Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 11:05:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sug_40765/07_2023/8sug_40765_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sug_40765/07_2023/8sug_40765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sug_40765/07_2023/8sug_40765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sug_40765/07_2023/8sug_40765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sug_40765/07_2023/8sug_40765_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sug_40765/07_2023/8sug_40765_neut.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.023 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 33 5.16 5 C 68376 2.51 5 N 20658 2.21 5 O 24288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A ASP 216": "OD1" <-> "OD2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "A ASP 418": "OD1" <-> "OD2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "A ASP 449": "OD1" <-> "OD2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B ASP 106": "OD1" <-> "OD2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 273": "OD1" <-> "OD2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B ASP 418": "OD1" <-> "OD2" Residue "B ASP 431": "OD1" <-> "OD2" Residue "B ASP 451": "OD1" <-> "OD2" Residue "C ASP 24": "OD1" <-> "OD2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C ASP 94": "OD1" <-> "OD2" Residue "C ASP 108": "OD1" <-> "OD2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 276": "OD1" <-> "OD2" Residue "C ASP 413": "OD1" <-> "OD2" Residue "C ASP 431": "OD1" <-> "OD2" Residue "C ASP 451": "OD1" <-> "OD2" Residue "C GLU 455": "OE1" <-> "OE2" Residue "D ASP 24": "OD1" <-> "OD2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D ASP 94": "OD1" <-> "OD2" Residue "D ASP 106": "OD1" <-> "OD2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 293": "OD1" <-> "OD2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D ASP 431": "OD1" <-> "OD2" Residue "E ASP 24": "OD1" <-> "OD2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E ASP 108": "OD1" <-> "OD2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E ASP 158": "OD1" <-> "OD2" Residue "E ASP 293": "OD1" <-> "OD2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 406": "OD1" <-> "OD2" Residue "E ASP 413": "OD1" <-> "OD2" Residue "E ASP 431": "OD1" <-> "OD2" Residue "E GLU 438": "OE1" <-> "OE2" Residue "E ASP 449": "OD1" <-> "OD2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 455": "OE1" <-> "OE2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F GLU 79": "OE1" <-> "OE2" Residue "F GLU 115": "OE1" <-> "OE2" Residue "F ASP 273": "OD1" <-> "OD2" Residue "F ASP 293": "OD1" <-> "OD2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 391": "OD1" <-> "OD2" Residue "F ASP 396": "OD1" <-> "OD2" Residue "F ASP 406": "OD1" <-> "OD2" Residue "F ASP 413": "OD1" <-> "OD2" Residue "F ASP 418": "OD1" <-> "OD2" Residue "F ASP 431": "OD1" <-> "OD2" Residue "F ASP 449": "OD1" <-> "OD2" Residue "F ASP 451": "OD1" <-> "OD2" Residue "F PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 24": "OD1" <-> "OD2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G GLU 223": "OE1" <-> "OE2" Residue "G PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 276": "OD1" <-> "OD2" Residue "G ASP 391": "OD1" <-> "OD2" Residue "G ASP 406": "OD1" <-> "OD2" Residue "G ASP 418": "OD1" <-> "OD2" Residue "G ASP 431": "OD1" <-> "OD2" Residue "G GLU 438": "OE1" <-> "OE2" Residue "G GLU 455": "OE1" <-> "OE2" Residue "H ASP 24": "OD1" <-> "OD2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "H ASP 94": "OD1" <-> "OD2" Residue "H ASP 106": "OD1" <-> "OD2" Residue "H ASP 108": "OD1" <-> "OD2" Residue "H GLU 115": "OE1" <-> "OE2" Residue "H ASP 128": "OD1" <-> "OD2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H ASP 158": "OD1" <-> "OD2" Residue "H ASP 255": "OD1" <-> "OD2" Residue "H ASP 293": "OD1" <-> "OD2" Residue "H GLU 305": "OE1" <-> "OE2" Residue "H PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 391": "OD1" <-> "OD2" Residue "H ASP 406": "OD1" <-> "OD2" Residue "H ASP 418": "OD1" <-> "OD2" Residue "H ASP 431": "OD1" <-> "OD2" Residue "H GLU 438": "OE1" <-> "OE2" Residue "H ASP 449": "OD1" <-> "OD2" Residue "H PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 455": "OE1" <-> "OE2" Residue "I ASP 70": "OD1" <-> "OD2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I ASP 108": "OD1" <-> "OD2" Residue "I GLU 115": "OE1" <-> "OE2" Residue "I GLU 122": "OE1" <-> "OE2" Residue "I GLU 223": "OE1" <-> "OE2" Residue "I PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 276": "OD1" <-> "OD2" Residue "I ASP 396": "OD1" <-> "OD2" Residue "I ASP 406": "OD1" <-> "OD2" Residue "I GLU 455": "OE1" <-> "OE2" Residue "J ASP 70": "OD1" <-> "OD2" Residue "J GLU 79": "OE1" <-> "OE2" Residue "J ASP 94": "OD1" <-> "OD2" Residue "J ASP 106": "OD1" <-> "OD2" Residue "J ASP 108": "OD1" <-> "OD2" Residue "J ASP 158": "OD1" <-> "OD2" Residue "J PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 391": "OD1" <-> "OD2" Residue "J ASP 406": "OD1" <-> "OD2" Residue "J ASP 418": "OD1" <-> "OD2" Residue "J ASP 431": "OD1" <-> "OD2" Residue "J GLU 438": "OE1" <-> "OE2" Residue "J ASP 449": "OD1" <-> "OD2" Residue "K ASP 44": "OD1" <-> "OD2" Residue "K ASP 70": "OD1" <-> "OD2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K ASP 94": "OD1" <-> "OD2" Residue "K ASP 108": "OD1" <-> "OD2" Residue "K GLU 115": "OE1" <-> "OE2" Residue "K ASP 139": "OD1" <-> "OD2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "K ASP 293": "OD1" <-> "OD2" Residue "K PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 333": "OE1" <-> "OE2" Residue "K TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 396": "OD1" <-> "OD2" Residue "K ASP 418": "OD1" <-> "OD2" Residue "K ASP 451": "OD1" <-> "OD2" Residue "K PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 455": "OE1" <-> "OE2" Residue "L ASP 24": "OD1" <-> "OD2" Residue "L ASP 94": "OD1" <-> "OD2" Residue "L GLU 122": "OE1" <-> "OE2" Residue "L PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 293": "OD1" <-> "OD2" Residue "L GLU 305": "OE1" <-> "OE2" Residue "L ASP 406": "OD1" <-> "OD2" Residue "L ASP 431": "OD1" <-> "OD2" Residue "L ASP 451": "OD1" <-> "OD2" Residue "L GLU 455": "OE1" <-> "OE2" Residue "M ASP 70": "OD1" <-> "OD2" Residue "M ASP 106": "OD1" <-> "OD2" Residue "M GLU 115": "OE1" <-> "OE2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 305": "OE1" <-> "OE2" Residue "M ASP 406": "OD1" <-> "OD2" Residue "M ASP 413": "OD1" <-> "OD2" Residue "M ASP 431": "OD1" <-> "OD2" Residue "M ASP 449": "OD1" <-> "OD2" Residue "N ASP 44": "OD1" <-> "OD2" Residue "N ASP 94": "OD1" <-> "OD2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N GLU 155": "OE1" <-> "OE2" Residue "N ASP 158": "OD1" <-> "OD2" Residue "N ASP 273": "OD1" <-> "OD2" Residue "N PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 406": "OD1" <-> "OD2" Residue "N ASP 431": "OD1" <-> "OD2" Residue "N ASP 449": "OD1" <-> "OD2" Residue "N PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 44": "OD1" <-> "OD2" Residue "O ASP 70": "OD1" <-> "OD2" Residue "O GLU 79": "OE1" <-> "OE2" Residue "O GLU 155": "OE1" <-> "OE2" Residue "O PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 305": "OE1" <-> "OE2" Residue "O ASP 329": "OD1" <-> "OD2" Residue "O ASP 391": "OD1" <-> "OD2" Residue "O ASP 396": "OD1" <-> "OD2" Residue "O ASP 431": "OD1" <-> "OD2" Residue "O ASP 449": "OD1" <-> "OD2" Residue "O ASP 451": "OD1" <-> "OD2" Residue "P ASP 24": "OD1" <-> "OD2" Residue "P ASP 70": "OD1" <-> "OD2" Residue "P ASP 94": "OD1" <-> "OD2" Residue "P ASP 106": "OD1" <-> "OD2" Residue "P GLU 122": "OE1" <-> "OE2" Residue "P GLU 155": "OE1" <-> "OE2" Residue "P ASP 158": "OD1" <-> "OD2" Residue "P ASP 276": "OD1" <-> "OD2" Residue "P ASP 293": "OD1" <-> "OD2" Residue "P PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 391": "OD1" <-> "OD2" Residue "P ASP 396": "OD1" <-> "OD2" Residue "P ASP 406": "OD1" <-> "OD2" Residue "P ASP 418": "OD1" <-> "OD2" Residue "P ASP 431": "OD1" <-> "OD2" Residue "P GLU 438": "OE1" <-> "OE2" Residue "P ASP 451": "OD1" <-> "OD2" Residue "P PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 455": "OE1" <-> "OE2" Residue "Q ASP 70": "OD1" <-> "OD2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q ASP 94": "OD1" <-> "OD2" Residue "Q ASP 108": "OD1" <-> "OD2" Residue "Q ASP 226": "OD1" <-> "OD2" Residue "Q PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 305": "OE1" <-> "OE2" Residue "Q ASP 329": "OD1" <-> "OD2" Residue "Q ASP 396": "OD1" <-> "OD2" Residue "Q ASP 406": "OD1" <-> "OD2" Residue "Q ASP 413": "OD1" <-> "OD2" Residue "Q GLU 438": "OE1" <-> "OE2" Residue "Q ASP 449": "OD1" <-> "OD2" Residue "Q ASP 451": "OD1" <-> "OD2" Residue "R GLU 79": "OE1" <-> "OE2" Residue "R ASP 94": "OD1" <-> "OD2" Residue "R GLU 115": "OE1" <-> "OE2" Residue "R GLU 122": "OE1" <-> "OE2" Residue "R ASP 158": "OD1" <-> "OD2" Residue "R GLU 305": "OE1" <-> "OE2" Residue "R PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 391": "OD1" <-> "OD2" Residue "R ASP 413": "OD1" <-> "OD2" Residue "R ASP 431": "OD1" <-> "OD2" Residue "R PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 455": "OE1" <-> "OE2" Residue "S ASP 24": "OD1" <-> "OD2" Residue "S ASP 44": "OD1" <-> "OD2" Residue "S ASP 70": "OD1" <-> "OD2" Residue "S GLU 79": "OE1" <-> "OE2" Residue "S ASP 94": "OD1" <-> "OD2" Residue "S ASP 108": "OD1" <-> "OD2" Residue "S GLU 115": "OE1" <-> "OE2" Residue "S GLU 155": "OE1" <-> "OE2" Residue "S ASP 273": "OD1" <-> "OD2" Residue "S ASP 276": "OD1" <-> "OD2" Residue "S ASP 293": "OD1" <-> "OD2" Residue "S PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 391": "OD1" <-> "OD2" Residue "S ASP 396": "OD1" <-> "OD2" Residue "S ASP 406": "OD1" <-> "OD2" Residue "S ASP 413": "OD1" <-> "OD2" Residue "S ASP 449": "OD1" <-> "OD2" Residue "S PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 455": "OE1" <-> "OE2" Residue "T ASP 24": "OD1" <-> "OD2" Residue "T ASP 44": "OD1" <-> "OD2" Residue "T ASP 70": "OD1" <-> "OD2" Residue "T GLU 79": "OE1" <-> "OE2" Residue "T ASP 106": "OD1" <-> "OD2" Residue "T GLU 223": "OE1" <-> "OE2" Residue "T PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 276": "OD1" <-> "OD2" Residue "T ASP 293": "OD1" <-> "OD2" Residue "T GLU 305": "OE1" <-> "OE2" Residue "T ASP 396": "OD1" <-> "OD2" Residue "T ASP 451": "OD1" <-> "OD2" Residue "T PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 24": "OD1" <-> "OD2" Residue "U ASP 70": "OD1" <-> "OD2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "U GLU 155": "OE1" <-> "OE2" Residue "U ASP 293": "OD1" <-> "OD2" Residue "U PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 406": "OD1" <-> "OD2" Residue "U ASP 413": "OD1" <-> "OD2" Residue "U ASP 431": "OD1" <-> "OD2" Residue "U ASP 451": "OD1" <-> "OD2" Residue "U PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 24": "OD1" <-> "OD2" Residue "V GLU 155": "OE1" <-> "OE2" Residue "V ASP 158": "OD1" <-> "OD2" Residue "V PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 431": "OD1" <-> "OD2" Residue "V GLU 438": "OE1" <-> "OE2" Residue "V ASP 451": "OD1" <-> "OD2" Residue "V PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 70": "OD1" <-> "OD2" Residue "W GLU 79": "OE1" <-> "OE2" Residue "W GLU 122": "OE1" <-> "OE2" Residue "W ASP 276": "OD1" <-> "OD2" Residue "W ASP 293": "OD1" <-> "OD2" Residue "W PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 391": "OD1" <-> "OD2" Residue "W ASP 406": "OD1" <-> "OD2" Residue "W PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 24": "OD1" <-> "OD2" Residue "X GLU 115": "OE1" <-> "OE2" Residue "X GLU 122": "OE1" <-> "OE2" Residue "X GLU 155": "OE1" <-> "OE2" Residue "X PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 293": "OD1" <-> "OD2" Residue "X ASP 329": "OD1" <-> "OD2" Residue "X ASP 396": "OD1" <-> "OD2" Residue "X ASP 406": "OD1" <-> "OD2" Residue "X ASP 413": "OD1" <-> "OD2" Residue "X ASP 418": "OD1" <-> "OD2" Residue "X ASP 449": "OD1" <-> "OD2" Residue "Y ASP 24": "OD1" <-> "OD2" Residue "Y ASP 70": "OD1" <-> "OD2" Residue "Y ASP 106": "OD1" <-> "OD2" Residue "Y GLU 155": "OE1" <-> "OE2" Residue "Y ASP 158": "OD1" <-> "OD2" Residue "Y PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 406": "OD1" <-> "OD2" Residue "Y ASP 413": "OD1" <-> "OD2" Residue "Y ASP 431": "OD1" <-> "OD2" Residue "Y GLU 438": "OE1" <-> "OE2" Residue "Y ASP 449": "OD1" <-> "OD2" Residue "Z ASP 24": "OD1" <-> "OD2" Residue "Z ASP 70": "OD1" <-> "OD2" Residue "Z GLU 79": "OE1" <-> "OE2" Residue "Z GLU 122": "OE1" <-> "OE2" Residue "Z GLU 155": "OE1" <-> "OE2" Residue "Z ASP 226": "OD1" <-> "OD2" Residue "Z ASP 293": "OD1" <-> "OD2" Residue "Z PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 391": "OD1" <-> "OD2" Residue "Z ASP 396": "OD1" <-> "OD2" Residue "Z ASP 406": "OD1" <-> "OD2" Residue "Z ASP 413": "OD1" <-> "OD2" Residue "Z ASP 418": "OD1" <-> "OD2" Residue "Z GLU 438": "OE1" <-> "OE2" Residue "Z PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 455": "OE1" <-> "OE2" Residue "a ASP 70": "OD1" <-> "OD2" Residue "a ASP 106": "OD1" <-> "OD2" Residue "a ASP 108": "OD1" <-> "OD2" Residue "a GLU 122": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "a ASP 158": "OD1" <-> "OD2" Residue "a PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 305": "OE1" <-> "OE2" Residue "a GLU 333": "OE1" <-> "OE2" Residue "a ASP 396": "OD1" <-> "OD2" Residue "a ASP 406": "OD1" <-> "OD2" Residue "a ASP 418": "OD1" <-> "OD2" Residue "a ASP 431": "OD1" <-> "OD2" Residue "a ASP 449": "OD1" <-> "OD2" Residue "a ASP 451": "OD1" <-> "OD2" Residue "a GLU 455": "OE1" <-> "OE2" Residue "b ASP 24": "OD1" <-> "OD2" Residue "b GLU 79": "OE1" <-> "OE2" Residue "b ASP 94": "OD1" <-> "OD2" Residue "b GLU 155": "OE1" <-> "OE2" Residue "b ASP 158": "OD1" <-> "OD2" Residue "b ASP 226": "OD1" <-> "OD2" Residue "b ASP 293": "OD1" <-> "OD2" Residue "b PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 391": "OD1" <-> "OD2" Residue "b ASP 396": "OD1" <-> "OD2" Residue "b ASP 406": "OD1" <-> "OD2" Residue "b GLU 438": "OE1" <-> "OE2" Residue "b GLU 455": "OE1" <-> "OE2" Residue "c ASP 24": "OD1" <-> "OD2" Residue "c ASP 44": "OD1" <-> "OD2" Residue "c ASP 106": "OD1" <-> "OD2" Residue "c GLU 155": "OE1" <-> "OE2" Residue "c ASP 158": "OD1" <-> "OD2" Residue "c PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 276": "OD1" <-> "OD2" Residue "c GLU 305": "OE1" <-> "OE2" Residue "c ASP 406": "OD1" <-> "OD2" Residue "c ASP 418": "OD1" <-> "OD2" Residue "c ASP 449": "OD1" <-> "OD2" Residue "c GLU 455": "OE1" <-> "OE2" Residue "d ASP 44": "OD1" <-> "OD2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "d ASP 94": "OD1" <-> "OD2" Residue "d ASP 293": "OD1" <-> "OD2" Residue "d PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 406": "OD1" <-> "OD2" Residue "d ASP 413": "OD1" <-> "OD2" Residue "d ASP 418": "OD1" <-> "OD2" Residue "d ASP 449": "OD1" <-> "OD2" Residue "d PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 455": "OE1" <-> "OE2" Residue "e ASP 24": "OD1" <-> "OD2" Residue "e ASP 70": "OD1" <-> "OD2" Residue "e GLU 79": "OE1" <-> "OE2" Residue "e ASP 106": "OD1" <-> "OD2" Residue "e GLU 115": "OE1" <-> "OE2" Residue "e ASP 293": "OD1" <-> "OD2" Residue "e PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 333": "OE1" <-> "OE2" Residue "e TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 391": "OD1" <-> "OD2" Residue "e ASP 396": "OD1" <-> "OD2" Residue "e ASP 413": "OD1" <-> "OD2" Residue "e ASP 418": "OD1" <-> "OD2" Residue "e PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 24": "OD1" <-> "OD2" Residue "f ASP 70": "OD1" <-> "OD2" Residue "f ASP 106": "OD1" <-> "OD2" Residue "f ASP 108": "OD1" <-> "OD2" Residue "f GLU 122": "OE1" <-> "OE2" Residue "f GLU 155": "OE1" <-> "OE2" Residue "f PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 255": "OD1" <-> "OD2" Residue "f GLU 305": "OE1" <-> "OE2" Residue "f ASP 406": "OD1" <-> "OD2" Residue "f ASP 431": "OD1" <-> "OD2" Residue "f ASP 449": "OD1" <-> "OD2" Residue "f GLU 455": "OE1" <-> "OE2" Residue "g ASP 44": "OD1" <-> "OD2" Residue "g ASP 70": "OD1" <-> "OD2" Residue "g ASP 106": "OD1" <-> "OD2" Residue "g ASP 108": "OD1" <-> "OD2" Residue "g GLU 115": "OE1" <-> "OE2" Residue "g ASP 158": "OD1" <-> "OD2" Residue "g GLU 223": "OE1" <-> "OE2" Residue "g PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 391": "OD1" <-> "OD2" Residue "g GLU 438": "OE1" <-> "OE2" Residue "g ASP 449": "OD1" <-> "OD2" Residue "g ASP 451": "OD1" <-> "OD2" Residue "g PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 113355 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "B" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "C" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "D" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "E" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "F" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "G" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "H" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "I" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "J" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "K" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "L" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "M" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "N" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "O" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "P" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "Q" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "R" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "S" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "T" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "U" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "V" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "W" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "X" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "Y" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "Z" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "a" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "b" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "c" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "d" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "e" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "f" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Chain: "g" Number of atoms: 3435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 484, 3430 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 480} bond proxies already assigned to first conformer: 3441 Time building chain proxies: 73.14, per 1000 atoms: 0.65 Number of scatterers: 113355 At special positions: 0 Unit cell: (190.44, 191.36, 323.84, 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 33 16.00 O 24288 8.00 N 20658 7.00 C 68376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 34.01 Conformation dependent library (CDL) restraints added in 26.3 seconds 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 29172 Finding SS restraints... Secondary structure from input PDB file: 334 helices and 198 sheets defined 47.5% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 11 through 35 Processing helix chain 'A' and resid 44 through 99 Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.595A pdb=" N ASN A 104 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 128 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 369 through 377 removed outlier: 3.658A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 449 removed outlier: 3.542A pdb=" N GLN A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA A 401 " --> pdb=" O GLY A 397 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 477 removed outlier: 4.131A pdb=" N GLU A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 488 Processing helix chain 'B' and resid 11 through 35 removed outlier: 3.632A pdb=" N GLN B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 99 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 108 through 128 Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 270 through 281 Processing helix chain 'B' and resid 369 through 377 removed outlier: 3.721A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 448 removed outlier: 3.741A pdb=" N GLN B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA B 401 " --> pdb=" O GLY B 397 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 477 Processing helix chain 'B' and resid 478 through 487 Processing helix chain 'C' and resid 11 through 35 Processing helix chain 'C' and resid 44 through 99 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 108 through 128 Processing helix chain 'C' and resid 217 through 226 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 369 through 377 removed outlier: 3.714A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 449 removed outlier: 4.026A pdb=" N ALA C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 477 removed outlier: 3.559A pdb=" N GLU C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA C 457 " --> pdb=" O ALA C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 488 Processing helix chain 'D' and resid 11 through 35 removed outlier: 3.699A pdb=" N GLN D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 99 Processing helix chain 'D' and resid 108 through 128 Processing helix chain 'D' and resid 217 through 226 Processing helix chain 'D' and resid 270 through 281 removed outlier: 3.525A pdb=" N LEU D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 377 removed outlier: 3.511A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 375 " --> pdb=" O GLN D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 449 removed outlier: 4.694A pdb=" N ILE D 402 " --> pdb=" O ALA D 398 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 477 Processing helix chain 'D' and resid 478 through 487 Processing helix chain 'E' and resid 11 through 35 removed outlier: 3.501A pdb=" N GLN E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 99 Processing helix chain 'E' and resid 100 through 104 Processing helix chain 'E' and resid 108 through 128 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 270 through 286 removed outlier: 4.730A pdb=" N SER E 283 " --> pdb=" O ASN E 279 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LYS E 284 " --> pdb=" O SER E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 449 Processing helix chain 'E' and resid 451 through 477 removed outlier: 3.522A pdb=" N GLU E 455 " --> pdb=" O ASP E 451 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA E 457 " --> pdb=" O ALA E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 488 removed outlier: 3.611A pdb=" N ARG E 488 " --> pdb=" O LEU E 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 35 removed outlier: 3.776A pdb=" N GLN F 15 " --> pdb=" O SER F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 99 Processing helix chain 'F' and resid 100 through 104 Processing helix chain 'F' and resid 108 through 128 Processing helix chain 'F' and resid 217 through 226 Processing helix chain 'F' and resid 270 through 286 removed outlier: 4.414A pdb=" N SER F 283 " --> pdb=" O ASN F 279 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LYS F 284 " --> pdb=" O SER F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 448 Processing helix chain 'F' and resid 451 through 477 removed outlier: 3.915A pdb=" N GLU F 455 " --> pdb=" O ASP F 451 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA F 457 " --> pdb=" O ALA F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 488 Processing helix chain 'G' and resid 9 through 11 No H-bonds generated for 'chain 'G' and resid 9 through 11' Processing helix chain 'G' and resid 12 through 35 Processing helix chain 'G' and resid 44 through 99 Processing helix chain 'G' and resid 100 through 104 removed outlier: 3.563A pdb=" N ASN G 104 " --> pdb=" O ASN G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 128 Processing helix chain 'G' and resid 217 through 226 Processing helix chain 'G' and resid 270 through 281 removed outlier: 3.779A pdb=" N LEU G 274 " --> pdb=" O SER G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 284 No H-bonds generated for 'chain 'G' and resid 282 through 284' Processing helix chain 'G' and resid 369 through 377 Processing helix chain 'G' and resid 396 through 449 removed outlier: 4.519A pdb=" N ILE G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN G 407 " --> pdb=" O ALA G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 477 removed outlier: 3.928A pdb=" N GLU G 455 " --> pdb=" O ASP G 451 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA G 457 " --> pdb=" O ALA G 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 488 Processing helix chain 'H' and resid 11 through 35 removed outlier: 3.710A pdb=" N GLN H 15 " --> pdb=" O SER H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 99 Processing helix chain 'H' and resid 100 through 104 Processing helix chain 'H' and resid 108 through 128 Processing helix chain 'H' and resid 217 through 226 Processing helix chain 'H' and resid 270 through 281 Processing helix chain 'H' and resid 281 through 286 Processing helix chain 'H' and resid 394 through 449 Processing helix chain 'H' and resid 451 through 477 removed outlier: 3.978A pdb=" N GLU H 455 " --> pdb=" O ASP H 451 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA H 457 " --> pdb=" O ALA H 453 " (cutoff:3.500A) Processing helix chain 'H' and resid 477 through 488 removed outlier: 4.581A pdb=" N GLN H 481 " --> pdb=" O ASN H 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 35 Processing helix chain 'I' and resid 44 through 99 Processing helix chain 'I' and resid 108 through 128 removed outlier: 3.512A pdb=" N ASP I 128 " --> pdb=" O THR I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 226 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 282 through 284 No H-bonds generated for 'chain 'I' and resid 282 through 284' Processing helix chain 'I' and resid 369 through 377 removed outlier: 3.504A pdb=" N VAL I 375 " --> pdb=" O GLN I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 449 removed outlier: 4.526A pdb=" N GLN I 399 " --> pdb=" O ALA I 395 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE I 402 " --> pdb=" O ALA I 398 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN I 407 " --> pdb=" O ALA I 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 477 removed outlier: 3.757A pdb=" N GLU I 455 " --> pdb=" O ASP I 451 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA I 457 " --> pdb=" O ALA I 453 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 488 Processing helix chain 'J' and resid 11 through 35 removed outlier: 3.683A pdb=" N GLN J 15 " --> pdb=" O SER J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 99 Processing helix chain 'J' and resid 100 through 104 removed outlier: 3.588A pdb=" N ASN J 104 " --> pdb=" O ASN J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 128 Processing helix chain 'J' and resid 217 through 226 Processing helix chain 'J' and resid 270 through 281 Processing helix chain 'J' and resid 282 through 284 No H-bonds generated for 'chain 'J' and resid 282 through 284' Processing helix chain 'J' and resid 369 through 377 removed outlier: 3.602A pdb=" N VAL J 375 " --> pdb=" O GLN J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 396 through 449 removed outlier: 4.632A pdb=" N ILE J 402 " --> pdb=" O ALA J 398 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN J 407 " --> pdb=" O ALA J 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 477 removed outlier: 3.832A pdb=" N GLU J 455 " --> pdb=" O ASP J 451 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA J 457 " --> pdb=" O ALA J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 478 through 487 Processing helix chain 'K' and resid 11 through 35 removed outlier: 3.816A pdb=" N GLN K 15 " --> pdb=" O SER K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 99 Processing helix chain 'K' and resid 100 through 104 removed outlier: 3.800A pdb=" N ASN K 104 " --> pdb=" O ASN K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 128 Processing helix chain 'K' and resid 217 through 226 Processing helix chain 'K' and resid 270 through 286 removed outlier: 4.859A pdb=" N SER K 283 " --> pdb=" O ASN K 279 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LYS K 284 " --> pdb=" O SER K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 394 through 449 Processing helix chain 'K' and resid 451 through 477 removed outlier: 3.526A pdb=" N GLU K 455 " --> pdb=" O ASP K 451 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ALA K 457 " --> pdb=" O ALA K 453 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 488 Processing helix chain 'L' and resid 11 through 35 Processing helix chain 'L' and resid 44 through 99 Processing helix chain 'L' and resid 100 through 104 Processing helix chain 'L' and resid 108 through 128 Processing helix chain 'L' and resid 217 through 226 Processing helix chain 'L' and resid 270 through 282 Processing helix chain 'L' and resid 369 through 377 Processing helix chain 'L' and resid 395 through 449 removed outlier: 4.465A pdb=" N GLN L 399 " --> pdb=" O ALA L 395 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE L 402 " --> pdb=" O ALA L 398 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN L 407 " --> pdb=" O ALA L 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 477 removed outlier: 3.636A pdb=" N GLU L 455 " --> pdb=" O ASP L 451 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA L 457 " --> pdb=" O ALA L 453 " (cutoff:3.500A) Processing helix chain 'L' and resid 478 through 488 Processing helix chain 'M' and resid 11 through 35 removed outlier: 3.974A pdb=" N GLN M 15 " --> pdb=" O SER M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 99 Processing helix chain 'M' and resid 100 through 104 Processing helix chain 'M' and resid 108 through 128 Processing helix chain 'M' and resid 217 through 226 Processing helix chain 'M' and resid 270 through 281 Processing helix chain 'M' and resid 282 through 284 No H-bonds generated for 'chain 'M' and resid 282 through 284' Processing helix chain 'M' and resid 369 through 377 removed outlier: 3.595A pdb=" N VAL M 375 " --> pdb=" O GLN M 371 " (cutoff:3.500A) Processing helix chain 'M' and resid 396 through 449 removed outlier: 4.519A pdb=" N ILE M 402 " --> pdb=" O ALA M 398 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN M 407 " --> pdb=" O ALA M 403 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 477 removed outlier: 3.978A pdb=" N GLU M 455 " --> pdb=" O ASP M 451 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA M 457 " --> pdb=" O ALA M 453 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 488 Processing helix chain 'N' and resid 11 through 35 removed outlier: 3.626A pdb=" N GLN N 15 " --> pdb=" O SER N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 99 Processing helix chain 'N' and resid 100 through 104 removed outlier: 3.500A pdb=" N ASN N 104 " --> pdb=" O ASN N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 128 Processing helix chain 'N' and resid 217 through 226 Processing helix chain 'N' and resid 270 through 286 removed outlier: 4.827A pdb=" N SER N 283 " --> pdb=" O ASN N 279 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LYS N 284 " --> pdb=" O SER N 280 " (cutoff:3.500A) Processing helix chain 'N' and resid 394 through 449 Processing helix chain 'N' and resid 451 through 477 removed outlier: 3.881A pdb=" N GLU N 455 " --> pdb=" O ASP N 451 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA N 457 " --> pdb=" O ALA N 453 " (cutoff:3.500A) Processing helix chain 'N' and resid 477 through 488 removed outlier: 4.604A pdb=" N GLN N 481 " --> pdb=" O ASN N 477 " (cutoff:3.500A) Processing helix chain 'O' and resid 11 through 35 Processing helix chain 'O' and resid 44 through 99 Processing helix chain 'O' and resid 100 through 104 Processing helix chain 'O' and resid 108 through 128 Processing helix chain 'O' and resid 217 through 226 Processing helix chain 'O' and resid 270 through 281 Processing helix chain 'O' and resid 369 through 377 Processing helix chain 'O' and resid 395 through 449 removed outlier: 4.475A pdb=" N GLN O 399 " --> pdb=" O ALA O 395 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE O 402 " --> pdb=" O ALA O 398 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN O 407 " --> pdb=" O ALA O 403 " (cutoff:3.500A) Processing helix chain 'O' and resid 454 through 477 Processing helix chain 'O' and resid 478 through 488 Processing helix chain 'P' and resid 11 through 35 removed outlier: 3.785A pdb=" N GLN P 15 " --> pdb=" O SER P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 99 Processing helix chain 'P' and resid 100 through 104 Processing helix chain 'P' and resid 108 through 128 Processing helix chain 'P' and resid 217 through 226 removed outlier: 3.533A pdb=" N ILE P 221 " --> pdb=" O SER P 217 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 286 removed outlier: 4.826A pdb=" N SER P 283 " --> pdb=" O ASN P 279 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS P 284 " --> pdb=" O SER P 280 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU P 285 " --> pdb=" O ASN P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 372 through 377 Processing helix chain 'P' and resid 394 through 448 Processing helix chain 'P' and resid 451 through 477 removed outlier: 3.643A pdb=" N GLU P 455 " --> pdb=" O ASP P 451 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA P 457 " --> pdb=" O ALA P 453 " (cutoff:3.500A) Processing helix chain 'P' and resid 478 through 487 Processing helix chain 'Q' and resid 11 through 35 removed outlier: 3.820A pdb=" N GLN Q 15 " --> pdb=" O SER Q 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 99 Processing helix chain 'Q' and resid 100 through 104 Processing helix chain 'Q' and resid 108 through 128 Processing helix chain 'Q' and resid 217 through 226 Processing helix chain 'Q' and resid 270 through 281 removed outlier: 3.515A pdb=" N LEU Q 274 " --> pdb=" O SER Q 270 " (cutoff:3.500A) Processing helix chain 'Q' and resid 282 through 284 No H-bonds generated for 'chain 'Q' and resid 282 through 284' Processing helix chain 'Q' and resid 369 through 377 removed outlier: 3.527A pdb=" N VAL Q 375 " --> pdb=" O GLN Q 371 " (cutoff:3.500A) Processing helix chain 'Q' and resid 396 through 449 removed outlier: 4.413A pdb=" N ILE Q 402 " --> pdb=" O ALA Q 398 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN Q 407 " --> pdb=" O ALA Q 403 " (cutoff:3.500A) Processing helix chain 'Q' and resid 451 through 477 removed outlier: 4.654A pdb=" N ALA Q 457 " --> pdb=" O ALA Q 453 " (cutoff:3.500A) Processing helix chain 'Q' and resid 478 through 488 removed outlier: 3.765A pdb=" N ALA Q 482 " --> pdb=" O GLN Q 478 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 35 removed outlier: 3.516A pdb=" N GLN R 15 " --> pdb=" O SER R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 99 Processing helix chain 'R' and resid 100 through 104 removed outlier: 3.871A pdb=" N ASN R 104 " --> pdb=" O ASN R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 128 Processing helix chain 'R' and resid 217 through 226 Processing helix chain 'R' and resid 270 through 281 Processing helix chain 'R' and resid 281 through 286 Processing helix chain 'R' and resid 372 through 377 Processing helix chain 'R' and resid 394 through 448 Processing helix chain 'R' and resid 451 through 477 removed outlier: 3.764A pdb=" N GLU R 455 " --> pdb=" O ASP R 451 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA R 457 " --> pdb=" O ALA R 453 " (cutoff:3.500A) Processing helix chain 'R' and resid 478 through 488 Processing helix chain 'S' and resid 11 through 35 removed outlier: 3.651A pdb=" N GLN S 15 " --> pdb=" O SER S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 99 Processing helix chain 'S' and resid 100 through 104 removed outlier: 3.521A pdb=" N ASN S 104 " --> pdb=" O ASN S 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 128 Processing helix chain 'S' and resid 217 through 226 Processing helix chain 'S' and resid 270 through 286 removed outlier: 5.055A pdb=" N SER S 283 " --> pdb=" O ASN S 279 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS S 284 " --> pdb=" O SER S 280 " (cutoff:3.500A) Processing helix chain 'S' and resid 372 through 377 Processing helix chain 'S' and resid 394 through 449 Processing helix chain 'S' and resid 451 through 477 removed outlier: 4.027A pdb=" N GLU S 455 " --> pdb=" O ASP S 451 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ALA S 457 " --> pdb=" O ALA S 453 " (cutoff:3.500A) Processing helix chain 'S' and resid 478 through 487 removed outlier: 3.572A pdb=" N ALA S 482 " --> pdb=" O GLN S 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 11 through 35 removed outlier: 3.735A pdb=" N GLN T 15 " --> pdb=" O SER T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 99 Processing helix chain 'T' and resid 108 through 128 Processing helix chain 'T' and resid 217 through 226 Processing helix chain 'T' and resid 270 through 281 Processing helix chain 'T' and resid 282 through 284 No H-bonds generated for 'chain 'T' and resid 282 through 284' Processing helix chain 'T' and resid 369 through 377 removed outlier: 3.575A pdb=" N VAL T 375 " --> pdb=" O GLN T 371 " (cutoff:3.500A) Processing helix chain 'T' and resid 396 through 449 removed outlier: 4.500A pdb=" N ILE T 402 " --> pdb=" O ALA T 398 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN T 407 " --> pdb=" O ALA T 403 " (cutoff:3.500A) Processing helix chain 'T' and resid 451 through 477 removed outlier: 3.976A pdb=" N GLU T 455 " --> pdb=" O ASP T 451 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA T 457 " --> pdb=" O ALA T 453 " (cutoff:3.500A) Processing helix chain 'T' and resid 478 through 487 Processing helix chain 'U' and resid 11 through 35 Processing helix chain 'U' and resid 44 through 99 Processing helix chain 'U' and resid 100 through 104 removed outlier: 3.880A pdb=" N ASN U 104 " --> pdb=" O ASN U 101 " (cutoff:3.500A) Processing helix chain 'U' and resid 108 through 128 Processing helix chain 'U' and resid 217 through 226 Processing helix chain 'U' and resid 270 through 281 Processing helix chain 'U' and resid 281 through 286 Processing helix chain 'U' and resid 394 through 449 Processing helix chain 'U' and resid 454 through 477 Processing helix chain 'U' and resid 478 through 488 Processing helix chain 'V' and resid 11 through 35 removed outlier: 3.841A pdb=" N GLN V 15 " --> pdb=" O SER V 11 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 99 Processing helix chain 'V' and resid 100 through 104 removed outlier: 3.708A pdb=" N ASN V 104 " --> pdb=" O ASN V 101 " (cutoff:3.500A) Processing helix chain 'V' and resid 108 through 128 Processing helix chain 'V' and resid 217 through 226 Processing helix chain 'V' and resid 270 through 281 Processing helix chain 'V' and resid 282 through 284 No H-bonds generated for 'chain 'V' and resid 282 through 284' Processing helix chain 'V' and resid 369 through 377 removed outlier: 3.522A pdb=" N VAL V 375 " --> pdb=" O GLN V 371 " (cutoff:3.500A) Processing helix chain 'V' and resid 396 through 448 removed outlier: 4.535A pdb=" N ILE V 402 " --> pdb=" O ALA V 398 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN V 407 " --> pdb=" O ALA V 403 " (cutoff:3.500A) Processing helix chain 'V' and resid 451 through 477 removed outlier: 3.841A pdb=" N GLU V 455 " --> pdb=" O ASP V 451 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA V 457 " --> pdb=" O ALA V 453 " (cutoff:3.500A) Processing helix chain 'V' and resid 478 through 488 removed outlier: 3.504A pdb=" N ALA V 482 " --> pdb=" O GLN V 478 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 35 removed outlier: 3.810A pdb=" N GLN W 15 " --> pdb=" O SER W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 99 Processing helix chain 'W' and resid 100 through 104 removed outlier: 3.519A pdb=" N ASN W 104 " --> pdb=" O ASN W 101 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 128 Processing helix chain 'W' and resid 217 through 226 Processing helix chain 'W' and resid 270 through 281 Processing helix chain 'W' and resid 281 through 286 Processing helix chain 'W' and resid 369 through 374 removed outlier: 4.435A pdb=" N SER W 373 " --> pdb=" O GLY W 369 " (cutoff:3.500A) Processing helix chain 'W' and resid 394 through 449 Processing helix chain 'W' and resid 451 through 477 removed outlier: 3.980A pdb=" N GLU W 455 " --> pdb=" O ASP W 451 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA W 457 " --> pdb=" O ALA W 453 " (cutoff:3.500A) Processing helix chain 'W' and resid 478 through 487 Processing helix chain 'X' and resid 11 through 35 Processing helix chain 'X' and resid 44 through 99 Processing helix chain 'X' and resid 100 through 104 Processing helix chain 'X' and resid 108 through 128 Processing helix chain 'X' and resid 217 through 226 Processing helix chain 'X' and resid 270 through 281 Processing helix chain 'X' and resid 369 through 377 removed outlier: 3.628A pdb=" N VAL X 375 " --> pdb=" O GLN X 371 " (cutoff:3.500A) Processing helix chain 'X' and resid 396 through 449 removed outlier: 4.624A pdb=" N ILE X 402 " --> pdb=" O ALA X 398 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN X 407 " --> pdb=" O ALA X 403 " (cutoff:3.500A) Processing helix chain 'X' and resid 451 through 477 removed outlier: 4.184A pdb=" N GLU X 455 " --> pdb=" O ASP X 451 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA X 457 " --> pdb=" O ALA X 453 " (cutoff:3.500A) Processing helix chain 'X' and resid 478 through 488 Processing helix chain 'Y' and resid 9 through 11 No H-bonds generated for 'chain 'Y' and resid 9 through 11' Processing helix chain 'Y' and resid 12 through 35 Processing helix chain 'Y' and resid 44 through 99 Processing helix chain 'Y' and resid 100 through 104 removed outlier: 3.684A pdb=" N ASN Y 104 " --> pdb=" O ASN Y 101 " (cutoff:3.500A) Processing helix chain 'Y' and resid 108 through 128 Processing helix chain 'Y' and resid 217 through 226 Processing helix chain 'Y' and resid 270 through 281 removed outlier: 3.514A pdb=" N LEU Y 274 " --> pdb=" O SER Y 270 " (cutoff:3.500A) Processing helix chain 'Y' and resid 282 through 284 No H-bonds generated for 'chain 'Y' and resid 282 through 284' Processing helix chain 'Y' and resid 369 through 377 removed outlier: 3.507A pdb=" N SER Y 373 " --> pdb=" O GLY Y 369 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL Y 375 " --> pdb=" O GLN Y 371 " (cutoff:3.500A) Processing helix chain 'Y' and resid 396 through 448 removed outlier: 4.717A pdb=" N ILE Y 402 " --> pdb=" O ALA Y 398 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN Y 407 " --> pdb=" O ALA Y 403 " (cutoff:3.500A) Processing helix chain 'Y' and resid 451 through 477 removed outlier: 3.722A pdb=" N GLU Y 455 " --> pdb=" O ASP Y 451 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA Y 457 " --> pdb=" O ALA Y 453 " (cutoff:3.500A) Processing helix chain 'Y' and resid 478 through 488 Processing helix chain 'Z' and resid 11 through 35 removed outlier: 3.690A pdb=" N GLN Z 15 " --> pdb=" O SER Z 11 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 99 Processing helix chain 'Z' and resid 100 through 104 Processing helix chain 'Z' and resid 108 through 128 Processing helix chain 'Z' and resid 217 through 226 Processing helix chain 'Z' and resid 270 through 286 removed outlier: 5.211A pdb=" N SER Z 283 " --> pdb=" O ASN Z 279 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LYS Z 284 " --> pdb=" O SER Z 280 " (cutoff:3.500A) Processing helix chain 'Z' and resid 369 through 374 removed outlier: 4.541A pdb=" N SER Z 373 " --> pdb=" O GLY Z 369 " (cutoff:3.500A) Processing helix chain 'Z' and resid 394 through 449 Processing helix chain 'Z' and resid 451 through 477 removed outlier: 4.179A pdb=" N GLU Z 455 " --> pdb=" O ASP Z 451 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA Z 457 " --> pdb=" O ALA Z 453 " (cutoff:3.500A) Processing helix chain 'Z' and resid 478 through 488 Processing helix chain 'a' and resid 11 through 35 removed outlier: 3.572A pdb=" N GLN a 15 " --> pdb=" O SER a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 99 Processing helix chain 'a' and resid 100 through 104 removed outlier: 3.783A pdb=" N ASN a 104 " --> pdb=" O ASN a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 128 Processing helix chain 'a' and resid 217 through 226 Processing helix chain 'a' and resid 270 through 281 Processing helix chain 'a' and resid 282 through 284 No H-bonds generated for 'chain 'a' and resid 282 through 284' Processing helix chain 'a' and resid 369 through 377 removed outlier: 3.590A pdb=" N SER a 373 " --> pdb=" O GLY a 369 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL a 375 " --> pdb=" O GLN a 371 " (cutoff:3.500A) Processing helix chain 'a' and resid 396 through 449 removed outlier: 4.889A pdb=" N ILE a 402 " --> pdb=" O ALA a 398 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN a 407 " --> pdb=" O ALA a 403 " (cutoff:3.500A) Processing helix chain 'a' and resid 454 through 477 Processing helix chain 'a' and resid 478 through 488 Processing helix chain 'b' and resid 11 through 35 removed outlier: 3.786A pdb=" N GLN b 15 " --> pdb=" O SER b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 99 Processing helix chain 'b' and resid 108 through 128 Processing helix chain 'b' and resid 217 through 226 Processing helix chain 'b' and resid 270 through 286 removed outlier: 4.587A pdb=" N SER b 283 " --> pdb=" O ASN b 279 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYS b 284 " --> pdb=" O SER b 280 " (cutoff:3.500A) Processing helix chain 'b' and resid 394 through 448 Processing helix chain 'b' and resid 451 through 477 removed outlier: 3.997A pdb=" N GLU b 455 " --> pdb=" O ASP b 451 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA b 457 " --> pdb=" O ALA b 453 " (cutoff:3.500A) Processing helix chain 'b' and resid 478 through 488 Processing helix chain 'c' and resid 11 through 35 removed outlier: 3.726A pdb=" N GLN c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 99 Processing helix chain 'c' and resid 100 through 104 Processing helix chain 'c' and resid 108 through 128 Processing helix chain 'c' and resid 217 through 226 Processing helix chain 'c' and resid 270 through 281 Processing helix chain 'c' and resid 369 through 377 removed outlier: 3.503A pdb=" N SER c 373 " --> pdb=" O GLY c 369 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL c 375 " --> pdb=" O GLN c 371 " (cutoff:3.500A) Processing helix chain 'c' and resid 396 through 449 removed outlier: 4.622A pdb=" N ILE c 402 " --> pdb=" O ALA c 398 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASN c 407 " --> pdb=" O ALA c 403 " (cutoff:3.500A) Processing helix chain 'c' and resid 451 through 477 removed outlier: 4.053A pdb=" N GLU c 455 " --> pdb=" O ASP c 451 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA c 457 " --> pdb=" O ALA c 453 " (cutoff:3.500A) Processing helix chain 'c' and resid 478 through 488 Processing helix chain 'd' and resid 11 through 35 Processing helix chain 'd' and resid 44 through 99 Processing helix chain 'd' and resid 100 through 104 removed outlier: 3.616A pdb=" N ASN d 104 " --> pdb=" O ASN d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 128 Processing helix chain 'd' and resid 217 through 226 Processing helix chain 'd' and resid 270 through 281 Processing helix chain 'd' and resid 281 through 286 Processing helix chain 'd' and resid 394 through 449 Processing helix chain 'd' and resid 454 through 477 Processing helix chain 'd' and resid 478 through 488 Processing helix chain 'e' and resid 11 through 35 removed outlier: 3.873A pdb=" N GLN e 15 " --> pdb=" O SER e 11 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 99 Processing helix chain 'e' and resid 100 through 104 Processing helix chain 'e' and resid 108 through 128 Processing helix chain 'e' and resid 217 through 226 Processing helix chain 'e' and resid 270 through 286 removed outlier: 4.805A pdb=" N SER e 283 " --> pdb=" O ASN e 279 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYS e 284 " --> pdb=" O SER e 280 " (cutoff:3.500A) Processing helix chain 'e' and resid 394 through 448 Processing helix chain 'e' and resid 451 through 477 removed outlier: 4.026A pdb=" N GLU e 455 " --> pdb=" O ASP e 451 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA e 457 " --> pdb=" O ALA e 453 " (cutoff:3.500A) Processing helix chain 'e' and resid 478 through 488 Processing helix chain 'f' and resid 11 through 35 removed outlier: 3.765A pdb=" N GLN f 15 " --> pdb=" O SER f 11 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 99 Processing helix chain 'f' and resid 100 through 104 removed outlier: 3.892A pdb=" N ASN f 104 " --> pdb=" O ASN f 101 " (cutoff:3.500A) Processing helix chain 'f' and resid 108 through 128 Processing helix chain 'f' and resid 217 through 226 Processing helix chain 'f' and resid 270 through 282 Processing helix chain 'f' and resid 369 through 377 removed outlier: 3.576A pdb=" N VAL f 375 " --> pdb=" O GLN f 371 " (cutoff:3.500A) Processing helix chain 'f' and resid 396 through 449 removed outlier: 4.563A pdb=" N ILE f 402 " --> pdb=" O ALA f 398 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN f 407 " --> pdb=" O ALA f 403 " (cutoff:3.500A) Processing helix chain 'f' and resid 451 through 477 removed outlier: 3.982A pdb=" N GLU f 455 " --> pdb=" O ASP f 451 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA f 457 " --> pdb=" O ALA f 453 " (cutoff:3.500A) Processing helix chain 'f' and resid 477 through 487 removed outlier: 4.681A pdb=" N GLN f 481 " --> pdb=" O ASN f 477 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 35 Processing helix chain 'g' and resid 44 through 99 Processing helix chain 'g' and resid 100 through 104 removed outlier: 3.932A pdb=" N ASN g 104 " --> pdb=" O ASN g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 108 through 128 Processing helix chain 'g' and resid 217 through 226 Processing helix chain 'g' and resid 270 through 286 removed outlier: 4.922A pdb=" N SER g 283 " --> pdb=" O ASN g 279 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LYS g 284 " --> pdb=" O SER g 280 " (cutoff:3.500A) Processing helix chain 'g' and resid 372 through 377 Processing helix chain 'g' and resid 394 through 449 Processing helix chain 'g' and resid 454 through 477 Processing helix chain 'g' and resid 478 through 488 removed outlier: 3.544A pdb=" N ALA g 482 " --> pdb=" O GLN g 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 146 through 148 Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 175 removed outlier: 3.725A pdb=" N GLN A 356 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 235 " --> pdb=" O GLN A 356 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A 358 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER A 233 " --> pdb=" O ASN A 358 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 297 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 175 removed outlier: 3.725A pdb=" N GLN A 356 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 235 " --> pdb=" O GLN A 356 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A 358 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER A 233 " --> pdb=" O ASN A 358 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL A 321 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 202 Processing sheet with id=AA5, first strand: chain 'A' and resid 261 through 263 removed outlier: 3.864A pdb=" N ASN A 261 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 148 Processing sheet with id=AA7, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.743A pdb=" N ARG B 235 " --> pdb=" O GLN B 356 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B 358 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER B 233 " --> pdb=" O ASN B 358 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 242 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU B 297 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.743A pdb=" N ARG B 235 " --> pdb=" O GLN B 356 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B 358 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER B 233 " --> pdb=" O ASN B 358 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 322 " --> pdb=" O ASP B 243 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL B 321 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 189 through 190 Processing sheet with id=AB1, first strand: chain 'B' and resid 200 through 202 Processing sheet with id=AB2, first strand: chain 'B' and resid 254 through 258 removed outlier: 4.693A pdb=" N ASP B 255 " --> pdb=" O GLY B 310 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 148 Processing sheet with id=AB4, first strand: chain 'C' and resid 173 through 175 removed outlier: 3.549A pdb=" N THR C 238 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 242 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C 297 " --> pdb=" O ALA C 242 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 173 through 175 removed outlier: 7.149A pdb=" N VAL C 321 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 189 through 190 Processing sheet with id=AB7, first strand: chain 'C' and resid 200 through 202 Processing sheet with id=AB8, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AB9, first strand: chain 'D' and resid 146 through 148 Processing sheet with id=AC1, first strand: chain 'D' and resid 173 through 175 removed outlier: 3.645A pdb=" N GLN D 356 " --> pdb=" O ARG D 235 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG D 235 " --> pdb=" O GLN D 356 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR D 238 " --> pdb=" O SER D 301 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 297 " --> pdb=" O ALA D 242 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 173 through 175 removed outlier: 3.645A pdb=" N GLN D 356 " --> pdb=" O ARG D 235 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG D 235 " --> pdb=" O GLN D 356 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS D 324 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL D 340 " --> pdb=" O VAL D 321 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL D 323 " --> pdb=" O ASN D 338 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ASN D 338 " --> pdb=" O VAL D 323 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 189 through 190 Processing sheet with id=AC4, first strand: chain 'D' and resid 200 through 202 Processing sheet with id=AC5, first strand: chain 'D' and resid 261 through 263 removed outlier: 3.781A pdb=" N ASN D 261 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASP D 255 " --> pdb=" O GLY D 310 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 146 through 148 Processing sheet with id=AC7, first strand: chain 'E' and resid 197 through 198 Processing sheet with id=AC8, first strand: chain 'E' and resid 207 through 208 Processing sheet with id=AC9, first strand: chain 'E' and resid 233 through 234 Processing sheet with id=AD1, first strand: chain 'E' and resid 244 through 248 removed outlier: 4.515A pdb=" N VAL E 247 " --> pdb=" O ALA E 318 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA E 318 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLY E 319 " --> pdb=" O ALA E 341 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ALA E 341 " --> pdb=" O GLY E 319 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL E 321 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS E 337 " --> pdb=" O VAL E 323 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 262 through 264 Processing sheet with id=AD3, first strand: chain 'F' and resid 146 through 148 Processing sheet with id=AD4, first strand: chain 'F' and resid 197 through 198 Processing sheet with id=AD5, first strand: chain 'F' and resid 207 through 208 Processing sheet with id=AD6, first strand: chain 'F' and resid 233 through 234 Processing sheet with id=AD7, first strand: chain 'F' and resid 244 through 248 removed outlier: 3.523A pdb=" N SER F 245 " --> pdb=" O GLN F 320 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL F 247 " --> pdb=" O ALA F 318 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA F 318 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLY F 319 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ALA F 341 " --> pdb=" O GLY F 319 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL F 321 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS F 337 " --> pdb=" O VAL F 323 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 254 through 258 removed outlier: 3.658A pdb=" N PHE F 254 " --> pdb=" O LEU F 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 146 through 148 Processing sheet with id=AE1, first strand: chain 'G' and resid 173 through 175 removed outlier: 3.553A pdb=" N ARG G 235 " --> pdb=" O GLN G 356 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN G 358 " --> pdb=" O SER G 233 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER G 233 " --> pdb=" O ASN G 358 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA G 242 " --> pdb=" O LEU G 297 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU G 297 " --> pdb=" O ALA G 242 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 173 through 175 removed outlier: 3.553A pdb=" N ARG G 235 " --> pdb=" O GLN G 356 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN G 358 " --> pdb=" O SER G 233 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER G 233 " --> pdb=" O ASN G 358 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL G 340 " --> pdb=" O VAL G 321 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL G 323 " --> pdb=" O ASN G 338 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASN G 338 " --> pdb=" O VAL G 323 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 189 through 190 removed outlier: 4.557A pdb=" N ASP G 255 " --> pdb=" O GLY G 310 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN G 261 " --> pdb=" O VAL G 258 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 208 through 209 Processing sheet with id=AE5, first strand: chain 'H' and resid 146 through 148 Processing sheet with id=AE6, first strand: chain 'H' and resid 207 through 208 removed outlier: 3.557A pdb=" N LYS H 208 " --> pdb=" O LEU H 201 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 233 through 234 Processing sheet with id=AE8, first strand: chain 'H' and resid 245 through 248 removed outlier: 3.716A pdb=" N SER H 245 " --> pdb=" O GLN H 320 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL H 247 " --> pdb=" O ALA H 318 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA H 318 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL H 340 " --> pdb=" O VAL H 321 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL H 323 " --> pdb=" O ASN H 338 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASN H 338 " --> pdb=" O VAL H 323 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 261 through 265 Processing sheet with id=AF1, first strand: chain 'H' and resid 287 through 288 Processing sheet with id=AF2, first strand: chain 'I' and resid 146 through 148 Processing sheet with id=AF3, first strand: chain 'I' and resid 173 through 175 removed outlier: 3.745A pdb=" N GLN I 356 " --> pdb=" O ARG I 235 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG I 235 " --> pdb=" O GLN I 356 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN I 358 " --> pdb=" O SER I 233 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER I 233 " --> pdb=" O ASN I 358 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR I 238 " --> pdb=" O SER I 301 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU I 297 " --> pdb=" O ALA I 242 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 173 through 175 removed outlier: 3.745A pdb=" N GLN I 356 " --> pdb=" O ARG I 235 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG I 235 " --> pdb=" O GLN I 356 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN I 358 " --> pdb=" O SER I 233 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER I 233 " --> pdb=" O ASN I 358 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA I 322 " --> pdb=" O ASP I 243 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL I 321 " --> pdb=" O VAL I 339 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 189 through 190 Processing sheet with id=AF6, first strand: chain 'I' and resid 208 through 209 removed outlier: 3.532A pdb=" N LEU I 201 " --> pdb=" O LYS I 208 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 256 through 258 Processing sheet with id=AF8, first strand: chain 'J' and resid 146 through 148 Processing sheet with id=AF9, first strand: chain 'J' and resid 173 through 175 removed outlier: 3.630A pdb=" N GLN J 356 " --> pdb=" O ARG J 235 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG J 235 " --> pdb=" O GLN J 356 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN J 358 " --> pdb=" O SER J 233 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER J 233 " --> pdb=" O ASN J 358 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU J 297 " --> pdb=" O ALA J 242 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 173 through 175 removed outlier: 3.630A pdb=" N GLN J 356 " --> pdb=" O ARG J 235 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG J 235 " --> pdb=" O GLN J 356 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN J 358 " --> pdb=" O SER J 233 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER J 233 " --> pdb=" O ASN J 358 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL J 321 " --> pdb=" O VAL J 339 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 188 through 190 removed outlier: 3.656A pdb=" N THR J 352 " --> pdb=" O THR J 188 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR J 190 " --> pdb=" O ILE J 350 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 200 through 202 Processing sheet with id=AG4, first strand: chain 'J' and resid 261 through 263 removed outlier: 3.835A pdb=" N ASN J 261 " --> pdb=" O VAL J 258 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP J 255 " --> pdb=" O GLY J 310 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 146 through 148 Processing sheet with id=AG6, first strand: chain 'K' and resid 197 through 198 Processing sheet with id=AG7, first strand: chain 'K' and resid 207 through 208 Processing sheet with id=AG8, first strand: chain 'K' and resid 233 through 234 Processing sheet with id=AG9, first strand: chain 'K' and resid 244 through 248 removed outlier: 4.295A pdb=" N VAL K 247 " --> pdb=" O ALA K 318 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA K 318 " --> pdb=" O VAL K 247 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL K 340 " --> pdb=" O VAL K 321 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL K 323 " --> pdb=" O ASN K 338 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASN K 338 " --> pdb=" O VAL K 323 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 262 through 265 removed outlier: 3.514A pdb=" N VAL K 263 " --> pdb=" O VAL K 256 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 287 through 288 Processing sheet with id=AH3, first strand: chain 'L' and resid 146 through 148 Processing sheet with id=AH4, first strand: chain 'L' and resid 173 through 175 removed outlier: 3.781A pdb=" N GLN L 356 " --> pdb=" O ARG L 235 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG L 235 " --> pdb=" O GLN L 356 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU L 297 " --> pdb=" O ALA L 242 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 173 through 175 removed outlier: 3.781A pdb=" N GLN L 356 " --> pdb=" O ARG L 235 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG L 235 " --> pdb=" O GLN L 356 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA L 322 " --> pdb=" O ASP L 243 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY L 319 " --> pdb=" O ALA L 341 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA L 341 " --> pdb=" O GLY L 319 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL L 321 " --> pdb=" O VAL L 339 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 189 through 190 Processing sheet with id=AH7, first strand: chain 'L' and resid 200 through 202 Processing sheet with id=AH8, first strand: chain 'L' and resid 254 through 258 removed outlier: 4.731A pdb=" N ASP L 255 " --> pdb=" O GLY L 310 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'M' and resid 146 through 148 Processing sheet with id=AI1, first strand: chain 'M' and resid 173 through 175 removed outlier: 3.681A pdb=" N ARG M 235 " --> pdb=" O GLN M 356 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN M 358 " --> pdb=" O SER M 233 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER M 233 " --> pdb=" O ASN M 358 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU M 297 " --> pdb=" O ALA M 242 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 173 through 175 removed outlier: 3.681A pdb=" N ARG M 235 " --> pdb=" O GLN M 356 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN M 358 " --> pdb=" O SER M 233 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER M 233 " --> pdb=" O ASN M 358 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL M 321 " --> pdb=" O VAL M 339 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 189 through 190 Processing sheet with id=AI4, first strand: chain 'M' and resid 208 through 209 removed outlier: 3.525A pdb=" N LYS M 208 " --> pdb=" O LEU M 201 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU M 201 " --> pdb=" O LYS M 208 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 261 through 263 removed outlier: 3.939A pdb=" N ASN M 261 " --> pdb=" O VAL M 258 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP M 255 " --> pdb=" O GLY M 310 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 146 through 148 Processing sheet with id=AI7, first strand: chain 'N' and resid 188 through 190 removed outlier: 3.781A pdb=" N THR N 352 " --> pdb=" O THR N 188 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'N' and resid 207 through 208 Processing sheet with id=AI9, first strand: chain 'N' and resid 233 through 234 removed outlier: 3.547A pdb=" N ASN N 358 " --> pdb=" O SER N 233 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 287 through 288 removed outlier: 3.699A pdb=" N ALA N 242 " --> pdb=" O LEU N 297 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP N 243 " --> pdb=" O ALA N 322 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA N 322 " --> pdb=" O ASP N 243 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL N 247 " --> pdb=" O ALA N 318 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ALA N 318 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL N 340 " --> pdb=" O VAL N 321 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL N 323 " --> pdb=" O ASN N 338 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASN N 338 " --> pdb=" O VAL N 323 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 262 through 264 Processing sheet with id=AJ3, first strand: chain 'O' and resid 146 through 148 Processing sheet with id=AJ4, first strand: chain 'O' and resid 173 through 176 removed outlier: 3.819A pdb=" N GLN O 356 " --> pdb=" O ARG O 235 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG O 235 " --> pdb=" O GLN O 356 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU O 297 " --> pdb=" O ALA O 242 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'O' and resid 173 through 176 removed outlier: 3.819A pdb=" N GLN O 356 " --> pdb=" O ARG O 235 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG O 235 " --> pdb=" O GLN O 356 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL O 321 " --> pdb=" O VAL O 339 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'O' and resid 189 through 190 Processing sheet with id=AJ7, first strand: chain 'O' and resid 208 through 209 removed outlier: 3.579A pdb=" N LEU O 201 " --> pdb=" O LYS O 208 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'O' and resid 261 through 263 removed outlier: 3.757A pdb=" N ASN O 261 " --> pdb=" O VAL O 258 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASP O 255 " --> pdb=" O GLY O 310 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'P' and resid 146 through 148 Processing sheet with id=AK1, first strand: chain 'P' and resid 188 through 190 removed outlier: 3.764A pdb=" N THR P 352 " --> pdb=" O THR P 188 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'P' and resid 207 through 208 Processing sheet with id=AK3, first strand: chain 'P' and resid 233 through 234 Processing sheet with id=AK4, first strand: chain 'P' and resid 297 through 299 removed outlier: 3.710A pdb=" N ALA P 242 " --> pdb=" O LEU P 297 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP P 243 " --> pdb=" O ALA P 322 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA P 322 " --> pdb=" O ASP P 243 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL P 247 " --> pdb=" O ALA P 318 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA P 318 " --> pdb=" O VAL P 247 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL P 340 " --> pdb=" O VAL P 321 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL P 323 " --> pdb=" O ASN P 338 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ASN P 338 " --> pdb=" O VAL P 323 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'P' and resid 262 through 264 removed outlier: 3.509A pdb=" N THR P 257 " --> pdb=" O LYS P 308 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'Q' and resid 146 through 148 Processing sheet with id=AK7, first strand: chain 'Q' and resid 173 through 175 removed outlier: 3.584A pdb=" N GLN Q 356 " --> pdb=" O ARG Q 235 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG Q 235 " --> pdb=" O GLN Q 356 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'Q' and resid 173 through 175 removed outlier: 3.584A pdb=" N GLN Q 356 " --> pdb=" O ARG Q 235 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG Q 235 " --> pdb=" O GLN Q 356 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL Q 340 " --> pdb=" O VAL Q 321 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL Q 323 " --> pdb=" O ASN Q 338 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASN Q 338 " --> pdb=" O VAL Q 323 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'Q' and resid 188 through 190 Processing sheet with id=AL1, first strand: chain 'Q' and resid 200 through 202 Processing sheet with id=AL2, first strand: chain 'Q' and resid 261 through 263 removed outlier: 3.886A pdb=" N ASN Q 261 " --> pdb=" O VAL Q 258 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP Q 255 " --> pdb=" O GLY Q 310 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'R' and resid 146 through 148 Processing sheet with id=AL4, first strand: chain 'R' and resid 188 through 190 removed outlier: 3.923A pdb=" N THR R 352 " --> pdb=" O THR R 188 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'R' and resid 207 through 208 Processing sheet with id=AL6, first strand: chain 'R' and resid 233 through 234 Processing sheet with id=AL7, first strand: chain 'R' and resid 243 through 248 removed outlier: 3.957A pdb=" N ASP R 243 " --> pdb=" O ALA R 322 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA R 322 " --> pdb=" O ASP R 243 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL R 247 " --> pdb=" O ALA R 318 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA R 318 " --> pdb=" O VAL R 247 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLY R 319 " --> pdb=" O ALA R 341 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA R 341 " --> pdb=" O GLY R 319 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL R 321 " --> pdb=" O VAL R 339 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'R' and resid 262 through 264 Processing sheet with id=AL9, first strand: chain 'R' and resid 287 through 288 Processing sheet with id=AM1, first strand: chain 'S' and resid 146 through 148 Processing sheet with id=AM2, first strand: chain 'S' and resid 188 through 190 removed outlier: 3.775A pdb=" N THR S 352 " --> pdb=" O THR S 188 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'S' and resid 207 through 208 Processing sheet with id=AM4, first strand: chain 'S' and resid 233 through 234 Processing sheet with id=AM5, first strand: chain 'S' and resid 244 through 248 removed outlier: 3.528A pdb=" N SER S 245 " --> pdb=" O GLN S 320 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL S 247 " --> pdb=" O ALA S 318 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA S 318 " --> pdb=" O VAL S 247 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL S 340 " --> pdb=" O VAL S 321 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL S 323 " --> pdb=" O ASN S 338 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN S 338 " --> pdb=" O VAL S 323 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'S' and resid 261 through 264 removed outlier: 3.525A pdb=" N THR S 257 " --> pdb=" O LYS S 308 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'S' and resid 287 through 288 Processing sheet with id=AM8, first strand: chain 'T' and resid 146 through 148 Processing sheet with id=AM9, first strand: chain 'T' and resid 173 through 175 removed outlier: 3.575A pdb=" N GLN T 356 " --> pdb=" O ARG T 235 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG T 235 " --> pdb=" O GLN T 356 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN T 358 " --> pdb=" O SER T 233 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER T 233 " --> pdb=" O ASN T 358 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'T' and resid 173 through 175 removed outlier: 3.575A pdb=" N GLN T 356 " --> pdb=" O ARG T 235 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG T 235 " --> pdb=" O GLN T 356 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN T 358 " --> pdb=" O SER T 233 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER T 233 " --> pdb=" O ASN T 358 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL T 321 " --> pdb=" O VAL T 339 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'T' and resid 189 through 190 Processing sheet with id=AN3, first strand: chain 'T' and resid 200 through 201 Processing sheet with id=AN4, first strand: chain 'T' and resid 261 through 263 removed outlier: 3.845A pdb=" N ASN T 261 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASP T 255 " --> pdb=" O GLY T 310 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'U' and resid 146 through 148 Processing sheet with id=AN6, first strand: chain 'U' and resid 197 through 198 Processing sheet with id=AN7, first strand: chain 'U' and resid 207 through 208 removed outlier: 3.573A pdb=" N LYS U 208 " --> pdb=" O LEU U 201 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'U' and resid 233 through 234 Processing sheet with id=AN9, first strand: chain 'U' and resid 244 through 248 removed outlier: 3.543A pdb=" N SER U 245 " --> pdb=" O GLN U 320 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL U 247 " --> pdb=" O ALA U 318 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA U 318 " --> pdb=" O VAL U 247 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL U 340 " --> pdb=" O VAL U 321 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'U' and resid 255 through 257 Processing sheet with id=AO2, first strand: chain 'U' and resid 287 through 288 Processing sheet with id=AO3, first strand: chain 'V' and resid 146 through 148 Processing sheet with id=AO4, first strand: chain 'V' and resid 173 through 175 removed outlier: 3.514A pdb=" N ARG V 235 " --> pdb=" O GLN V 356 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN V 358 " --> pdb=" O SER V 233 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER V 233 " --> pdb=" O ASN V 358 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU V 297 " --> pdb=" O ALA V 242 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'V' and resid 173 through 175 removed outlier: 3.514A pdb=" N ARG V 235 " --> pdb=" O GLN V 356 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN V 358 " --> pdb=" O SER V 233 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER V 233 " --> pdb=" O ASN V 358 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL V 321 " --> pdb=" O VAL V 339 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'V' and resid 189 through 190 removed outlier: 3.806A pdb=" N ASN V 261 " --> pdb=" O VAL V 258 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'V' and resid 200 through 202 Processing sheet with id=AO8, first strand: chain 'W' and resid 146 through 148 Processing sheet with id=AO9, first strand: chain 'W' and resid 207 through 208 removed outlier: 3.781A pdb=" N LYS W 208 " --> pdb=" O LEU W 201 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU W 201 " --> pdb=" O LYS W 208 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'W' and resid 233 through 234 Processing sheet with id=AP2, first strand: chain 'W' and resid 244 through 248 removed outlier: 3.524A pdb=" N SER W 245 " --> pdb=" O GLN W 320 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL W 247 " --> pdb=" O ALA W 318 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA W 318 " --> pdb=" O VAL W 247 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL W 340 " --> pdb=" O VAL W 321 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'W' and resid 262 through 264 removed outlier: 5.469A pdb=" N ASP W 255 " --> pdb=" O GLY W 310 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'W' and resid 287 through 288 Processing sheet with id=AP5, first strand: chain 'X' and resid 146 through 148 Processing sheet with id=AP6, first strand: chain 'X' and resid 173 through 175 removed outlier: 3.623A pdb=" N GLN X 356 " --> pdb=" O ARG X 235 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG X 235 " --> pdb=" O GLN X 356 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN X 358 " --> pdb=" O SER X 233 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER X 233 " --> pdb=" O ASN X 358 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU X 297 " --> pdb=" O ALA X 242 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'X' and resid 173 through 175 removed outlier: 3.623A pdb=" N GLN X 356 " --> pdb=" O ARG X 235 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG X 235 " --> pdb=" O GLN X 356 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN X 358 " --> pdb=" O SER X 233 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER X 233 " --> pdb=" O ASN X 358 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS X 324 " --> pdb=" O THR X 241 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL X 321 " --> pdb=" O VAL X 339 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'X' and resid 188 through 190 removed outlier: 4.539A pdb=" N ASP X 255 " --> pdb=" O GLY X 310 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'X' and resid 200 through 202 Processing sheet with id=AQ1, first strand: chain 'Y' and resid 146 through 148 Processing sheet with id=AQ2, first strand: chain 'Y' and resid 173 through 175 removed outlier: 3.695A pdb=" N ASN Y 358 " --> pdb=" O SER Y 233 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER Y 233 " --> pdb=" O ASN Y 358 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU Y 297 " --> pdb=" O ALA Y 242 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'Y' and resid 173 through 175 removed outlier: 3.695A pdb=" N ASN Y 358 " --> pdb=" O SER Y 233 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER Y 233 " --> pdb=" O ASN Y 358 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL Y 321 " --> pdb=" O VAL Y 339 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'Y' and resid 188 through 190 Processing sheet with id=AQ5, first strand: chain 'Y' and resid 200 through 202 Processing sheet with id=AQ6, first strand: chain 'Y' and resid 261 through 263 removed outlier: 3.689A pdb=" N ASN Y 261 " --> pdb=" O VAL Y 258 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP Y 255 " --> pdb=" O GLY Y 310 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'Z' and resid 146 through 148 Processing sheet with id=AQ8, first strand: chain 'Z' and resid 188 through 190 removed outlier: 3.941A pdb=" N THR Z 352 " --> pdb=" O THR Z 188 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'Z' and resid 207 through 208 Processing sheet with id=AR1, first strand: chain 'Z' and resid 233 through 234 Processing sheet with id=AR2, first strand: chain 'Z' and resid 243 through 248 removed outlier: 3.852A pdb=" N ASP Z 243 " --> pdb=" O ALA Z 322 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA Z 322 " --> pdb=" O ASP Z 243 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER Z 245 " --> pdb=" O GLN Z 320 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL Z 247 " --> pdb=" O ALA Z 318 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA Z 318 " --> pdb=" O VAL Z 247 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL Z 340 " --> pdb=" O VAL Z 321 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL Z 323 " --> pdb=" O ASN Z 338 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASN Z 338 " --> pdb=" O VAL Z 323 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'Z' and resid 262 through 264 removed outlier: 3.501A pdb=" N VAL Z 263 " --> pdb=" O VAL Z 256 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'Z' and resid 287 through 288 Processing sheet with id=AR5, first strand: chain 'a' and resid 146 through 148 Processing sheet with id=AR6, first strand: chain 'a' and resid 173 through 175 removed outlier: 3.727A pdb=" N GLN a 356 " --> pdb=" O ARG a 235 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG a 235 " --> pdb=" O GLN a 356 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'a' and resid 173 through 175 removed outlier: 3.727A pdb=" N GLN a 356 " --> pdb=" O ARG a 235 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG a 235 " --> pdb=" O GLN a 356 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL a 340 " --> pdb=" O VAL a 321 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL a 323 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ASN a 338 " --> pdb=" O VAL a 323 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'a' and resid 189 through 190 Processing sheet with id=AR9, first strand: chain 'a' and resid 200 through 202 Processing sheet with id=AS1, first strand: chain 'a' and resid 262 through 263 Processing sheet with id=AS2, first strand: chain 'b' and resid 146 through 148 Processing sheet with id=AS3, first strand: chain 'b' and resid 188 through 190 removed outlier: 4.048A pdb=" N THR b 352 " --> pdb=" O THR b 188 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'b' and resid 207 through 208 Processing sheet with id=AS5, first strand: chain 'b' and resid 233 through 234 Processing sheet with id=AS6, first strand: chain 'b' and resid 245 through 248 removed outlier: 3.583A pdb=" N SER b 245 " --> pdb=" O GLN b 320 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL b 247 " --> pdb=" O ALA b 318 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA b 318 " --> pdb=" O VAL b 247 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL b 340 " --> pdb=" O VAL b 321 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL b 323 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN b 338 " --> pdb=" O VAL b 323 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'b' and resid 262 through 264 removed outlier: 3.553A pdb=" N THR b 257 " --> pdb=" O LYS b 308 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'c' and resid 146 through 148 Processing sheet with id=AS9, first strand: chain 'c' and resid 173 through 175 removed outlier: 3.824A pdb=" N GLN c 356 " --> pdb=" O ARG c 235 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG c 235 " --> pdb=" O GLN c 356 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR c 238 " --> pdb=" O SER c 301 " (cutoff:3.500A) Processing sheet with id=AT1, first strand: chain 'c' and resid 173 through 175 removed outlier: 3.824A pdb=" N GLN c 356 " --> pdb=" O ARG c 235 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG c 235 " --> pdb=" O GLN c 356 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS c 324 " --> pdb=" O THR c 241 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL c 321 " --> pdb=" O VAL c 339 " (cutoff:3.500A) Processing sheet with id=AT2, first strand: chain 'c' and resid 188 through 190 Processing sheet with id=AT3, first strand: chain 'c' and resid 200 through 202 Processing sheet with id=AT4, first strand: chain 'c' and resid 261 through 263 removed outlier: 3.991A pdb=" N ASN c 261 " --> pdb=" O VAL c 258 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP c 255 " --> pdb=" O GLY c 310 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'd' and resid 146 through 148 Processing sheet with id=AT6, first strand: chain 'd' and resid 207 through 208 removed outlier: 3.597A pdb=" N LYS d 208 " --> pdb=" O LEU d 201 " (cutoff:3.500A) Processing sheet with id=AT7, first strand: chain 'd' and resid 233 through 234 Processing sheet with id=AT8, first strand: chain 'd' and resid 244 through 248 removed outlier: 3.574A pdb=" N SER d 245 " --> pdb=" O GLN d 320 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL d 247 " --> pdb=" O ALA d 318 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA d 318 " --> pdb=" O VAL d 247 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLY d 319 " --> pdb=" O ALA d 341 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA d 341 " --> pdb=" O GLY d 319 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL d 321 " --> pdb=" O VAL d 339 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'd' and resid 262 through 265 Processing sheet with id=AU1, first strand: chain 'd' and resid 287 through 288 Processing sheet with id=AU2, first strand: chain 'e' and resid 146 through 148 Processing sheet with id=AU3, first strand: chain 'e' and resid 207 through 208 Processing sheet with id=AU4, first strand: chain 'e' and resid 233 through 234 Processing sheet with id=AU5, first strand: chain 'e' and resid 245 through 248 removed outlier: 4.513A pdb=" N VAL e 247 " --> pdb=" O ALA e 318 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA e 318 " --> pdb=" O VAL e 247 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL e 340 " --> pdb=" O VAL e 321 " (cutoff:3.500A) Processing sheet with id=AU6, first strand: chain 'e' and resid 255 through 257 Processing sheet with id=AU7, first strand: chain 'f' and resid 146 through 148 Processing sheet with id=AU8, first strand: chain 'f' and resid 173 through 175 removed outlier: 3.601A pdb=" N ARG f 235 " --> pdb=" O GLN f 356 " (cutoff:3.500A) Processing sheet with id=AU9, first strand: chain 'f' and resid 173 through 175 removed outlier: 3.601A pdb=" N ARG f 235 " --> pdb=" O GLN f 356 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL f 321 " --> pdb=" O VAL f 339 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL f 339 " --> pdb=" O VAL f 321 " (cutoff:3.500A) Processing sheet with id=AV1, first strand: chain 'f' and resid 189 through 190 removed outlier: 3.772A pdb=" N THR f 190 " --> pdb=" O ILE f 350 " (cutoff:3.500A) Processing sheet with id=AV2, first strand: chain 'f' and resid 200 through 202 Processing sheet with id=AV3, first strand: chain 'f' and resid 261 through 263 Processing sheet with id=AV4, first strand: chain 'g' and resid 146 through 148 Processing sheet with id=AV5, first strand: chain 'g' and resid 207 through 208 Processing sheet with id=AV6, first strand: chain 'g' and resid 233 through 234 Processing sheet with id=AV7, first strand: chain 'g' and resid 244 through 248 removed outlier: 4.417A pdb=" N VAL g 247 " --> pdb=" O ALA g 318 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA g 318 " --> pdb=" O VAL g 247 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY g 319 " --> pdb=" O ALA g 341 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA g 341 " --> pdb=" O GLY g 319 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL g 321 " --> pdb=" O VAL g 339 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS g 337 " --> pdb=" O VAL g 323 " (cutoff:3.500A) Processing sheet with id=AV8, first strand: chain 'g' and resid 262 through 264 Processing sheet with id=AV9, first strand: chain 'g' and resid 287 through 288 7114 hydrogen bonds defined for protein. 20388 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: 50.48 Time building geometry restraints manager: 36.94 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: 40920 1.34 - 1.46: 13469 1.46 - 1.58: 59494 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 113949 Sorted by residual: bond pdb=" N ALA G 168 " pdb=" CA ALA G 168 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.40e+00 bond pdb=" N ALA D 168 " pdb=" CA ALA D 168 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.04e+00 bond pdb=" N ALA O 168 " pdb=" CA ALA O 168 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.96e+00 bond pdb=" N ALA f 168 " pdb=" CA ALA f 168 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.96e+00 bond pdb=" N ALA I 168 " pdb=" CA ALA I 168 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.87e+00 ... (remaining 113944 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.31: 421 106.31 - 112.53: 61907 112.53 - 118.75: 31580 118.75 - 124.97: 60747 124.97 - 131.19: 313 Bond angle restraints: 154968 Sorted by residual: angle pdb=" N ALA g 388 " pdb=" CA ALA g 388 " pdb=" C ALA g 388 " ideal model delta sigma weight residual 114.75 106.89 7.86 1.26e+00 6.30e-01 3.89e+01 angle pdb=" N ALA K 388 " pdb=" CA ALA K 388 " pdb=" C ALA K 388 " ideal model delta sigma weight residual 114.56 106.88 7.68 1.27e+00 6.20e-01 3.66e+01 angle pdb=" N ALA F 388 " pdb=" CA ALA F 388 " pdb=" C ALA F 388 " ideal model delta sigma weight residual 114.75 107.26 7.49 1.26e+00 6.30e-01 3.53e+01 angle pdb=" N ALA W 388 " pdb=" CA ALA W 388 " pdb=" C ALA W 388 " ideal model delta sigma weight residual 114.75 107.28 7.47 1.26e+00 6.30e-01 3.51e+01 angle pdb=" N ALA H 388 " pdb=" CA ALA H 388 " pdb=" C ALA H 388 " ideal model delta sigma weight residual 114.75 107.32 7.43 1.26e+00 6.30e-01 3.48e+01 ... (remaining 154963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 63696 18.00 - 35.99: 4297 35.99 - 53.99: 787 53.99 - 71.99: 186 71.99 - 89.99: 103 Dihedral angle restraints: 69069 sinusoidal: 23727 harmonic: 45342 Sorted by residual: dihedral pdb=" CA SER A 167 " pdb=" C SER A 167 " pdb=" N ALA A 168 " pdb=" CA ALA A 168 " ideal model delta harmonic sigma weight residual -180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA LYS D 136 " pdb=" C LYS D 136 " pdb=" N LEU D 137 " pdb=" CA LEU D 137 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA SER C 167 " pdb=" C SER C 167 " pdb=" N ALA C 168 " pdb=" CA ALA C 168 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 69066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 15620 0.046 - 0.093: 2952 0.093 - 0.139: 827 0.139 - 0.185: 33 0.185 - 0.231: 5 Chirality restraints: 19437 Sorted by residual: chirality pdb=" CB ILE N 212 " pdb=" CA ILE N 212 " pdb=" CG1 ILE N 212 " pdb=" CG2 ILE N 212 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB ILE A 291 " pdb=" CA ILE A 291 " pdb=" CG1 ILE A 291 " pdb=" CG2 ILE A 291 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB ILE O 291 " pdb=" CA ILE O 291 " pdb=" CG1 ILE O 291 " pdb=" CG2 ILE O 291 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 19434 not shown) Planarity restraints: 20823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 206 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C GLN B 206 " -0.029 2.00e-02 2.50e+03 pdb=" O GLN B 206 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL B 207 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 94 " -0.007 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" CG ASP A 94 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP A 94 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP A 94 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA g 220 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C ALA g 220 " 0.026 2.00e-02 2.50e+03 pdb=" O ALA g 220 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE g 221 " -0.009 2.00e-02 2.50e+03 ... (remaining 20820 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 4024 2.69 - 3.24: 131655 3.24 - 3.79: 192623 3.79 - 4.35: 245612 4.35 - 4.90: 386967 Nonbonded interactions: 960881 Sorted by model distance: nonbonded pdb=" O GLY K 143 " pdb=" OG SER L 290 " model vdw 2.137 2.440 nonbonded pdb=" OG SER K 301 " pdb=" OE1 GLU K 305 " model vdw 2.153 2.440 nonbonded pdb=" OG1 THR X 269 " pdb=" OD2 ASP X 273 " model vdw 2.156 2.440 nonbonded pdb=" O ASN U 101 " pdb=" OG SER U 105 " model vdw 2.172 2.440 nonbonded pdb=" OG1 THR a 269 " pdb=" OD2 ASP a 273 " model vdw 2.181 2.440 ... (remaining 960876 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' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'B' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'C' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'D' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'E' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'F' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'G' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'H' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'I' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'J' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'K' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'L' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'M' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'N' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'O' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'P' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'Q' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'R' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'S' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'T' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'U' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'V' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'W' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'X' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'Y' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'Z' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'a' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'b' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'c' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'd' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'e' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'f' and (resid 5 through 242 or resid 244 through 488)) selection = (chain 'g' and (resid 5 through 242 or resid 244 through 488)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 22.230 Check model and map are aligned: 1.220 Set scattering table: 0.730 Process input model: 272.700 Find NCS groups from input model: 6.850 Set up NCS constraints: 0.530 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 309.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 : 0.002 0.032 113949 Z= 0.164 Angle : 0.726 14.190 154968 Z= 0.456 Chirality : 0.039 0.231 19437 Planarity : 0.002 0.027 20823 Dihedral : 13.567 89.985 39897 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.37 % Favored : 91.28 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.06), residues: 15939 helix: 0.59 (0.06), residues: 7032 sheet: -3.29 (0.08), residues: 2412 loop : -3.44 (0.06), residues: 6495 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4327 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4327 time to evaluate : 8.766 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 4327 average time/residue: 0.9876 time to fit residues: 7228.2813 Evaluate side-chains 2837 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2837 time to evaluate : 10.248 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.5933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1584 random chunks: chunk 1337 optimal weight: 0.6980 chunk 1200 optimal weight: 0.0010 chunk 666 optimal weight: 8.9990 chunk 410 optimal weight: 7.9990 chunk 809 optimal weight: 20.0000 chunk 641 optimal weight: 7.9990 chunk 1241 optimal weight: 0.9980 chunk 480 optimal weight: 10.0000 chunk 754 optimal weight: 20.0000 chunk 924 optimal weight: 1.9990 chunk 1438 optimal weight: 10.0000 overall best weight: 2.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN A 57 GLN ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN A 177 ASN A 253 ASN A 281 ASN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN B 253 ASN B 358 ASN B 371 GLN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN C 57 GLN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN C 399 GLN C 478 GLN D 23 ASN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 104 ASN D 120 GLN ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 ASN ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 ASN ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 GLN ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 ASN E 26 ASN E 57 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN E 177 ASN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 462 ASN F 17 ASN ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN F 119 GLN F 231 ASN F 272 GLN F 277 GLN F 312 GLN ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN G 253 ASN ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 399 GLN G 428 ASN G 475 GLN H 6 ASN H 17 ASN H 69 ASN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 462 ASN ** H 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 466 GLN ** H 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN I 83 GLN ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 253 ASN I 435 ASN ** J 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN ** J 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 253 ASN ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 423 GLN ** J 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 ASN K 49 GLN K 83 GLN ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN K 104 ASN K 206 GLN ** K 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 467 GLN ** K 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 ASN ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 GLN L 83 GLN L 90 GLN L 98 GLN L 152 ASN L 253 ASN L 407 ASN L 439 ASN L 463 GLN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN M 120 GLN M 253 ASN M 272 GLN ** M 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 378 ASN M 399 GLN ** M 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 462 ASN M 463 GLN N 17 ASN N 19 ASN ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 GLN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 277 GLN N 432 ASN ** O 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 23 ASN O 49 GLN O 90 GLN O 101 ASN O 119 GLN ** O 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 206 GLN O 253 ASN O 272 GLN ** O 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 428 ASN O 432 ASN P 23 ASN P 56 ASN P 84 GLN P 152 ASN ** P 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 281 ASN P 415 GLN P 432 ASN P 439 ASN P 462 ASN ** P 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 467 GLN Q 17 ASN Q 49 GLN ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN Q 152 ASN ** Q 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 206 GLN ** Q 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 326 GLN Q 415 GLN ** Q 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 462 ASN Q 466 GLN R 62 ASN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 277 GLN R 281 ASN R 312 GLN R 435 ASN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 30 GLN S 56 ASN ** S 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 279 ASN S 312 GLN ** S 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 466 GLN S 467 GLN ** S 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN T 56 ASN ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 253 ASN T 277 GLN ** T 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 481 GLN U 17 ASN U 30 GLN U 57 GLN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 104 ASN ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 162 GLN ** U 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 281 ASN ** U 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 466 GLN V 23 ASN V 57 GLN V 120 GLN V 253 ASN V 399 GLN V 428 ASN V 432 ASN V 478 GLN V 481 GLN ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 49 GLN ** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 98 GLN ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 104 ASN W 120 GLN W 163 ASN W 281 ASN W 312 GLN ** W 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 432 ASN W 439 ASN X 26 ASN ** X 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 GLN X 84 GLN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 435 ASN ** X 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 478 GLN Y 13 ASN ** Y 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 56 ASN Y 57 GLN ** Y 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN ** Y 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 177 ASN Y 253 ASN ** Y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 383 GLN Y 399 GLN ** Y 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 17 ASN Z 56 ASN Z 83 GLN Z 90 GLN Z 148 GLN Z 272 GLN Z 279 ASN ** Z 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 415 GLN Z 466 GLN Z 477 ASN a 17 ASN ** a 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 104 ASN a 206 GLN a 253 ASN a 277 GLN a 428 ASN ** a 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 466 GLN ** a 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 56 ASN b 87 ASN b 120 GLN b 200 ASN b 272 GLN b 277 GLN b 432 ASN b 439 ASN ** c 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 23 ASN c 177 ASN ** c 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 277 GLN ** c 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 415 GLN c 424 ASN c 439 ASN c 462 ASN c 467 GLN d 101 ASN ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 272 GLN d 312 GLN e 23 ASN e 26 ASN e 49 GLN e 200 ASN e 209 ASN ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 466 GLN ** e 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 481 GLN f 17 ASN f 56 ASN ** f 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 101 ASN f 120 GLN f 177 ASN f 253 ASN f 277 GLN ** f 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 84 GLN g 104 ASN ** g 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 279 ASN ** g 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 113949 Z= 0.214 Angle : 0.658 12.068 154968 Z= 0.359 Chirality : 0.043 0.276 19437 Planarity : 0.004 0.126 20823 Dihedral : 4.836 30.236 16764 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.22 % Favored : 90.47 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.06), residues: 15939 helix: 1.63 (0.06), residues: 7051 sheet: -2.57 (0.10), residues: 2167 loop : -3.14 (0.06), residues: 6721 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3437 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 3411 time to evaluate : 8.866 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 3 residues processed: 3431 average time/residue: 0.9317 time to fit residues: 5570.1938 Evaluate side-chains 2599 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2596 time to evaluate : 8.888 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.8693 time to fit residues: 16.3700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1584 random chunks: chunk 799 optimal weight: 9.9990 chunk 446 optimal weight: 20.0000 chunk 1197 optimal weight: 7.9990 chunk 979 optimal weight: 3.9990 chunk 396 optimal weight: 8.9990 chunk 1441 optimal weight: 4.9990 chunk 1556 optimal weight: 8.9990 chunk 1283 optimal weight: 9.9990 chunk 1429 optimal weight: 0.0980 chunk 491 optimal weight: 3.9990 chunk 1156 optimal weight: 4.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN B 358 ASN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 GLN ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 120 GLN D 162 GLN ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN E 57 GLN E 67 ASN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 GLN E 423 GLN ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN ** F 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 ASN G 13 ASN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN ** G 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 356 GLN ** G 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 ASN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 261 ASN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 ASN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 253 ASN ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 435 ASN J 49 GLN ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 439 ASN J 442 ASN ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 467 GLN L 6 ASN ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN ** L 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 439 ASN ** M 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 ASN N 69 ASN ** N 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 GLN ** N 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 439 ASN ** O 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 ASN ** O 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 432 ASN ** O 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 GLN P 83 GLN P 163 ASN ** P 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 383 GLN P 439 ASN ** Q 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN ** Q 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 326 GLN Q 415 GLN ** Q 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 462 ASN Q 466 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 GLN R 277 GLN ** R 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 GLN ** S 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 ASN ** S 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 467 GLN T 49 GLN T 52 ASN T 76 GLN ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 272 GLN ** T 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 428 ASN ** T 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 462 ASN U 57 GLN ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 378 ASN U 428 ASN ** U 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 281 ASN V 356 GLN V 428 ASN V 432 ASN V 478 GLN ** W 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 415 GLN W 428 ASN W 432 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 ASN Y 56 ASN Y 83 GLN ** Y 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 356 GLN Z 17 ASN ** Z 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 378 ASN Z 383 GLN ** Z 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 466 GLN ** a 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 49 GLN ** a 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 104 ASN a 435 ASN ** a 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 277 GLN b 439 ASN c 30 GLN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 424 ASN c 439 ASN c 466 GLN ** d 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 415 GLN d 478 GLN e 17 ASN ** e 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 83 GLN e 272 GLN ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 312 GLN ** e 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 466 GLN ** e 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 356 GLN ** f 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 6 ASN ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 113 GLN g 162 GLN ** g 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 462 ASN Total number of N/Q/H flips: 102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 113949 Z= 0.244 Angle : 0.664 12.022 154968 Z= 0.366 Chirality : 0.044 0.439 19437 Planarity : 0.004 0.096 20823 Dihedral : 5.000 31.882 16764 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.52 % Favored : 90.19 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.07), residues: 15939 helix: 1.86 (0.06), residues: 6951 sheet: -2.32 (0.10), residues: 1939 loop : -2.86 (0.06), residues: 7049 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3239 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 3225 time to evaluate : 9.070 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 3236 average time/residue: 0.9413 time to fit residues: 5329.4567 Evaluate side-chains 2456 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2449 time to evaluate : 8.896 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.8133 time to fit residues: 22.4462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1584 random chunks: chunk 1423 optimal weight: 1.9990 chunk 1083 optimal weight: 5.9990 chunk 747 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 687 optimal weight: 5.9990 chunk 967 optimal weight: 5.9990 chunk 1446 optimal weight: 7.9990 chunk 1531 optimal weight: 0.9990 chunk 755 optimal weight: 0.9990 chunk 1370 optimal weight: 30.0000 chunk 412 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 462 ASN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 162 GLN ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN E 57 GLN E 67 ASN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN F 277 GLN ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 ASN G 13 ASN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 356 GLN ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 466 GLN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 200 ASN H 209 ASN H 261 ASN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 439 ASN ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 281 ASN ** K 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN L 98 GLN L 356 GLN ** M 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 442 ASN N 56 ASN ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN O 90 GLN ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 119 GLN O 281 ASN ** O 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN P 76 GLN P 83 GLN P 84 GLN ** P 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 383 GLN ** P 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 428 ASN P 432 ASN P 439 ASN P 467 GLN Q 17 ASN ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 177 ASN ** Q 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 326 GLN Q 415 GLN ** Q 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 466 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 442 ASN S 467 GLN ** S 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 466 GLN ** U 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 23 ASN ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 399 GLN V 428 ASN ** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 113 GLN W 415 GLN W 462 ASN X 49 GLN ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 ASN ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 56 ASN Y 57 GLN Y 83 GLN ** Y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 356 GLN ** Y 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 17 ASN Z 30 GLN ** Z 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 466 GLN ** a 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 49 GLN ** a 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 173 GLN a 272 GLN a 358 ASN ** a 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 432 ASN b 439 ASN b 462 ASN ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 424 ASN ** c 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 466 GLN ** e 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 356 GLN ** f 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 84 GLN g 200 ASN ** g 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 478 GLN g 481 GLN Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 113949 Z= 0.215 Angle : 0.656 13.415 154968 Z= 0.358 Chirality : 0.043 0.249 19437 Planarity : 0.004 0.139 20823 Dihedral : 4.960 33.680 16764 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.76 % Favored : 89.97 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.07), residues: 15939 helix: 1.91 (0.06), residues: 6998 sheet: -2.09 (0.10), residues: 2017 loop : -2.78 (0.07), residues: 6924 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3188 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 3178 time to evaluate : 9.210 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 3184 average time/residue: 0.9448 time to fit residues: 5273.1019 Evaluate side-chains 2442 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2441 time to evaluate : 8.913 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.8798 time to fit residues: 13.3436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1584 random chunks: chunk 1275 optimal weight: 8.9990 chunk 869 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 1140 optimal weight: 1.9990 chunk 631 optimal weight: 5.9990 chunk 1306 optimal weight: 8.9990 chunk 1058 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 781 optimal weight: 9.9990 chunk 1374 optimal weight: 9.9990 chunk 386 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 ASN ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 162 GLN ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 GLN D 423 GLN D 428 ASN ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 ASN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 ASN F 478 GLN G 13 ASN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 466 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 ASN H 104 ASN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 ASN H 261 ASN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 GLN ** H 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 GLN ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 GLN ** J 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 439 ASN ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 400 ASN ** K 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 467 GLN ** M 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 432 ASN M 462 ASN ** M 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN N 84 GLN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 439 ASN N 466 GLN ** O 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 23 ASN O 84 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 ASN ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 272 GLN O 281 ASN ** O 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 356 GLN ** P 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 GLN ** P 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 439 ASN P 466 GLN ** Q 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 326 GLN Q 415 GLN ** Q 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 462 ASN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 400 ASN R 466 GLN S 17 ASN ** S 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 463 GLN S 467 GLN S 477 ASN ** S 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 104 ASN ** U 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 200 ASN U 206 GLN U 209 ASN ** U 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 17 ASN V 26 ASN V 30 GLN ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 GLN ** V 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 399 GLN ** V 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 428 ASN ** V 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 466 GLN ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 415 GLN ** W 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 GLN X 52 ASN ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 ASN Y 17 ASN Y 57 GLN Y 83 GLN Y 87 ASN ** Y 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 383 GLN ** Y 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 ASN ** Z 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 462 ASN Z 466 GLN a 17 ASN a 49 GLN ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 83 GLN ** a 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 272 GLN ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 439 ASN ** c 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 424 ASN ** c 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 466 GLN ** d 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 76 GLN ** e 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 466 GLN ** e 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 30 GLN ** f 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 281 ASN ** f 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 19 ASN ** g 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 62 ASN ** g 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 84 GLN g 101 ASN g 277 GLN g 281 ASN ** g 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 481 GLN Total number of N/Q/H flips: 94 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 113949 Z= 0.305 Angle : 0.728 12.794 154968 Z= 0.403 Chirality : 0.045 0.289 19437 Planarity : 0.004 0.107 20823 Dihedral : 5.370 31.471 16764 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 28.14 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.88 % Favored : 88.90 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.07), residues: 15939 helix: 1.66 (0.06), residues: 6958 sheet: -1.89 (0.11), residues: 2024 loop : -2.80 (0.07), residues: 6957 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3076 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 3065 time to evaluate : 8.840 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 3073 average time/residue: 0.9588 time to fit residues: 5179.4476 Evaluate side-chains 2333 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2329 time to evaluate : 8.856 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.8788 time to fit residues: 18.1763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1584 random chunks: chunk 515 optimal weight: 7.9990 chunk 1378 optimal weight: 7.9990 chunk 302 optimal weight: 8.9990 chunk 898 optimal weight: 0.0270 chunk 377 optimal weight: 6.9990 chunk 1532 optimal weight: 2.9990 chunk 1272 optimal weight: 1.9990 chunk 709 optimal weight: 8.9990 chunk 127 optimal weight: 30.0000 chunk 506 optimal weight: 30.0000 chunk 804 optimal weight: 6.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 462 ASN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN C 83 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN D 98 GLN D 120 GLN D 162 GLN ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN E 90 GLN E 98 GLN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 ASN ** E 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN ** F 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 ASN G 13 ASN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN G 104 ASN ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 ASN ** H 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 439 ASN ** H 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 ASN ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 463 GLN ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 ASN ** J 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 439 ASN ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 400 ASN ** K 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 432 ASN ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 84 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 ASN ** O 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 424 ASN ** P 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 GLN ** P 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 432 ASN P 439 ASN ** Q 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 326 GLN Q 415 GLN ** Q 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 462 ASN Q 475 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 467 GLN ** S 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 428 ASN U 435 ASN ** U 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 466 GLN U 475 GLN V 23 ASN ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 GLN V 356 GLN V 428 ASN V 432 ASN ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 49 GLN ** W 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 415 GLN W 428 ASN ** W 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 ASN Y 57 GLN Y 83 GLN Y 87 ASN ** Y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 407 ASN Y 477 ASN Z 17 ASN ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 279 ASN ** Z 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 415 GLN ** Z 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 478 GLN ** a 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 49 GLN a 76 GLN a 83 GLN ** a 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 439 ASN ** b 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 462 ASN ** d 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 23 ASN ** e 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 162 GLN ** f 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 356 GLN f 415 GLN f 432 ASN ** f 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 23 ASN ** g 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 84 GLN g 277 GLN g 320 GLN ** g 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 481 GLN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 113949 Z= 0.246 Angle : 0.699 14.631 154968 Z= 0.383 Chirality : 0.045 0.281 19437 Planarity : 0.004 0.089 20823 Dihedral : 5.220 32.886 16764 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 25.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.07 % Favored : 89.69 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.07), residues: 15939 helix: 1.77 (0.06), residues: 6935 sheet: -1.84 (0.11), residues: 2159 loop : -2.71 (0.07), residues: 6845 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3062 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 3056 time to evaluate : 8.857 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 3061 average time/residue: 0.9539 time to fit residues: 5151.4202 Evaluate side-chains 2376 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2375 time to evaluate : 8.873 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.8067 time to fit residues: 13.4037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1584 random chunks: chunk 1477 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 873 optimal weight: 10.0000 chunk 1119 optimal weight: 0.9990 chunk 867 optimal weight: 10.0000 chunk 1290 optimal weight: 0.8980 chunk 855 optimal weight: 0.9990 chunk 1526 optimal weight: 7.9990 chunk 955 optimal weight: 3.9990 chunk 930 optimal weight: 6.9990 chunk 704 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN B 356 GLN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN C 83 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 162 GLN ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 ASN ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN E 67 ASN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN F 277 GLN F 281 ASN ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 ASN ** F 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 ASN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 439 ASN ** H 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 463 GLN ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 439 ASN ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 467 GLN ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 432 ASN ** M 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN N 120 GLN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 ASN ** O 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 475 GLN ** P 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN P 84 GLN ** P 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 432 ASN P 439 ASN ** Q 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 GLN ** Q 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 326 GLN Q 415 GLN ** Q 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 462 ASN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 383 GLN ** S 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 467 GLN ** T 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 GLN ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 432 ASN V 466 GLN ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 415 GLN ** W 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 ASN ** Y 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN Y 162 GLN ** Y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 415 GLN ** Z 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 467 GLN a 17 ASN ** a 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 49 GLN ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 83 GLN ** a 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 272 GLN ** a 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 277 GLN ** b 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 439 ASN ** b 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 90 GLN ** c 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 462 ASN ** d 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 281 ASN ** e 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 466 GLN ** e 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 356 GLN f 432 ASN ** f 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 277 GLN g 356 GLN ** g 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 481 GLN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 113949 Z= 0.214 Angle : 0.688 13.696 154968 Z= 0.374 Chirality : 0.044 0.273 19437 Planarity : 0.004 0.076 20823 Dihedral : 5.115 31.248 16764 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.18 % Favored : 89.60 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.07), residues: 15939 helix: 1.83 (0.06), residues: 6905 sheet: -1.71 (0.11), residues: 2184 loop : -2.71 (0.07), residues: 6850 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3078 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 3070 time to evaluate : 9.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 3075 average time/residue: 0.9586 time to fit residues: 5204.9445 Evaluate side-chains 2370 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2370 time to evaluate : 8.897 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.7550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1584 random chunks: chunk 944 optimal weight: 7.9990 chunk 609 optimal weight: 3.9990 chunk 911 optimal weight: 0.7980 chunk 459 optimal weight: 20.0000 chunk 299 optimal weight: 0.8980 chunk 295 optimal weight: 5.9990 chunk 970 optimal weight: 5.9990 chunk 1040 optimal weight: 0.6980 chunk 754 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 1200 optimal weight: 0.0970 overall best weight: 1.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 ASN ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN C 83 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN D 98 GLN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 162 GLN ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN F 281 ASN ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 ASN G 13 ASN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN H 261 ASN H 277 GLN ** H 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 439 ASN ** H 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 253 ASN I 281 ASN I 463 GLN ** J 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 ASN ** J 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 ASN ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN L 177 ASN L 462 ASN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 432 ASN N 30 GLN N 83 GLN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 231 ASN ** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN O 119 GLN ** O 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 GLN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN P 84 GLN ** P 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 439 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 326 GLN Q 415 GLN ** Q 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 462 ASN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 400 ASN ** S 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 23 ASN ** S 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 424 ASN ** S 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 467 GLN ** S 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 84 GLN ** T 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 383 GLN ** U 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 272 GLN U 435 ASN ** U 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 23 ASN V 49 GLN V 57 GLN ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 GLN ** V 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 356 GLN ** V 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 424 ASN ** V 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 432 ASN ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 52 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 467 GLN Y 13 ASN ** Y 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN ** Y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 17 ASN ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 49 GLN ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 439 ASN ** a 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 439 ASN ** b 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 98 GLN ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 466 GLN ** e 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 90 GLN f 120 GLN f 281 ASN f 356 GLN ** f 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 84 GLN ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 113 GLN g 120 GLN g 277 GLN g 374 GLN g 428 ASN ** g 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 481 GLN Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 113949 Z= 0.192 Angle : 0.689 13.598 154968 Z= 0.371 Chirality : 0.044 0.315 19437 Planarity : 0.003 0.074 20823 Dihedral : 4.982 30.644 16764 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.48 % Favored : 90.32 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.07), residues: 15939 helix: 1.84 (0.06), residues: 6890 sheet: -1.60 (0.11), residues: 2167 loop : -2.68 (0.07), residues: 6882 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3106 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 3094 time to evaluate : 8.094 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 3101 average time/residue: 0.9329 time to fit residues: 5101.5328 Evaluate side-chains 2413 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2412 time to evaluate : 9.004 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7910 time to fit residues: 13.2899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1584 random chunks: chunk 1388 optimal weight: 10.0000 chunk 1462 optimal weight: 0.0570 chunk 1334 optimal weight: 4.9990 chunk 1422 optimal weight: 8.9990 chunk 856 optimal weight: 0.8980 chunk 619 optimal weight: 7.9990 chunk 1117 optimal weight: 2.9990 chunk 436 optimal weight: 0.9980 chunk 1285 optimal weight: 9.9990 chunk 1345 optimal weight: 7.9990 chunk 1417 optimal weight: 6.9990 overall best weight: 1.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 GLN ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN E 57 GLN E 67 ASN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN F 281 ASN ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 ASN G 13 ASN G 49 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN H 261 ASN H 277 GLN ** H 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 439 ASN ** H 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 253 ASN ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 ASN ** J 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 466 GLN ** K 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 467 GLN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 432 ASN ** M 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 ASN ** O 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** P 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 439 ASN Q 17 ASN Q 49 GLN ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 326 GLN Q 415 GLN ** Q 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 462 ASN Q 475 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN S 23 ASN S 162 GLN ** S 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 463 GLN S 467 GLN ** S 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN T 84 GLN ** T 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 399 GLN ** U 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 GLN V 57 GLN ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 356 GLN ** V 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 424 ASN ** V 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 432 ASN V 466 GLN ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 415 GLN W 432 ASN ** W 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 ASN Y 23 ASN ** Y 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN ** Y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 415 GLN ** Z 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 17 ASN ** a 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 49 GLN ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 439 ASN ** a 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 467 GLN ** b 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 439 ASN b 466 GLN ** b 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 76 GLN ** d 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 466 GLN ** e 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 281 ASN ** f 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 356 GLN ** f 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 84 GLN g 277 GLN g 481 GLN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 113949 Z= 0.205 Angle : 0.698 13.586 154968 Z= 0.379 Chirality : 0.044 0.296 19437 Planarity : 0.004 0.148 20823 Dihedral : 4.973 43.035 16764 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.88 % Favored : 89.92 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.07), residues: 15939 helix: 1.83 (0.06), residues: 6877 sheet: -1.48 (0.11), residues: 2167 loop : -2.66 (0.07), residues: 6895 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3049 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 3044 time to evaluate : 8.956 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 3046 average time/residue: 0.9574 time to fit residues: 5167.1038 Evaluate side-chains 2365 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2364 time to evaluate : 8.889 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.9148 time to fit residues: 13.3426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1584 random chunks: chunk 934 optimal weight: 0.0060 chunk 1504 optimal weight: 30.0000 chunk 918 optimal weight: 3.9990 chunk 713 optimal weight: 2.9990 chunk 1045 optimal weight: 9.9990 chunk 1578 optimal weight: 3.9990 chunk 1452 optimal weight: 20.0000 chunk 1256 optimal weight: 6.9990 chunk 130 optimal weight: 0.0570 chunk 970 optimal weight: 5.9990 chunk 770 optimal weight: 4.9990 overall best weight: 2.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN C 57 GLN C 83 GLN C 101 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN D 98 GLN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 GLN ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN E 57 GLN E 67 ASN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN F 277 GLN F 281 ASN ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 ASN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN H 277 GLN ** H 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 439 ASN ** H 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 ASN ** J 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 462 ASN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 432 ASN ** M 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN O 281 ASN ** O 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 439 ASN ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 326 GLN Q 415 GLN ** Q 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 462 ASN ** Q 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN S 23 ASN ** S 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 467 GLN ** S 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 GLN V 57 GLN ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 356 GLN ** V 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 424 ASN ** V 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 432 ASN ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 415 GLN W 432 ASN ** W 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 ASN ** Y 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN Y 148 GLN ** Y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 17 ASN ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 49 GLN ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 439 ASN ** a 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 467 GLN b 49 GLN ** b 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 439 ASN ** b 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 76 GLN d 101 ASN ** d 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 356 GLN ** f 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 277 GLN ** g 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 462 ASN g 481 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 113949 Z= 0.213 Angle : 0.712 13.468 154968 Z= 0.386 Chirality : 0.045 0.295 19437 Planarity : 0.004 0.218 20823 Dihedral : 4.974 36.644 16764 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.89 % Favored : 89.92 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.07), residues: 15939 helix: 1.77 (0.06), residues: 6892 sheet: -1.47 (0.11), residues: 2235 loop : -2.65 (0.07), residues: 6812 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31878 Ramachandran restraints generated. 15939 Oldfield, 0 Emsley, 15939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2978 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2974 time to evaluate : 8.102 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 2977 average time/residue: 0.9043 time to fit residues: 4763.2893 Evaluate side-chains 2330 residues out of total 11847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2330 time to evaluate : 8.889 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.6913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1584 random chunks: chunk 998 optimal weight: 0.0010 chunk 1338 optimal weight: 5.9990 chunk 384 optimal weight: 20.0000 chunk 1158 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 349 optimal weight: 0.0020 chunk 1258 optimal weight: 10.0000 chunk 526 optimal weight: 5.9990 chunk 1292 optimal weight: 8.9990 chunk 159 optimal weight: 20.0000 chunk 231 optimal weight: 0.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN E 57 GLN E 67 ASN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 475 GLN ** E 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN F 277 GLN F 281 ASN ** F 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 ASN ** F 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 ASN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 439 ASN G 442 ASN ** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN H 277 GLN ** H 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 439 ASN ** H 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 463 GLN ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 ASN ** J 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 462 ASN ** K 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN L 462 ASN L 467 GLN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 432 ASN M 466 GLN ** M 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 ASN N 83 GLN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN O 200 ASN O 281 ASN ** O 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** P 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 439 ASN ** Q 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 326 GLN Q 415 GLN ** Q 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 462 ASN Q 475 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN S 23 ASN ** S 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 467 GLN ** S 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 272 GLN ** U 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 GLN V 57 GLN ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 356 GLN ** V 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 432 ASN ** W 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 ASN ** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 415 GLN W 432 ASN ** W 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 462 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 ASN ** Y 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN ** Y 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 279 ASN ** Y 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 467 GLN a 17 ASN a 49 GLN ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 83 GLN ** a 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 439 ASN ** a 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 467 GLN ** b 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 439 ASN ** b 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 356 GLN ** f 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 277 GLN g 428 ASN g 481 GLN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.110253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.084000 restraints weight = 661337.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.088224 restraints weight = 378843.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.091355 restraints weight = 251457.729| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 113949 Z= 0.209 Angle : 0.709 12.804 154968 Z= 0.385 Chirality : 0.045 0.290 19437 Planarity : 0.004 0.182 20823 Dihedral : 4.962 31.795 16764 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.87 % Favored : 89.93 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.07), residues: 15939 helix: 1.74 (0.06), residues: 6897 sheet: -1.54 (0.11), residues: 2326 loop : -2.64 (0.07), residues: 6716 =============================================================================== Job complete usr+sys time: 61955.46 seconds wall clock time: 1066 minutes 50.65 seconds (64010.65 seconds total)