Starting phenix.real_space_refine on Tue Mar 26 02:49:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vk3_43299/03_2024/8vk3_43299_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vk3_43299/03_2024/8vk3_43299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vk3_43299/03_2024/8vk3_43299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vk3_43299/03_2024/8vk3_43299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vk3_43299/03_2024/8vk3_43299_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vk3_43299/03_2024/8vk3_43299_updated.pdb" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.026 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 8 5.49 5 S 988 5.16 5 C 94716 2.51 5 N 25444 2.21 5 O 27692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 19": "OD1" <-> "OD2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1038": "OD1" <-> "OD2" Residue "A ASP 1113": "OD1" <-> "OD2" Residue "A ASP 1208": "OD1" <-> "OD2" Residue "A TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1466": "OD1" <-> "OD2" Residue "A GLU 1480": "OE1" <-> "OE2" Residue "A PHE 1540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1544": "OE1" <-> "OE2" Residue "A ASP 1617": "OD1" <-> "OD2" Residue "A ASP 1714": "OD1" <-> "OD2" Residue "A GLU 1795": "OE1" <-> "OE2" Residue "A ASP 1968": "OD1" <-> "OD2" Residue "A PHE 1999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2027": "OE1" <-> "OE2" Residue "A GLU 2206": "OE1" <-> "OE2" Residue "A ASP 2321": "OD1" <-> "OD2" Residue "A GLU 2348": "OE1" <-> "OE2" Residue "A GLU 2372": "OE1" <-> "OE2" Residue "A ASP 2517": "OD1" <-> "OD2" Residue "A GLU 2546": "OE1" <-> "OE2" Residue "A PHE 2629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2630": "OD1" <-> "OD2" Residue "A GLU 2650": "OE1" <-> "OE2" Residue "A PHE 2958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2969": "OD1" <-> "OD2" Residue "A PHE 2974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2988": "OE1" <-> "OE2" Residue "A TYR 3010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3102": "OE1" <-> "OE2" Residue "A GLU 3210": "OE1" <-> "OE2" Residue "A TYR 3214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3291": "OE1" <-> "OE2" Residue "A PHE 3399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3441": "OE1" <-> "OE2" Residue "A GLU 3456": "OE1" <-> "OE2" Residue "A PHE 3459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3547": "OD1" <-> "OD2" Residue "A TYR 3577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3760": "OE1" <-> "OE2" Residue "A GLU 3828": "OE1" <-> "OE2" Residue "A ASP 3865": "OD1" <-> "OD2" Residue "A GLU 3931": "OE1" <-> "OE2" Residue "A ASP 3944": "OD1" <-> "OD2" Residue "A GLU 3970": "OE1" <-> "OE2" Residue "A ASP 4009": "OD1" <-> "OD2" Residue "A ASP 4021": "OD1" <-> "OD2" Residue "A ASP 4049": "OD1" <-> "OD2" Residue "A PHE 4096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4171": "OE1" <-> "OE2" Residue "A GLU 4247": "OE1" <-> "OE2" Residue "A PHE 4562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4867": "OE1" <-> "OE2" Residue "A GLU 4898": "OE1" <-> "OE2" Residue "A TYR 4910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4915": "OD1" <-> "OD2" Residue "A GLU 4946": "OE1" <-> "OE2" Residue "A PHE 4957": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 42": "OD1" <-> "OD2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "J ASP 67": "OD1" <-> "OD2" Residue "I PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "G ASP 42": "OD1" <-> "OD2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "K PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 67": "OD1" <-> "OD2" Residue "N ASP 67": "OD1" <-> "OD2" Residue "P ASP 67": "OD1" <-> "OD2" Residue "D ASP 19": "OD1" <-> "OD2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 141": "OD1" <-> "OD2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D ASP 229": "OD1" <-> "OD2" Residue "D ASP 238": "OD1" <-> "OD2" Residue "D TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "D GLU 464": "OE1" <-> "OE2" Residue "D TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1038": "OD1" <-> "OD2" Residue "D ASP 1113": "OD1" <-> "OD2" Residue "D ASP 1208": "OD1" <-> "OD2" Residue "D TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1466": "OD1" <-> "OD2" Residue "D GLU 1480": "OE1" <-> "OE2" Residue "D PHE 1540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1544": "OE1" <-> "OE2" Residue "D ASP 1617": "OD1" <-> "OD2" Residue "D ASP 1714": "OD1" <-> "OD2" Residue "D GLU 1795": "OE1" <-> "OE2" Residue "D ASP 1968": "OD1" <-> "OD2" Residue "D PHE 1999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2027": "OE1" <-> "OE2" Residue "D GLU 2206": "OE1" <-> "OE2" Residue "D ASP 2321": "OD1" <-> "OD2" Residue "D GLU 2348": "OE1" <-> "OE2" Residue "D GLU 2372": "OE1" <-> "OE2" Residue "D ASP 2517": "OD1" <-> "OD2" Residue "D GLU 2546": "OE1" <-> "OE2" Residue "D PHE 2629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2630": "OD1" <-> "OD2" Residue "D GLU 2650": "OE1" <-> "OE2" Residue "D PHE 2958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2969": "OD1" <-> "OD2" Residue "D PHE 2974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2988": "OE1" <-> "OE2" Residue "D TYR 3010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3102": "OE1" <-> "OE2" Residue "D GLU 3210": "OE1" <-> "OE2" Residue "D TYR 3214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 3220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3291": "OE1" <-> "OE2" Residue "D PHE 3399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3441": "OE1" <-> "OE2" Residue "D GLU 3456": "OE1" <-> "OE2" Residue "D PHE 3459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3547": "OD1" <-> "OD2" Residue "D TYR 3577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3760": "OE1" <-> "OE2" Residue "D GLU 3828": "OE1" <-> "OE2" Residue "D ASP 3865": "OD1" <-> "OD2" Residue "D GLU 3931": "OE1" <-> "OE2" Residue "D ASP 3944": "OD1" <-> "OD2" Residue "D GLU 3970": "OE1" <-> "OE2" Residue "D ASP 4009": "OD1" <-> "OD2" Residue "D ASP 4021": "OD1" <-> "OD2" Residue "D ASP 4049": "OD1" <-> "OD2" Residue "D PHE 4096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4171": "OE1" <-> "OE2" Residue "D GLU 4247": "OE1" <-> "OE2" Residue "D PHE 4562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4867": "OE1" <-> "OE2" Residue "D GLU 4898": "OE1" <-> "OE2" Residue "D TYR 4910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4915": "OD1" <-> "OD2" Residue "D GLU 4946": "OE1" <-> "OE2" Residue "D PHE 4957": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 19": "OD1" <-> "OD2" Residue "B PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 141": "OD1" <-> "OD2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B ASP 238": "OD1" <-> "OD2" Residue "B TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1038": "OD1" <-> "OD2" Residue "B ASP 1113": "OD1" <-> "OD2" Residue "B ASP 1208": "OD1" <-> "OD2" Residue "B TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1466": "OD1" <-> "OD2" Residue "B GLU 1480": "OE1" <-> "OE2" Residue "B PHE 1540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1544": "OE1" <-> "OE2" Residue "B ASP 1617": "OD1" <-> "OD2" Residue "B ASP 1714": "OD1" <-> "OD2" Residue "B GLU 1795": "OE1" <-> "OE2" Residue "B ASP 1968": "OD1" <-> "OD2" Residue "B PHE 1999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2027": "OE1" <-> "OE2" Residue "B GLU 2206": "OE1" <-> "OE2" Residue "B ASP 2321": "OD1" <-> "OD2" Residue "B GLU 2348": "OE1" <-> "OE2" Residue "B GLU 2372": "OE1" <-> "OE2" Residue "B ASP 2517": "OD1" <-> "OD2" Residue "B GLU 2546": "OE1" <-> "OE2" Residue "B PHE 2629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2630": "OD1" <-> "OD2" Residue "B GLU 2650": "OE1" <-> "OE2" Residue "B PHE 2958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2969": "OD1" <-> "OD2" Residue "B PHE 2974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2988": "OE1" <-> "OE2" Residue "B TYR 3010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3102": "OE1" <-> "OE2" Residue "B GLU 3210": "OE1" <-> "OE2" Residue "B TYR 3214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3291": "OE1" <-> "OE2" Residue "B PHE 3399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3441": "OE1" <-> "OE2" Residue "B GLU 3456": "OE1" <-> "OE2" Residue "B PHE 3459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3547": "OD1" <-> "OD2" Residue "B TYR 3577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3760": "OE1" <-> "OE2" Residue "B GLU 3828": "OE1" <-> "OE2" Residue "B ASP 3865": "OD1" <-> "OD2" Residue "B GLU 3931": "OE1" <-> "OE2" Residue "B ASP 3944": "OD1" <-> "OD2" Residue "B GLU 3970": "OE1" <-> "OE2" Residue "B ASP 4009": "OD1" <-> "OD2" Residue "B ASP 4021": "OD1" <-> "OD2" Residue "B ASP 4049": "OD1" <-> "OD2" Residue "B PHE 4096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4171": "OE1" <-> "OE2" Residue "B GLU 4247": "OE1" <-> "OE2" Residue "B PHE 4562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4867": "OE1" <-> "OE2" Residue "B GLU 4898": "OE1" <-> "OE2" Residue "B TYR 4910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4915": "OD1" <-> "OD2" Residue "B GLU 4946": "OE1" <-> "OE2" Residue "B PHE 4957": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 19": "OD1" <-> "OD2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C ASP 238": "OD1" <-> "OD2" Residue "C TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "C GLU 464": "OE1" <-> "OE2" Residue "C TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1038": "OD1" <-> "OD2" Residue "C ASP 1113": "OD1" <-> "OD2" Residue "C ASP 1208": "OD1" <-> "OD2" Residue "C TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1466": "OD1" <-> "OD2" Residue "C GLU 1480": "OE1" <-> "OE2" Residue "C PHE 1540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1544": "OE1" <-> "OE2" Residue "C ASP 1617": "OD1" <-> "OD2" Residue "C ASP 1714": "OD1" <-> "OD2" Residue "C GLU 1795": "OE1" <-> "OE2" Residue "C ASP 1968": "OD1" <-> "OD2" Residue "C PHE 1999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2027": "OE1" <-> "OE2" Residue "C GLU 2206": "OE1" <-> "OE2" Residue "C ASP 2321": "OD1" <-> "OD2" Residue "C GLU 2348": "OE1" <-> "OE2" Residue "C GLU 2372": "OE1" <-> "OE2" Residue "C ASP 2517": "OD1" <-> "OD2" Residue "C GLU 2546": "OE1" <-> "OE2" Residue "C PHE 2629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2630": "OD1" <-> "OD2" Residue "C GLU 2650": "OE1" <-> "OE2" Residue "C PHE 2958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2969": "OD1" <-> "OD2" Residue "C PHE 2974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2988": "OE1" <-> "OE2" Residue "C TYR 3010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3102": "OE1" <-> "OE2" Residue "C GLU 3210": "OE1" <-> "OE2" Residue "C TYR 3214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3291": "OE1" <-> "OE2" Residue "C PHE 3399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3441": "OE1" <-> "OE2" Residue "C GLU 3456": "OE1" <-> "OE2" Residue "C PHE 3459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3547": "OD1" <-> "OD2" Residue "C TYR 3577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3760": "OE1" <-> "OE2" Residue "C GLU 3828": "OE1" <-> "OE2" Residue "C ASP 3865": "OD1" <-> "OD2" Residue "C GLU 3931": "OE1" <-> "OE2" Residue "C ASP 3944": "OD1" <-> "OD2" Residue "C GLU 3970": "OE1" <-> "OE2" Residue "C ASP 4009": "OD1" <-> "OD2" Residue "C ASP 4021": "OD1" <-> "OD2" Residue "C ASP 4049": "OD1" <-> "OD2" Residue "C PHE 4096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4171": "OE1" <-> "OE2" Residue "C GLU 4247": "OE1" <-> "OE2" Residue "C PHE 4562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4867": "OE1" <-> "OE2" Residue "C GLU 4898": "OE1" <-> "OE2" Residue "C TYR 4910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4915": "OD1" <-> "OD2" Residue "C GLU 4946": "OE1" <-> "OE2" Residue "C PHE 4957": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.46s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 148852 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 34809 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4374, 34804 Classifications: {'peptide': 4374} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 220, 'TRANS': 4151} Chain breaks: 13 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 4374, 34804 Classifications: {'peptide': 4374} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 220, 'TRANS': 4151} Chain breaks: 13 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 35587 Chain: "E" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'TRANS': 92} Chain: "I" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 737 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'TRANS': 93} Chain: "H" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 737 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'TRANS': 93} Chain: "M" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 737 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'TRANS': 93} Chain: "O" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 737 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'TRANS': 93} Chain: "L" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'TRANS': 92} Chain: "N" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'TRANS': 92} Chain: "P" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'TRANS': 92} Chain: "D" Number of atoms: 34809 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4374, 34804 Classifications: {'peptide': 4374} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 220, 'TRANS': 4151} Chain breaks: 13 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 4374, 34804 Classifications: {'peptide': 4374} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 220, 'TRANS': 4151} Chain breaks: 13 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 35587 Chain: "B" Number of atoms: 34809 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4374, 34804 Classifications: {'peptide': 4374} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 220, 'TRANS': 4151} Chain breaks: 13 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 4374, 34804 Classifications: {'peptide': 4374} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 220, 'TRANS': 4151} Chain breaks: 13 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 35587 Chain: "C" Number of atoms: 34809 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4374, 34804 Classifications: {'peptide': 4374} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 220, 'TRANS': 4151} Chain breaks: 13 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 4374, 34804 Classifications: {'peptide': 4374} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 220, 'TRANS': 4151} Chain breaks: 13 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 35587 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {' ZN': 1, 'PCW': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {' ZN': 1, 'PCW': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {' ZN': 1, 'PCW': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {' ZN': 1, 'PCW': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34135 SG CYS A4956 194.267 169.726 86.657 1.00 74.33 S ATOM 34160 SG CYS A4959 191.857 169.741 89.641 1.00 74.00 S ATOM 78124 SG CYS D4956 169.716 172.348 86.639 1.00 74.33 S ATOM 78149 SG CYS D4959 169.731 174.758 89.623 1.00 74.00 S ATOM A09Z9 SG CYS B4956 196.885 194.260 86.640 1.00 74.33 S ATOM A09ZY SG CYS B4959 196.869 191.850 89.624 1.00 74.00 S ATOM A10U6 SG CYS C4956 172.344 196.888 86.639 1.00 74.33 S ATOM A10UV SG CYS C4959 174.754 196.872 89.624 1.00 74.00 S Time building chain proxies: 102.79, per 1000 atoms: 0.69 Number of scatterers: 148852 At special positions: 0 Unit cell: (367.443, 367.443, 210.924, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 988 16.00 P 8 15.00 O 27692 8.00 N 25444 7.00 C 94716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A3171 " - pdb=" SG CYS A3241 " distance=2.03 Simple disulfide: pdb=" SG CYS A4874 " - pdb=" SG CYS A4880 " distance=2.03 Simple disulfide: pdb=" SG CYS D3171 " - pdb=" SG CYS D3241 " distance=2.03 Simple disulfide: pdb=" SG CYS D4874 " - pdb=" SG CYS D4880 " distance=2.03 Simple disulfide: pdb=" SG CYS B3171 " - pdb=" SG CYS B3241 " distance=2.03 Simple disulfide: pdb=" SG CYS B4874 " - pdb=" SG CYS B4880 " distance=2.03 Simple disulfide: pdb=" SG CYS C3171 " - pdb=" SG CYS C3241 " distance=2.03 Simple disulfide: pdb=" SG CYS C4874 " - pdb=" SG CYS C4880 " distance=2.03 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: 46.48 Conformation dependent library (CDL) restraints added in 38.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A8001 " pdb="ZN ZN A8001 " - pdb=" NE2 HIS A4976 " pdb="ZN ZN A8001 " - pdb=" ND1 HIS A4981 " pdb="ZN ZN A8001 " - pdb=" SG CYS A4959 " pdb="ZN ZN A8001 " - pdb=" SG CYS A4956 " pdb=" ZN B8001 " pdb="ZN ZN B8001 " - pdb=" NE2 HIS B4976 " pdb="ZN ZN B8001 " - pdb=" ND1 HIS B4981 " pdb="ZN ZN B8001 " - pdb=" SG CYS B4959 " pdb="ZN ZN B8001 " - pdb=" SG CYS B4956 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4976 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4981 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4959 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4956 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4976 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4981 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4959 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4956 " Number of angles added : 4 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 34960 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 748 helices and 84 sheets defined 60.3% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 48.42 Creating SS restraints... Processing helix chain 'A' and resid 62 through 67 removed outlier: 4.355A pdb=" N CYS A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 67' Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.777A pdb=" N HIS A 256 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ALA A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 257' Processing helix chain 'A' and resid 304 through 309 removed outlier: 5.061A pdb=" N HIS A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 395 through 423 removed outlier: 3.776A pdb=" N PHE A 422 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 461 through 483 Processing helix chain 'A' and resid 484 through 498 removed outlier: 4.507A pdb=" N TYR A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.735A pdb=" N PHE A 507 " --> pdb=" O HIS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 532 removed outlier: 4.317A pdb=" N SER A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLU A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 545 removed outlier: 3.812A pdb=" N LEU A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE A 541 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER A 542 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 553 removed outlier: 4.117A pdb=" N LYS A 551 " --> pdb=" O TRP A 547 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 572 Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 580 through 594 removed outlier: 3.513A pdb=" N LEU A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 610 removed outlier: 3.593A pdb=" N LEU A 601 " --> pdb=" O ASN A 597 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 609 " --> pdb=" O CYS A 605 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N CYS A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 630 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 811 through 816 removed outlier: 4.510A pdb=" N ALA A 815 " --> pdb=" O PRO A 811 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL A 816 " --> pdb=" O CYS A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 816' Processing helix chain 'A' and resid 848 through 854 removed outlier: 4.092A pdb=" N PHE A 852 " --> pdb=" O SER A 848 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL A 853 " --> pdb=" O HIS A 849 " (cutoff:3.500A) Proline residue: A 854 - end of helix No H-bonds generated for 'chain 'A' and resid 848 through 854' Processing helix chain 'A' and resid 866 through 891 removed outlier: 3.709A pdb=" N ILE A 871 " --> pdb=" O HIS A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 936 Processing helix chain 'A' and resid 944 through 951 removed outlier: 4.518A pdb=" N GLU A 948 " --> pdb=" O ASP A 944 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASP A 949 " --> pdb=" O GLU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 962 removed outlier: 4.501A pdb=" N MET A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1005 Processing helix chain 'A' and resid 1024 through 1029 removed outlier: 3.776A pdb=" N LEU A1028 " --> pdb=" O PRO A1024 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP A1029 " --> pdb=" O TYR A1025 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1024 through 1029' Processing helix chain 'A' and resid 1030 through 1049 removed outlier: 3.540A pdb=" N ALA A1043 " --> pdb=" O SER A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1074 removed outlier: 4.925A pdb=" N ARG A1074 " --> pdb=" O GLY A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1223 removed outlier: 7.102A pdb=" N GLU A1222 " --> pdb=" O CYS A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1431 Processing helix chain 'A' and resid 1445 through 1450 removed outlier: 3.923A pdb=" N VAL A1449 " --> pdb=" O GLU A1445 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TRP A1450 " --> pdb=" O PRO A1446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1445 through 1450' Processing helix chain 'A' and resid 1497 through 1503 removed outlier: 4.433A pdb=" N PHE A1501 " --> pdb=" O TRP A1497 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A1502 " --> pdb=" O GLY A1498 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N SER A1503 " --> pdb=" O GLY A1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1497 through 1503' Processing helix chain 'A' and resid 1575 through 1581 removed outlier: 3.823A pdb=" N ALA A1579 " --> pdb=" O PRO A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1650 through 1657 removed outlier: 4.306A pdb=" N LEU A1654 " --> pdb=" O ASP A1650 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER A1655 " --> pdb=" O ILE A1651 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU A1656 " --> pdb=" O LEU A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1676 Processing helix chain 'A' and resid 1679 through 1690 removed outlier: 3.877A pdb=" N SER A1688 " --> pdb=" O HIS A1684 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS A1689 " --> pdb=" O ALA A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1701 Processing helix chain 'A' and resid 1705 through 1720 Processing helix chain 'A' and resid 1721 through 1733 removed outlier: 4.193A pdb=" N SER A1733 " --> pdb=" O ARG A1729 " (cutoff:3.500A) Processing helix chain 'A' and resid 1740 through 1747 removed outlier: 5.706A pdb=" N THR A1747 " --> pdb=" O THR A1743 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1827 Processing helix chain 'A' and resid 1835 through 1854 Proline residue: A1842 - end of helix Processing helix chain 'A' and resid 1857 through 1869 Processing helix chain 'A' and resid 1926 through 1931 removed outlier: 4.898A pdb=" N LYS A1931 " --> pdb=" O LEU A1927 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1985 removed outlier: 5.342A pdb=" N PHE A1985 " --> pdb=" O LEU A1981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1988 through 2001 removed outlier: 3.759A pdb=" N ARG A1994 " --> pdb=" O ALA A1990 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU A1998 " --> pdb=" O ARG A1994 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A1999 " --> pdb=" O ARG A1995 " (cutoff:3.500A) Processing helix chain 'A' and resid 2002 through 2012 Processing helix chain 'A' and resid 2025 through 2044 removed outlier: 3.657A pdb=" N GLU A2031 " --> pdb=" O GLU A2027 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A2032 " --> pdb=" O ILE A2028 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2110 Processing helix chain 'A' and resid 2114 through 2131 removed outlier: 3.810A pdb=" N GLY A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2142 Proline residue: A2140 - end of helix Processing helix chain 'A' and resid 2146 through 2170 removed outlier: 3.887A pdb=" N VAL A2150 " --> pdb=" O SER A2146 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU A2151 " --> pdb=" O VAL A2147 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP A2152 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A2167 " --> pdb=" O ILE A2163 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE A2168 " --> pdb=" O ARG A2164 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL A2169 " --> pdb=" O SER A2165 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN A2170 " --> pdb=" O LEU A2166 " (cutoff:3.500A) Processing helix chain 'A' and resid 2172 through 2190 removed outlier: 5.492A pdb=" N LYS A2190 " --> pdb=" O ILE A2186 " (cutoff:3.500A) Processing helix chain 'A' and resid 2195 through 2203 Processing helix chain 'A' and resid 2204 through 2220 removed outlier: 5.209A pdb=" N GLY A2219 " --> pdb=" O VAL A2215 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU A2220 " --> pdb=" O LEU A2216 " (cutoff:3.500A) Processing helix chain 'A' and resid 2226 through 2245 removed outlier: 4.084A pdb=" N SER A2244 " --> pdb=" O PHE A2240 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ARG A2245 " --> pdb=" O CYS A2241 " (cutoff:3.500A) Processing helix chain 'A' and resid 2246 through 2255 removed outlier: 3.644A pdb=" N HIS A2254 " --> pdb=" O SER A2250 " (cutoff:3.500A) Processing helix chain 'A' and resid 2256 through 2263 removed outlier: 4.245A pdb=" N GLY A2263 " --> pdb=" O LEU A2259 " (cutoff:3.500A) Processing helix chain 'A' and resid 2272 through 2282 removed outlier: 3.523A pdb=" N VAL A2281 " --> pdb=" O ALA A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2284 through 2291 Processing helix chain 'A' and resid 2292 through 2309 Processing helix chain 'A' and resid 2311 through 2318 Processing helix chain 'A' and resid 2325 through 2341 removed outlier: 3.755A pdb=" N ARG A2331 " --> pdb=" O CYS A2327 " (cutoff:3.500A) Processing helix chain 'A' and resid 2347 through 2362 Proline residue: A2362 - end of helix Processing helix chain 'A' and resid 2376 through 2391 Proline residue: A2391 - end of helix Processing helix chain 'A' and resid 2418 through 2438 Processing helix chain 'A' and resid 2440 through 2447 Processing helix chain 'A' and resid 2448 through 2463 Proline residue: A2463 - end of helix Processing helix chain 'A' and resid 2464 through 2473 Processing helix chain 'A' and resid 2496 through 2510 removed outlier: 3.866A pdb=" N LYS A2500 " --> pdb=" O VAL A2496 " (cutoff:3.500A) Processing helix chain 'A' and resid 2515 through 2526 Processing helix chain 'A' and resid 2527 through 2539 removed outlier: 3.607A pdb=" N ASP A2538 " --> pdb=" O ALA A2534 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N THR A2539 " --> pdb=" O ALA A2535 " (cutoff:3.500A) Processing helix chain 'A' and resid 2545 through 2567 removed outlier: 5.048A pdb=" N LEU A2560 " --> pdb=" O CYS A2556 " (cutoff:3.500A) Proline residue: A2561 - end of helix Processing helix chain 'A' and resid 2576 through 2594 removed outlier: 3.949A pdb=" N GLY A2593 " --> pdb=" O ARG A2589 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG A2594 " --> pdb=" O LEU A2590 " (cutoff:3.500A) Processing helix chain 'A' and resid 2597 through 2615 removed outlier: 3.685A pdb=" N TYR A2614 " --> pdb=" O ALA A2610 " (cutoff:3.500A) Processing helix chain 'A' and resid 2616 through 2631 removed outlier: 3.906A pdb=" N LEU A2620 " --> pdb=" O ARG A2616 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN A2621 " --> pdb=" O PRO A2617 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N HIS A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU A2623 " --> pdb=" O MET A2619 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A2629 " --> pdb=" O ARG A2625 " (cutoff:3.500A) Processing helix chain 'A' and resid 2637 through 2653 Proline residue: A2641 - end of helix Processing helix chain 'A' and resid 2669 through 2690 Processing helix chain 'A' and resid 2693 through 2712 Proline residue: A2702 - end of helix Proline residue: A2712 - end of helix Processing helix chain 'A' and resid 2742 through 2747 removed outlier: 5.126A pdb=" N ILE A2747 " --> pdb=" O THR A2743 " (cutoff:3.500A) Processing helix chain 'A' and resid 2749 through 2775 Processing helix chain 'A' and resid 2799 through 2821 Proline residue: A2809 - end of helix Processing helix chain 'A' and resid 2869 through 2899 Processing helix chain 'A' and resid 2908 through 2913 removed outlier: 5.395A pdb=" N THR A2913 " --> pdb=" O TYR A2909 " (cutoff:3.500A) Processing helix chain 'A' and resid 2916 through 2935 removed outlier: 4.657A pdb=" N ASP A2920 " --> pdb=" O GLU A2916 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS A2923 " --> pdb=" O ARG A2919 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A2927 " --> pdb=" O LYS A2923 " (cutoff:3.500A) Processing helix chain 'A' and resid 2941 through 2948 removed outlier: 3.821A pdb=" N MET A2945 " --> pdb=" O GLY A2941 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASP A2948 " --> pdb=" O ASP A2944 " (cutoff:3.500A) Processing helix chain 'A' and resid 2950 through 2984 removed outlier: 6.084A pdb=" N PHE A2956 " --> pdb=" O ILE A2952 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALA A2957 " --> pdb=" O GLU A2953 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE A2958 " --> pdb=" O LYS A2954 " (cutoff:3.500A) Processing helix chain 'A' and resid 2992 through 3015 removed outlier: 4.279A pdb=" N LEU A3004 " --> pdb=" O ALA A3000 " (cutoff:3.500A) Proline residue: A3005 - end of helix Processing helix chain 'A' and resid 3033 through 3052 Processing helix chain 'A' and resid 3054 through 3059 Processing helix chain 'A' and resid 3060 through 3076 removed outlier: 4.732A pdb=" N ALA A3064 " --> pdb=" O THR A3060 " (cutoff:3.500A) Processing helix chain 'A' and resid 3077 through 3084 removed outlier: 4.409A pdb=" N VAL A3081 " --> pdb=" O ASP A3077 " (cutoff:3.500A) Processing helix chain 'A' and resid 3086 through 3113 Processing helix chain 'A' and resid 3124 through 3152 removed outlier: 5.266A pdb=" N LEU A3138 " --> pdb=" O THR A3134 " (cutoff:3.500A) Proline residue: A3139 - end of helix Processing helix chain 'A' and resid 3160 through 3180 removed outlier: 3.612A pdb=" N SER A3172 " --> pdb=" O ARG A3168 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A3179 " --> pdb=" O SER A3175 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ARG A3180 " --> pdb=" O LEU A3176 " (cutoff:3.500A) Processing helix chain 'A' and resid 3181 through 3202 removed outlier: 3.817A pdb=" N LYS A3186 " --> pdb=" O PRO A3182 " (cutoff:3.500A) Proline residue: A3189 - end of helix Processing helix chain 'A' and resid 3208 through 3216 removed outlier: 4.087A pdb=" N ASN A3212 " --> pdb=" O GLU A3208 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU A3213 " --> pdb=" O PRO A3209 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR A3214 " --> pdb=" O GLU A3210 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN A3215 " --> pdb=" O LEU A3211 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ALA A3216 " --> pdb=" O ASN A3212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3208 through 3216' Processing helix chain 'A' and resid 3218 through 3223 Processing helix chain 'A' and resid 3224 through 3232 removed outlier: 4.437A pdb=" N ARG A3228 " --> pdb=" O SER A3224 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA A3229 " --> pdb=" O PRO A3225 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE A3230 " --> pdb=" O ARG A3226 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A3231 " --> pdb=" O GLU A3227 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLY A3232 " --> pdb=" O ARG A3228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3224 through 3232' Processing helix chain 'A' and resid 3236 through 3242 removed outlier: 3.532A pdb=" N MET A3240 " --> pdb=" O SER A3236 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N CYS A3241 " --> pdb=" O VAL A3237 " (cutoff:3.500A) Proline residue: A3242 - end of helix No H-bonds generated for 'chain 'A' and resid 3236 through 3242' Processing helix chain 'A' and resid 3246 through 3261 Processing helix chain 'A' and resid 3263 through 3268 removed outlier: 3.835A pdb=" N MET A3267 " --> pdb=" O ARG A3263 " (cutoff:3.500A) Proline residue: A3268 - end of helix No H-bonds generated for 'chain 'A' and resid 3263 through 3268' Processing helix chain 'A' and resid 3269 through 3289 removed outlier: 4.574A pdb=" N LEU A3275 " --> pdb=" O ILE A3271 " (cutoff:3.500A) Proline residue: A3276 - end of helix Proline residue: A3283 - end of helix removed outlier: 3.658A pdb=" N ARG A3288 " --> pdb=" O ARG A3284 " (cutoff:3.500A) Processing helix chain 'A' and resid 3309 through 3328 Processing helix chain 'A' and resid 3333 through 3348 removed outlier: 4.799A pdb=" N LYS A3337 " --> pdb=" O ALA A3333 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A3338 " --> pdb=" O SER A3334 " (cutoff:3.500A) Proline residue: A3345 - end of helix removed outlier: 4.322A pdb=" N SER A3348 " --> pdb=" O GLN A3344 " (cutoff:3.500A) Processing helix chain 'A' and resid 3351 through 3384 removed outlier: 4.708A pdb=" N LEU A3355 " --> pdb=" O ARG A3351 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ARG A3356 " --> pdb=" O PRO A3352 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A3360 " --> pdb=" O ARG A3356 " (cutoff:3.500A) Proline residue: A3361 - end of helix removed outlier: 4.406A pdb=" N ALA A3384 " --> pdb=" O LEU A3380 " (cutoff:3.500A) Processing helix chain 'A' and resid 3390 through 3414 removed outlier: 6.731A pdb=" N LEU A3394 " --> pdb=" O GLU A3390 " (cutoff:3.500A) Proline residue: A3411 - end of helix Processing helix chain 'A' and resid 3420 through 3428 Proline residue: A3428 - end of helix Processing helix chain 'A' and resid 3429 through 3449 Processing helix chain 'A' and resid 3450 through 3464 removed outlier: 3.759A pdb=" N ARG A3454 " --> pdb=" O HIS A3450 " (cutoff:3.500A) Processing helix chain 'A' and resid 3466 through 3472 removed outlier: 4.047A pdb=" N PHE A3470 " --> pdb=" O ASN A3466 " (cutoff:3.500A) Processing helix chain 'A' and resid 3509 through 3527 removed outlier: 3.622A pdb=" N LEU A3515 " --> pdb=" O ILE A3511 " (cutoff:3.500A) Proline residue: A3520 - end of helix removed outlier: 3.579A pdb=" N MET A3525 " --> pdb=" O ILE A3521 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ALA A3527 " --> pdb=" O LEU A3523 " (cutoff:3.500A) Processing helix chain 'A' and resid 3528 through 3544 removed outlier: 5.271A pdb=" N ASP A3532 " --> pdb=" O PRO A3528 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU A3533 " --> pdb=" O THR A3529 " (cutoff:3.500A) Processing helix chain 'A' and resid 3546 through 3558 removed outlier: 3.744A pdb=" N LEU A3558 " --> pdb=" O LEU A3554 " (cutoff:3.500A) Processing helix chain 'A' and resid 3563 through 3568 Proline residue: A3568 - end of helix Processing helix chain 'A' and resid 3569 through 3581 Proline residue: A3581 - end of helix Processing helix chain 'A' and resid 3589 through 3613 Proline residue: A3613 - end of helix Processing helix chain 'A' and resid 3634 through 3639 removed outlier: 4.720A pdb=" N MET A3639 " --> pdb=" O ALA A3635 " (cutoff:3.500A) Processing helix chain 'A' and resid 3646 through 3662 Processing helix chain 'A' and resid 3670 through 3681 removed outlier: 5.546A pdb=" N ALA A3681 " --> pdb=" O ASP A3677 " (cutoff:3.500A) Processing helix chain 'A' and resid 3683 through 3688 removed outlier: 3.736A pdb=" N GLU A3687 " --> pdb=" O GLU A3683 " (cutoff:3.500A) Processing helix chain 'A' and resid 3697 through 3712 Processing helix chain 'A' and resid 3720 through 3735 removed outlier: 3.557A pdb=" N ASP A3728 " --> pdb=" O MET A3724 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS A3734 " --> pdb=" O MET A3730 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N HIS A3735 " --> pdb=" O ALA A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3755 through 3775 removed outlier: 3.636A pdb=" N LEU A3773 " --> pdb=" O GLN A3769 " (cutoff:3.500A) Processing helix chain 'A' and resid 3777 through 3790 removed outlier: 4.204A pdb=" N LYS A3790 " --> pdb=" O ILE A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3794 through 3809 Processing helix chain 'A' and resid 3812 through 3827 Processing helix chain 'A' and resid 3829 through 3842 Processing helix chain 'A' and resid 3846 through 3860 removed outlier: 4.875A pdb=" N GLY A3860 " --> pdb=" O ALA A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3880 through 3896 removed outlier: 3.612A pdb=" N CYS A3895 " --> pdb=" O LEU A3891 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3908 removed outlier: 4.240A pdb=" N ARG A3907 " --> pdb=" O GLN A3903 " (cutoff:3.500A) Processing helix chain 'A' and resid 3917 through 3942 removed outlier: 4.610A pdb=" N GLY A3942 " --> pdb=" O TRP A3938 " (cutoff:3.500A) Processing helix chain 'A' and resid 3947 through 3973 Processing helix chain 'A' and resid 3976 through 3987 removed outlier: 4.729A pdb=" N ARG A3987 " --> pdb=" O LEU A3983 " (cutoff:3.500A) Processing helix chain 'A' and resid 3988 through 4010 removed outlier: 3.713A pdb=" N ASP A4009 " --> pdb=" O LYS A4005 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER A4010 " --> pdb=" O LEU A4006 " (cutoff:3.500A) Processing helix chain 'A' and resid 4012 through 4035 Processing helix chain 'A' and resid 4041 through 4055 Processing helix chain 'A' and resid 4056 through 4074 removed outlier: 4.750A pdb=" N LYS A4072 " --> pdb=" O PHE A4068 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP A4073 " --> pdb=" O LEU A4069 " (cutoff:3.500A) Processing helix chain 'A' and resid 4077 through 4085 removed outlier: 5.135A pdb=" N THR A4085 " --> pdb=" O GLN A4081 " (cutoff:3.500A) Processing helix chain 'A' and resid 4092 through 4104 Processing helix chain 'A' and resid 4107 through 4119 removed outlier: 4.436A pdb=" N GLU A4119 " --> pdb=" O LEU A4115 " (cutoff:3.500A) Processing helix chain 'A' and resid 4127 through 4158 removed outlier: 4.420A pdb=" N PHE A4135 " --> pdb=" O PHE A4131 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN A4136 " --> pdb=" O ALA A4132 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU A4137 " --> pdb=" O ASN A4133 " (cutoff:3.500A) Proline residue: A4138 - end of helix removed outlier: 3.870A pdb=" N ASP A4141 " --> pdb=" O GLU A4137 " (cutoff:3.500A) Proline residue: A4158 - end of helix Processing helix chain 'A' and resid 4160 through 4171 removed outlier: 3.508A pdb=" N LEU A4169 " --> pdb=" O ASN A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4172 through 4178 Processing helix chain 'A' and resid 4201 through 4210 Processing helix chain 'A' and resid 4211 through 4227 Processing helix chain 'A' and resid 4232 through 4255 Processing helix chain 'A' and resid 4538 through 4557 Processing helix chain 'A' and resid 4558 through 4578 removed outlier: 4.362A pdb=" N PHE A4577 " --> pdb=" O PHE A4573 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N TYR A4578 " --> pdb=" O ILE A4574 " (cutoff:3.500A) Processing helix chain 'A' and resid 4636 through 4681 removed outlier: 4.110A pdb=" N VAL A4664 " --> pdb=" O ASN A4660 " (cutoff:3.500A) Proline residue: A4665 - end of helix Processing helix chain 'A' and resid 4694 through 4705 removed outlier: 3.848A pdb=" N GLN A4698 " --> pdb=" O ASP A4694 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU A4702 " --> pdb=" O GLN A4698 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL A4703 " --> pdb=" O TRP A4699 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A4704 " --> pdb=" O ASP A4700 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASN A4705 " --> pdb=" O ARG A4701 " (cutoff:3.500A) Processing helix chain 'A' and resid 4717 through 4727 Processing helix chain 'A' and resid 4731 through 4740 Processing helix chain 'A' and resid 4742 through 4752 Processing helix chain 'A' and resid 4761 through 4770 removed outlier: 4.339A pdb=" N TRP A4765 " --> pdb=" O GLY A4761 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP A4770 " --> pdb=" O ILE A4766 " (cutoff:3.500A) Processing helix chain 'A' and resid 4771 through 4784 Processing helix chain 'A' and resid 4785 through 4803 removed outlier: 3.789A pdb=" N HIS A4801 " --> pdb=" O SER A4797 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A4802 " --> pdb=" O LEU A4798 " (cutoff:3.500A) Processing helix chain 'A' and resid 4804 through 4818 removed outlier: 4.549A pdb=" N ALA A4808 " --> pdb=" O ASN A4804 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA A4809 " --> pdb=" O PHE A4805 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N HIS A4810 " --> pdb=" O PHE A4806 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU A4811 " --> pdb=" O PHE A4807 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A4812 " --> pdb=" O ALA A4808 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP A4813 " --> pdb=" O ALA A4809 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE A4814 " --> pdb=" O HIS A4810 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA A4815 " --> pdb=" O LEU A4811 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET A4816 " --> pdb=" O LEU A4812 " (cutoff:3.500A) Processing helix chain 'A' and resid 4819 through 4830 removed outlier: 3.592A pdb=" N SER A4827 " --> pdb=" O THR A4823 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A4828 " --> pdb=" O ILE A4824 " (cutoff:3.500A) Processing helix chain 'A' and resid 4831 through 4856 Processing helix chain 'A' and resid 4857 through 4862 removed outlier: 4.370A pdb=" N TYR A4861 " --> pdb=" O PHE A4857 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN A4862 " --> pdb=" O ARG A4858 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4857 through 4862' Processing helix chain 'A' and resid 4876 through 4891 removed outlier: 4.181A pdb=" N VAL A4889 " --> pdb=" O MET A4885 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG A4890 " --> pdb=" O TYR A4886 " (cutoff:3.500A) Processing helix chain 'A' and resid 4894 through 4899 removed outlier: 4.211A pdb=" N GLU A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) Processing helix chain 'A' and resid 4907 through 4922 Processing helix chain 'A' and resid 4926 through 4955 Processing helix chain 'A' and resid 4962 through 4968 removed outlier: 3.871A pdb=" N PHE A4966 " --> pdb=" O GLY A4962 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A4968 " --> pdb=" O ASP A4964 " (cutoff:3.500A) Processing helix chain 'A' and resid 4971 through 4979 Processing helix chain 'A' and resid 4982 through 4997 removed outlier: 5.334A pdb=" N ASP A4997 " --> pdb=" O LEU A4993 " (cutoff:3.500A) Processing helix chain 'A' and resid 5002 through 5015 Processing helix chain 'A' and resid 5025 through 5031 Processing helix chain 'A' and resid 323 through 328 removed outlier: 4.979A pdb=" N VAL A 326 " --> pdb=" O LYS A 323 " (cutoff:3.500A) Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 3582 through 3588 removed outlier: 4.952A pdb=" N GLU A3585 " --> pdb=" O GLY A3582 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASP A3586 " --> pdb=" O ARG A3583 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ALA A3587 " --> pdb=" O GLU A3584 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASP A3588 " --> pdb=" O GLU A3585 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3582 through 3588' Processing helix chain 'A' and resid 5016 through 5021 removed outlier: 4.454A pdb=" N PHE A5019 " --> pdb=" O CYS A5016 " (cutoff:3.500A) Proline residue: A5021 - end of helix Processing helix chain 'A' and resid 4683 through 4688 Processing helix chain 'D' and resid 62 through 67 removed outlier: 4.355A pdb=" N CYS D 66 " --> pdb=" O ASP D 62 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 67' Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.777A pdb=" N HIS D 256 " --> pdb=" O PRO D 252 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ALA D 257 " --> pdb=" O VAL D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 257' Processing helix chain 'D' and resid 304 through 309 removed outlier: 5.061A pdb=" N HIS D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 371 Processing helix chain 'D' and resid 395 through 423 removed outlier: 3.777A pdb=" N PHE D 422 " --> pdb=" O GLY D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 454 Processing helix chain 'D' and resid 461 through 483 Processing helix chain 'D' and resid 484 through 498 removed outlier: 4.507A pdb=" N TYR D 498 " --> pdb=" O ARG D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 508 removed outlier: 3.735A pdb=" N PHE D 507 " --> pdb=" O HIS D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 532 removed outlier: 4.317A pdb=" N SER D 515 " --> pdb=" O GLU D 511 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS D 517 " --> pdb=" O ALA D 513 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLU D 518 " --> pdb=" O GLU D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 545 removed outlier: 3.812A pdb=" N LEU D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE D 541 " --> pdb=" O ASN D 537 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER D 542 " --> pdb=" O CYS D 538 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 553 removed outlier: 4.117A pdb=" N LYS D 551 " --> pdb=" O TRP D 547 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D 552 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP D 553 " --> pdb=" O VAL D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 572 Processing helix chain 'D' and resid 573 through 579 Processing helix chain 'D' and resid 580 through 594 removed outlier: 3.514A pdb=" N LEU D 591 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 610 removed outlier: 3.593A pdb=" N LEU D 601 " --> pdb=" O ASN D 597 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS D 608 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL D 609 " --> pdb=" O CYS D 605 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N CYS D 610 " --> pdb=" O SER D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 630 Proline residue: D 628 - end of helix Processing helix chain 'D' and resid 811 through 816 removed outlier: 4.509A pdb=" N ALA D 815 " --> pdb=" O PRO D 811 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL D 816 " --> pdb=" O CYS D 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 811 through 816' Processing helix chain 'D' and resid 848 through 854 removed outlier: 4.093A pdb=" N PHE D 852 " --> pdb=" O SER D 848 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL D 853 " --> pdb=" O HIS D 849 " (cutoff:3.500A) Proline residue: D 854 - end of helix No H-bonds generated for 'chain 'D' and resid 848 through 854' Processing helix chain 'D' and resid 866 through 891 removed outlier: 3.710A pdb=" N ILE D 871 " --> pdb=" O HIS D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 936 Processing helix chain 'D' and resid 944 through 951 removed outlier: 4.518A pdb=" N GLU D 948 " --> pdb=" O ASP D 944 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASP D 949 " --> pdb=" O GLU D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 957 through 962 removed outlier: 4.502A pdb=" N MET D 962 " --> pdb=" O LYS D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 1005 Processing helix chain 'D' and resid 1024 through 1029 removed outlier: 3.777A pdb=" N LEU D1028 " --> pdb=" O PRO D1024 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ASP D1029 " --> pdb=" O TYR D1025 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1024 through 1029' Processing helix chain 'D' and resid 1030 through 1049 removed outlier: 3.540A pdb=" N ALA D1043 " --> pdb=" O SER D1039 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1074 removed outlier: 4.925A pdb=" N ARG D1074 " --> pdb=" O GLY D1070 " (cutoff:3.500A) Processing helix chain 'D' and resid 1218 through 1223 removed outlier: 7.101A pdb=" N GLU D1222 " --> pdb=" O CYS D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1424 through 1431 Processing helix chain 'D' and resid 1445 through 1450 removed outlier: 3.923A pdb=" N VAL D1449 " --> pdb=" O GLU D1445 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N TRP D1450 " --> pdb=" O PRO D1446 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1445 through 1450' Processing helix chain 'D' and resid 1497 through 1503 removed outlier: 4.433A pdb=" N PHE D1501 " --> pdb=" O TRP D1497 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL D1502 " --> pdb=" O GLY D1498 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N SER D1503 " --> pdb=" O GLY D1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1497 through 1503' Processing helix chain 'D' and resid 1575 through 1581 removed outlier: 3.823A pdb=" N ALA D1579 " --> pdb=" O PRO D1575 " (cutoff:3.500A) Processing helix chain 'D' and resid 1650 through 1657 removed outlier: 4.306A pdb=" N LEU D1654 " --> pdb=" O ASP D1650 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER D1655 " --> pdb=" O ILE D1651 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLU D1656 " --> pdb=" O LEU D1652 " (cutoff:3.500A) Processing helix chain 'D' and resid 1658 through 1676 Processing helix chain 'D' and resid 1679 through 1690 removed outlier: 3.877A pdb=" N SER D1688 " --> pdb=" O HIS D1684 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS D1689 " --> pdb=" O ALA D1685 " (cutoff:3.500A) Processing helix chain 'D' and resid 1691 through 1701 Processing helix chain 'D' and resid 1705 through 1720 Processing helix chain 'D' and resid 1721 through 1733 removed outlier: 4.193A pdb=" N SER D1733 " --> pdb=" O ARG D1729 " (cutoff:3.500A) Processing helix chain 'D' and resid 1740 through 1747 removed outlier: 5.705A pdb=" N THR D1747 " --> pdb=" O THR D1743 " (cutoff:3.500A) Processing helix chain 'D' and resid 1805 through 1827 Processing helix chain 'D' and resid 1835 through 1854 Proline residue: D1842 - end of helix Processing helix chain 'D' and resid 1857 through 1869 Processing helix chain 'D' and resid 1926 through 1931 removed outlier: 4.898A pdb=" N LYS D1931 " --> pdb=" O LEU D1927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1933 through 1985 removed outlier: 5.341A pdb=" N PHE D1985 " --> pdb=" O LEU D1981 " (cutoff:3.500A) Processing helix chain 'D' and resid 1988 through 2001 removed outlier: 3.759A pdb=" N ARG D1994 " --> pdb=" O ALA D1990 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU D1998 " --> pdb=" O ARG D1994 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE D1999 " --> pdb=" O ARG D1995 " (cutoff:3.500A) Processing helix chain 'D' and resid 2002 through 2012 Processing helix chain 'D' and resid 2025 through 2044 removed outlier: 3.657A pdb=" N GLU D2031 " --> pdb=" O GLU D2027 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D2032 " --> pdb=" O ILE D2028 " (cutoff:3.500A) Processing helix chain 'D' and resid 2094 through 2110 Processing helix chain 'D' and resid 2114 through 2131 removed outlier: 3.810A pdb=" N GLY D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) Processing helix chain 'D' and resid 2132 through 2142 Proline residue: D2140 - end of helix Processing helix chain 'D' and resid 2146 through 2170 removed outlier: 3.887A pdb=" N VAL D2150 " --> pdb=" O SER D2146 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU D2151 " --> pdb=" O VAL D2147 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP D2152 " --> pdb=" O SER D2148 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D2167 " --> pdb=" O ILE D2163 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE D2168 " --> pdb=" O ARG D2164 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL D2169 " --> pdb=" O SER D2165 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN D2170 " --> pdb=" O LEU D2166 " (cutoff:3.500A) Processing helix chain 'D' and resid 2172 through 2190 removed outlier: 5.492A pdb=" N LYS D2190 " --> pdb=" O ILE D2186 " (cutoff:3.500A) Processing helix chain 'D' and resid 2195 through 2203 Processing helix chain 'D' and resid 2204 through 2220 removed outlier: 5.210A pdb=" N GLY D2219 " --> pdb=" O VAL D2215 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU D2220 " --> pdb=" O LEU D2216 " (cutoff:3.500A) Processing helix chain 'D' and resid 2226 through 2245 removed outlier: 4.085A pdb=" N SER D2244 " --> pdb=" O PHE D2240 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG D2245 " --> pdb=" O CYS D2241 " (cutoff:3.500A) Processing helix chain 'D' and resid 2246 through 2255 removed outlier: 3.644A pdb=" N HIS D2254 " --> pdb=" O SER D2250 " (cutoff:3.500A) Processing helix chain 'D' and resid 2256 through 2263 removed outlier: 4.245A pdb=" N GLY D2263 " --> pdb=" O LEU D2259 " (cutoff:3.500A) Processing helix chain 'D' and resid 2272 through 2282 removed outlier: 3.522A pdb=" N VAL D2281 " --> pdb=" O ALA D2277 " (cutoff:3.500A) Processing helix chain 'D' and resid 2284 through 2291 Processing helix chain 'D' and resid 2292 through 2309 Processing helix chain 'D' and resid 2311 through 2318 Processing helix chain 'D' and resid 2325 through 2341 removed outlier: 3.756A pdb=" N ARG D2331 " --> pdb=" O CYS D2327 " (cutoff:3.500A) Processing helix chain 'D' and resid 2347 through 2362 Proline residue: D2362 - end of helix Processing helix chain 'D' and resid 2376 through 2391 Proline residue: D2391 - end of helix Processing helix chain 'D' and resid 2418 through 2438 Processing helix chain 'D' and resid 2440 through 2447 Processing helix chain 'D' and resid 2448 through 2463 Proline residue: D2463 - end of helix Processing helix chain 'D' and resid 2464 through 2473 Processing helix chain 'D' and resid 2496 through 2510 removed outlier: 3.865A pdb=" N LYS D2500 " --> pdb=" O VAL D2496 " (cutoff:3.500A) Processing helix chain 'D' and resid 2515 through 2526 Processing helix chain 'D' and resid 2527 through 2539 removed outlier: 3.606A pdb=" N ASP D2538 " --> pdb=" O ALA D2534 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N THR D2539 " --> pdb=" O ALA D2535 " (cutoff:3.500A) Processing helix chain 'D' and resid 2545 through 2567 removed outlier: 5.048A pdb=" N LEU D2560 " --> pdb=" O CYS D2556 " (cutoff:3.500A) Proline residue: D2561 - end of helix Processing helix chain 'D' and resid 2576 through 2594 removed outlier: 3.949A pdb=" N GLY D2593 " --> pdb=" O ARG D2589 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG D2594 " --> pdb=" O LEU D2590 " (cutoff:3.500A) Processing helix chain 'D' and resid 2597 through 2615 removed outlier: 3.685A pdb=" N TYR D2614 " --> pdb=" O ALA D2610 " (cutoff:3.500A) Processing helix chain 'D' and resid 2616 through 2631 removed outlier: 3.905A pdb=" N LEU D2620 " --> pdb=" O ARG D2616 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN D2621 " --> pdb=" O PRO D2617 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N HIS D2622 " --> pdb=" O SER D2618 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU D2623 " --> pdb=" O MET D2619 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE D2629 " --> pdb=" O ARG D2625 " (cutoff:3.500A) Processing helix chain 'D' and resid 2637 through 2653 Proline residue: D2641 - end of helix Processing helix chain 'D' and resid 2669 through 2690 Processing helix chain 'D' and resid 2693 through 2712 Proline residue: D2702 - end of helix Proline residue: D2712 - end of helix Processing helix chain 'D' and resid 2742 through 2747 removed outlier: 5.126A pdb=" N ILE D2747 " --> pdb=" O THR D2743 " (cutoff:3.500A) Processing helix chain 'D' and resid 2749 through 2775 Processing helix chain 'D' and resid 2799 through 2821 Proline residue: D2809 - end of helix Processing helix chain 'D' and resid 2869 through 2899 Processing helix chain 'D' and resid 2908 through 2913 removed outlier: 5.396A pdb=" N THR D2913 " --> pdb=" O TYR D2909 " (cutoff:3.500A) Processing helix chain 'D' and resid 2916 through 2935 removed outlier: 4.658A pdb=" N ASP D2920 " --> pdb=" O GLU D2916 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS D2923 " --> pdb=" O ARG D2919 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU D2927 " --> pdb=" O LYS D2923 " (cutoff:3.500A) Processing helix chain 'D' and resid 2941 through 2948 removed outlier: 3.820A pdb=" N MET D2945 " --> pdb=" O GLY D2941 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASP D2948 " --> pdb=" O ASP D2944 " (cutoff:3.500A) Processing helix chain 'D' and resid 2950 through 2984 removed outlier: 6.084A pdb=" N PHE D2956 " --> pdb=" O ILE D2952 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALA D2957 " --> pdb=" O GLU D2953 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE D2958 " --> pdb=" O LYS D2954 " (cutoff:3.500A) Processing helix chain 'D' and resid 2992 through 3015 removed outlier: 4.279A pdb=" N LEU D3004 " --> pdb=" O ALA D3000 " (cutoff:3.500A) Proline residue: D3005 - end of helix Processing helix chain 'D' and resid 3033 through 3052 Processing helix chain 'D' and resid 3054 through 3059 Processing helix chain 'D' and resid 3060 through 3076 removed outlier: 4.732A pdb=" N ALA D3064 " --> pdb=" O THR D3060 " (cutoff:3.500A) Processing helix chain 'D' and resid 3077 through 3084 removed outlier: 4.409A pdb=" N VAL D3081 " --> pdb=" O ASP D3077 " (cutoff:3.500A) Processing helix chain 'D' and resid 3086 through 3113 Processing helix chain 'D' and resid 3124 through 3152 removed outlier: 5.266A pdb=" N LEU D3138 " --> pdb=" O THR D3134 " (cutoff:3.500A) Proline residue: D3139 - end of helix Processing helix chain 'D' and resid 3160 through 3180 removed outlier: 3.612A pdb=" N SER D3172 " --> pdb=" O ARG D3168 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR D3179 " --> pdb=" O SER D3175 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ARG D3180 " --> pdb=" O LEU D3176 " (cutoff:3.500A) Processing helix chain 'D' and resid 3181 through 3202 removed outlier: 3.818A pdb=" N LYS D3186 " --> pdb=" O PRO D3182 " (cutoff:3.500A) Proline residue: D3189 - end of helix Processing helix chain 'D' and resid 3208 through 3216 removed outlier: 4.088A pdb=" N ASN D3212 " --> pdb=" O GLU D3208 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU D3213 " --> pdb=" O PRO D3209 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR D3214 " --> pdb=" O GLU D3210 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN D3215 " --> pdb=" O LEU D3211 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ALA D3216 " --> pdb=" O ASN D3212 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3208 through 3216' Processing helix chain 'D' and resid 3218 through 3223 Processing helix chain 'D' and resid 3224 through 3232 removed outlier: 4.437A pdb=" N ARG D3228 " --> pdb=" O SER D3224 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA D3229 " --> pdb=" O PRO D3225 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE D3230 " --> pdb=" O ARG D3226 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU D3231 " --> pdb=" O GLU D3227 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLY D3232 " --> pdb=" O ARG D3228 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3224 through 3232' Processing helix chain 'D' and resid 3236 through 3242 removed outlier: 3.532A pdb=" N MET D3240 " --> pdb=" O SER D3236 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N CYS D3241 " --> pdb=" O VAL D3237 " (cutoff:3.500A) Proline residue: D3242 - end of helix No H-bonds generated for 'chain 'D' and resid 3236 through 3242' Processing helix chain 'D' and resid 3246 through 3261 Processing helix chain 'D' and resid 3263 through 3268 removed outlier: 3.835A pdb=" N MET D3267 " --> pdb=" O ARG D3263 " (cutoff:3.500A) Proline residue: D3268 - end of helix No H-bonds generated for 'chain 'D' and resid 3263 through 3268' Processing helix chain 'D' and resid 3269 through 3289 removed outlier: 4.574A pdb=" N LEU D3275 " --> pdb=" O ILE D3271 " (cutoff:3.500A) Proline residue: D3276 - end of helix Proline residue: D3283 - end of helix removed outlier: 3.658A pdb=" N ARG D3288 " --> pdb=" O ARG D3284 " (cutoff:3.500A) Processing helix chain 'D' and resid 3309 through 3328 Processing helix chain 'D' and resid 3333 through 3348 removed outlier: 4.800A pdb=" N LYS D3337 " --> pdb=" O ALA D3333 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG D3338 " --> pdb=" O SER D3334 " (cutoff:3.500A) Proline residue: D3345 - end of helix removed outlier: 4.323A pdb=" N SER D3348 " --> pdb=" O GLN D3344 " (cutoff:3.500A) Processing helix chain 'D' and resid 3351 through 3384 removed outlier: 4.707A pdb=" N LEU D3355 " --> pdb=" O ARG D3351 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG D3356 " --> pdb=" O PRO D3352 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE D3360 " --> pdb=" O ARG D3356 " (cutoff:3.500A) Proline residue: D3361 - end of helix removed outlier: 4.405A pdb=" N ALA D3384 " --> pdb=" O LEU D3380 " (cutoff:3.500A) Processing helix chain 'D' and resid 3390 through 3414 removed outlier: 6.731A pdb=" N LEU D3394 " --> pdb=" O GLU D3390 " (cutoff:3.500A) Proline residue: D3411 - end of helix Processing helix chain 'D' and resid 3420 through 3428 Proline residue: D3428 - end of helix Processing helix chain 'D' and resid 3429 through 3449 Processing helix chain 'D' and resid 3450 through 3464 removed outlier: 3.759A pdb=" N ARG D3454 " --> pdb=" O HIS D3450 " (cutoff:3.500A) Processing helix chain 'D' and resid 3466 through 3472 removed outlier: 4.046A pdb=" N PHE D3470 " --> pdb=" O ASN D3466 " (cutoff:3.500A) Processing helix chain 'D' and resid 3509 through 3527 removed outlier: 3.622A pdb=" N LEU D3515 " --> pdb=" O ILE D3511 " (cutoff:3.500A) Proline residue: D3520 - end of helix removed outlier: 3.579A pdb=" N MET D3525 " --> pdb=" O ILE D3521 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ALA D3527 " --> pdb=" O LEU D3523 " (cutoff:3.500A) Processing helix chain 'D' and resid 3528 through 3544 removed outlier: 5.271A pdb=" N ASP D3532 " --> pdb=" O PRO D3528 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU D3533 " --> pdb=" O THR D3529 " (cutoff:3.500A) Processing helix chain 'D' and resid 3546 through 3558 removed outlier: 3.744A pdb=" N LEU D3558 " --> pdb=" O LEU D3554 " (cutoff:3.500A) Processing helix chain 'D' and resid 3563 through 3568 Proline residue: D3568 - end of helix Processing helix chain 'D' and resid 3569 through 3581 Proline residue: D3581 - end of helix Processing helix chain 'D' and resid 3589 through 3613 Proline residue: D3613 - end of helix Processing helix chain 'D' and resid 3634 through 3639 removed outlier: 4.720A pdb=" N MET D3639 " --> pdb=" O ALA D3635 " (cutoff:3.500A) Processing helix chain 'D' and resid 3646 through 3662 Processing helix chain 'D' and resid 3670 through 3681 removed outlier: 5.546A pdb=" N ALA D3681 " --> pdb=" O ASP D3677 " (cutoff:3.500A) Processing helix chain 'D' and resid 3683 through 3688 removed outlier: 3.736A pdb=" N GLU D3687 " --> pdb=" O GLU D3683 " (cutoff:3.500A) Processing helix chain 'D' and resid 3697 through 3712 Processing helix chain 'D' and resid 3720 through 3735 removed outlier: 3.558A pdb=" N ASP D3728 " --> pdb=" O MET D3724 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS D3734 " --> pdb=" O MET D3730 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N HIS D3735 " --> pdb=" O ALA D3731 " (cutoff:3.500A) Processing helix chain 'D' and resid 3755 through 3775 removed outlier: 3.636A pdb=" N LEU D3773 " --> pdb=" O GLN D3769 " (cutoff:3.500A) Processing helix chain 'D' and resid 3777 through 3790 removed outlier: 4.203A pdb=" N LYS D3790 " --> pdb=" O ILE D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3794 through 3809 Processing helix chain 'D' and resid 3812 through 3827 Processing helix chain 'D' and resid 3829 through 3842 Processing helix chain 'D' and resid 3846 through 3860 removed outlier: 4.875A pdb=" N GLY D3860 " --> pdb=" O ALA D3856 " (cutoff:3.500A) Processing helix chain 'D' and resid 3880 through 3896 removed outlier: 3.612A pdb=" N CYS D3895 " --> pdb=" O LEU D3891 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3908 removed outlier: 4.239A pdb=" N ARG D3907 " --> pdb=" O GLN D3903 " (cutoff:3.500A) Processing helix chain 'D' and resid 3917 through 3942 removed outlier: 4.610A pdb=" N GLY D3942 " --> pdb=" O TRP D3938 " (cutoff:3.500A) Processing helix chain 'D' and resid 3947 through 3973 Processing helix chain 'D' and resid 3976 through 3987 removed outlier: 4.729A pdb=" N ARG D3987 " --> pdb=" O LEU D3983 " (cutoff:3.500A) Processing helix chain 'D' and resid 3988 through 4010 removed outlier: 3.713A pdb=" N ASP D4009 " --> pdb=" O LYS D4005 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER D4010 " --> pdb=" O LEU D4006 " (cutoff:3.500A) Processing helix chain 'D' and resid 4012 through 4035 Processing helix chain 'D' and resid 4041 through 4055 Processing helix chain 'D' and resid 4056 through 4074 removed outlier: 4.750A pdb=" N LYS D4072 " --> pdb=" O PHE D4068 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP D4073 " --> pdb=" O LEU D4069 " (cutoff:3.500A) Processing helix chain 'D' and resid 4077 through 4085 removed outlier: 5.135A pdb=" N THR D4085 " --> pdb=" O GLN D4081 " (cutoff:3.500A) Processing helix chain 'D' and resid 4092 through 4104 Processing helix chain 'D' and resid 4107 through 4119 removed outlier: 4.436A pdb=" N GLU D4119 " --> pdb=" O LEU D4115 " (cutoff:3.500A) Processing helix chain 'D' and resid 4127 through 4158 removed outlier: 4.421A pdb=" N PHE D4135 " --> pdb=" O PHE D4131 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN D4136 " --> pdb=" O ALA D4132 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU D4137 " --> pdb=" O ASN D4133 " (cutoff:3.500A) Proline residue: D4138 - end of helix removed outlier: 3.870A pdb=" N ASP D4141 " --> pdb=" O GLU D4137 " (cutoff:3.500A) Proline residue: D4158 - end of helix Processing helix chain 'D' and resid 4160 through 4171 removed outlier: 3.508A pdb=" N LEU D4169 " --> pdb=" O ASN D4165 " (cutoff:3.500A) Processing helix chain 'D' and resid 4172 through 4178 Processing helix chain 'D' and resid 4201 through 4210 Processing helix chain 'D' and resid 4211 through 4227 Processing helix chain 'D' and resid 4232 through 4255 Processing helix chain 'D' and resid 4538 through 4557 Processing helix chain 'D' and resid 4558 through 4578 removed outlier: 4.362A pdb=" N PHE D4577 " --> pdb=" O PHE D4573 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR D4578 " --> pdb=" O ILE D4574 " (cutoff:3.500A) Processing helix chain 'D' and resid 4636 through 4681 removed outlier: 4.109A pdb=" N VAL D4664 " --> pdb=" O ASN D4660 " (cutoff:3.500A) Proline residue: D4665 - end of helix Processing helix chain 'D' and resid 4694 through 4705 removed outlier: 3.848A pdb=" N GLN D4698 " --> pdb=" O ASP D4694 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU D4702 " --> pdb=" O GLN D4698 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL D4703 " --> pdb=" O TRP D4699 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU D4704 " --> pdb=" O ASP D4700 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ASN D4705 " --> pdb=" O ARG D4701 " (cutoff:3.500A) Processing helix chain 'D' and resid 4717 through 4727 Processing helix chain 'D' and resid 4731 through 4740 Processing helix chain 'D' and resid 4742 through 4752 Processing helix chain 'D' and resid 4761 through 4770 removed outlier: 4.339A pdb=" N TRP D4765 " --> pdb=" O GLY D4761 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP D4770 " --> pdb=" O ILE D4766 " (cutoff:3.500A) Processing helix chain 'D' and resid 4771 through 4784 Processing helix chain 'D' and resid 4785 through 4803 removed outlier: 3.789A pdb=" N HIS D4801 " --> pdb=" O SER D4797 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR D4802 " --> pdb=" O LEU D4798 " (cutoff:3.500A) Processing helix chain 'D' and resid 4804 through 4818 removed outlier: 4.548A pdb=" N ALA D4808 " --> pdb=" O ASN D4804 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA D4809 " --> pdb=" O PHE D4805 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N HIS D4810 " --> pdb=" O PHE D4806 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU D4811 " --> pdb=" O PHE D4807 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU D4812 " --> pdb=" O ALA D4808 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP D4813 " --> pdb=" O ALA D4809 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE D4814 " --> pdb=" O HIS D4810 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA D4815 " --> pdb=" O LEU D4811 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET D4816 " --> pdb=" O LEU D4812 " (cutoff:3.500A) Processing helix chain 'D' and resid 4819 through 4830 removed outlier: 3.592A pdb=" N SER D4827 " --> pdb=" O THR D4823 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D4828 " --> pdb=" O ILE D4824 " (cutoff:3.500A) Processing helix chain 'D' and resid 4831 through 4856 Processing helix chain 'D' and resid 4857 through 4862 removed outlier: 4.370A pdb=" N TYR D4861 " --> pdb=" O PHE D4857 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN D4862 " --> pdb=" O ARG D4858 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4857 through 4862' Processing helix chain 'D' and resid 4876 through 4891 removed outlier: 4.181A pdb=" N VAL D4889 " --> pdb=" O MET D4885 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG D4890 " --> pdb=" O TYR D4886 " (cutoff:3.500A) Processing helix chain 'D' and resid 4894 through 4899 removed outlier: 4.211A pdb=" N GLU D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) Processing helix chain 'D' and resid 4907 through 4922 Processing helix chain 'D' and resid 4926 through 4955 Processing helix chain 'D' and resid 4962 through 4968 removed outlier: 3.870A pdb=" N PHE D4966 " --> pdb=" O GLY D4962 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR D4968 " --> pdb=" O ASP D4964 " (cutoff:3.500A) Processing helix chain 'D' and resid 4971 through 4979 Processing helix chain 'D' and resid 4982 through 4997 removed outlier: 5.334A pdb=" N ASP D4997 " --> pdb=" O LEU D4993 " (cutoff:3.500A) Processing helix chain 'D' and resid 5002 through 5015 Processing helix chain 'D' and resid 5025 through 5031 Processing helix chain 'D' and resid 323 through 328 removed outlier: 4.979A pdb=" N VAL D 326 " --> pdb=" O LYS D 323 " (cutoff:3.500A) Proline residue: D 328 - end of helix Processing helix chain 'D' and resid 3582 through 3588 removed outlier: 4.953A pdb=" N GLU D3585 " --> pdb=" O GLY D3582 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASP D3586 " --> pdb=" O ARG D3583 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ALA D3587 " --> pdb=" O GLU D3584 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASP D3588 " --> pdb=" O GLU D3585 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3582 through 3588' Processing helix chain 'D' and resid 5016 through 5021 removed outlier: 4.454A pdb=" N PHE D5019 " --> pdb=" O CYS D5016 " (cutoff:3.500A) Proline residue: D5021 - end of helix Processing helix chain 'D' and resid 4683 through 4688 Processing helix chain 'B' and resid 62 through 67 removed outlier: 4.355A pdb=" N CYS B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 67' Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.777A pdb=" N HIS B 256 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 257' Processing helix chain 'B' and resid 304 through 309 removed outlier: 5.062A pdb=" N HIS B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 395 through 423 removed outlier: 3.776A pdb=" N PHE B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 461 through 483 Processing helix chain 'B' and resid 484 through 498 removed outlier: 4.507A pdb=" N TYR B 498 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 508 removed outlier: 3.735A pdb=" N PHE B 507 " --> pdb=" O HIS B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 532 removed outlier: 4.316A pdb=" N SER B 515 " --> pdb=" O GLU B 511 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TRP B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLU B 518 " --> pdb=" O GLU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 545 removed outlier: 3.812A pdb=" N LEU B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE B 541 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER B 542 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 553 removed outlier: 4.117A pdb=" N LYS B 551 " --> pdb=" O TRP B 547 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 572 Processing helix chain 'B' and resid 573 through 579 Processing helix chain 'B' and resid 580 through 594 removed outlier: 3.513A pdb=" N LEU B 591 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 610 removed outlier: 3.592A pdb=" N LEU B 601 " --> pdb=" O ASN B 597 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS B 608 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 609 " --> pdb=" O CYS B 605 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N CYS B 610 " --> pdb=" O SER B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 630 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 811 through 816 removed outlier: 4.510A pdb=" N ALA B 815 " --> pdb=" O PRO B 811 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL B 816 " --> pdb=" O CYS B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 816' Processing helix chain 'B' and resid 848 through 854 removed outlier: 4.092A pdb=" N PHE B 852 " --> pdb=" O SER B 848 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL B 853 " --> pdb=" O HIS B 849 " (cutoff:3.500A) Proline residue: B 854 - end of helix No H-bonds generated for 'chain 'B' and resid 848 through 854' Processing helix chain 'B' and resid 866 through 891 removed outlier: 3.709A pdb=" N ILE B 871 " --> pdb=" O HIS B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 936 Processing helix chain 'B' and resid 944 through 951 removed outlier: 4.518A pdb=" N GLU B 948 " --> pdb=" O ASP B 944 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP B 949 " --> pdb=" O GLU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 962 removed outlier: 4.502A pdb=" N MET B 962 " --> pdb=" O LYS B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 1005 Processing helix chain 'B' and resid 1024 through 1029 removed outlier: 3.777A pdb=" N LEU B1028 " --> pdb=" O PRO B1024 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP B1029 " --> pdb=" O TYR B1025 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1024 through 1029' Processing helix chain 'B' and resid 1030 through 1049 removed outlier: 3.540A pdb=" N ALA B1043 " --> pdb=" O SER B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1074 removed outlier: 4.926A pdb=" N ARG B1074 " --> pdb=" O GLY B1070 " (cutoff:3.500A) Processing helix chain 'B' and resid 1218 through 1223 removed outlier: 7.101A pdb=" N GLU B1222 " --> pdb=" O CYS B1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 1424 through 1431 Processing helix chain 'B' and resid 1445 through 1450 removed outlier: 3.923A pdb=" N VAL B1449 " --> pdb=" O GLU B1445 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TRP B1450 " --> pdb=" O PRO B1446 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1445 through 1450' Processing helix chain 'B' and resid 1497 through 1503 removed outlier: 4.433A pdb=" N PHE B1501 " --> pdb=" O TRP B1497 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL B1502 " --> pdb=" O GLY B1498 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N SER B1503 " --> pdb=" O GLY B1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1497 through 1503' Processing helix chain 'B' and resid 1575 through 1581 removed outlier: 3.823A pdb=" N ALA B1579 " --> pdb=" O PRO B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1650 through 1657 removed outlier: 4.306A pdb=" N LEU B1654 " --> pdb=" O ASP B1650 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER B1655 " --> pdb=" O ILE B1651 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU B1656 " --> pdb=" O LEU B1652 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1676 Processing helix chain 'B' and resid 1679 through 1690 removed outlier: 3.876A pdb=" N SER B1688 " --> pdb=" O HIS B1684 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS B1689 " --> pdb=" O ALA B1685 " (cutoff:3.500A) Processing helix chain 'B' and resid 1691 through 1701 Processing helix chain 'B' and resid 1705 through 1720 Processing helix chain 'B' and resid 1721 through 1733 removed outlier: 4.192A pdb=" N SER B1733 " --> pdb=" O ARG B1729 " (cutoff:3.500A) Processing helix chain 'B' and resid 1740 through 1747 removed outlier: 5.706A pdb=" N THR B1747 " --> pdb=" O THR B1743 " (cutoff:3.500A) Processing helix chain 'B' and resid 1805 through 1827 Processing helix chain 'B' and resid 1835 through 1854 Proline residue: B1842 - end of helix Processing helix chain 'B' and resid 1857 through 1869 Processing helix chain 'B' and resid 1926 through 1931 removed outlier: 4.897A pdb=" N LYS B1931 " --> pdb=" O LEU B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1933 through 1985 removed outlier: 5.342A pdb=" N PHE B1985 " --> pdb=" O LEU B1981 " (cutoff:3.500A) Processing helix chain 'B' and resid 1988 through 2001 removed outlier: 3.760A pdb=" N ARG B1994 " --> pdb=" O ALA B1990 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU B1998 " --> pdb=" O ARG B1994 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE B1999 " --> pdb=" O ARG B1995 " (cutoff:3.500A) Processing helix chain 'B' and resid 2002 through 2012 Processing helix chain 'B' and resid 2025 through 2044 removed outlier: 3.657A pdb=" N GLU B2031 " --> pdb=" O GLU B2027 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B2032 " --> pdb=" O ILE B2028 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2110 Processing helix chain 'B' and resid 2114 through 2131 removed outlier: 3.811A pdb=" N GLY B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) Processing helix chain 'B' and resid 2132 through 2142 Proline residue: B2140 - end of helix Processing helix chain 'B' and resid 2146 through 2170 removed outlier: 3.887A pdb=" N VAL B2150 " --> pdb=" O SER B2146 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU B2151 " --> pdb=" O VAL B2147 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP B2152 " --> pdb=" O SER B2148 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B2167 " --> pdb=" O ILE B2163 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE B2168 " --> pdb=" O ARG B2164 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL B2169 " --> pdb=" O SER B2165 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN B2170 " --> pdb=" O LEU B2166 " (cutoff:3.500A) Processing helix chain 'B' and resid 2172 through 2190 removed outlier: 5.492A pdb=" N LYS B2190 " --> pdb=" O ILE B2186 " (cutoff:3.500A) Processing helix chain 'B' and resid 2195 through 2203 Processing helix chain 'B' and resid 2204 through 2220 removed outlier: 5.209A pdb=" N GLY B2219 " --> pdb=" O VAL B2215 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU B2220 " --> pdb=" O LEU B2216 " (cutoff:3.500A) Processing helix chain 'B' and resid 2226 through 2245 removed outlier: 4.085A pdb=" N SER B2244 " --> pdb=" O PHE B2240 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG B2245 " --> pdb=" O CYS B2241 " (cutoff:3.500A) Processing helix chain 'B' and resid 2246 through 2255 removed outlier: 3.644A pdb=" N HIS B2254 " --> pdb=" O SER B2250 " (cutoff:3.500A) Processing helix chain 'B' and resid 2256 through 2263 removed outlier: 4.246A pdb=" N GLY B2263 " --> pdb=" O LEU B2259 " (cutoff:3.500A) Processing helix chain 'B' and resid 2272 through 2282 removed outlier: 3.523A pdb=" N VAL B2281 " --> pdb=" O ALA B2277 " (cutoff:3.500A) Processing helix chain 'B' and resid 2284 through 2291 Processing helix chain 'B' and resid 2292 through 2309 Processing helix chain 'B' and resid 2311 through 2318 Processing helix chain 'B' and resid 2325 through 2341 removed outlier: 3.756A pdb=" N ARG B2331 " --> pdb=" O CYS B2327 " (cutoff:3.500A) Processing helix chain 'B' and resid 2347 through 2362 Proline residue: B2362 - end of helix Processing helix chain 'B' and resid 2376 through 2391 Proline residue: B2391 - end of helix Processing helix chain 'B' and resid 2418 through 2438 Processing helix chain 'B' and resid 2440 through 2447 Processing helix chain 'B' and resid 2448 through 2463 Proline residue: B2463 - end of helix Processing helix chain 'B' and resid 2464 through 2473 Processing helix chain 'B' and resid 2496 through 2510 removed outlier: 3.865A pdb=" N LYS B2500 " --> pdb=" O VAL B2496 " (cutoff:3.500A) Processing helix chain 'B' and resid 2515 through 2526 Processing helix chain 'B' and resid 2527 through 2539 removed outlier: 3.607A pdb=" N ASP B2538 " --> pdb=" O ALA B2534 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N THR B2539 " --> pdb=" O ALA B2535 " (cutoff:3.500A) Processing helix chain 'B' and resid 2545 through 2567 removed outlier: 5.047A pdb=" N LEU B2560 " --> pdb=" O CYS B2556 " (cutoff:3.500A) Proline residue: B2561 - end of helix Processing helix chain 'B' and resid 2576 through 2594 removed outlier: 3.948A pdb=" N GLY B2593 " --> pdb=" O ARG B2589 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG B2594 " --> pdb=" O LEU B2590 " (cutoff:3.500A) Processing helix chain 'B' and resid 2597 through 2615 removed outlier: 3.686A pdb=" N TYR B2614 " --> pdb=" O ALA B2610 " (cutoff:3.500A) Processing helix chain 'B' and resid 2616 through 2631 removed outlier: 3.906A pdb=" N LEU B2620 " --> pdb=" O ARG B2616 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN B2621 " --> pdb=" O PRO B2617 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N HIS B2622 " --> pdb=" O SER B2618 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU B2623 " --> pdb=" O MET B2619 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B2629 " --> pdb=" O ARG B2625 " (cutoff:3.500A) Processing helix chain 'B' and resid 2637 through 2653 Proline residue: B2641 - end of helix Processing helix chain 'B' and resid 2669 through 2690 Processing helix chain 'B' and resid 2693 through 2712 Proline residue: B2702 - end of helix Proline residue: B2712 - end of helix Processing helix chain 'B' and resid 2742 through 2747 removed outlier: 5.125A pdb=" N ILE B2747 " --> pdb=" O THR B2743 " (cutoff:3.500A) Processing helix chain 'B' and resid 2749 through 2775 Processing helix chain 'B' and resid 2799 through 2821 Proline residue: B2809 - end of helix Processing helix chain 'B' and resid 2869 through 2899 Processing helix chain 'B' and resid 2908 through 2913 removed outlier: 5.395A pdb=" N THR B2913 " --> pdb=" O TYR B2909 " (cutoff:3.500A) Processing helix chain 'B' and resid 2916 through 2935 removed outlier: 4.657A pdb=" N ASP B2920 " --> pdb=" O GLU B2916 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS B2923 " --> pdb=" O ARG B2919 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B2927 " --> pdb=" O LYS B2923 " (cutoff:3.500A) Processing helix chain 'B' and resid 2941 through 2948 removed outlier: 3.821A pdb=" N MET B2945 " --> pdb=" O GLY B2941 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASP B2948 " --> pdb=" O ASP B2944 " (cutoff:3.500A) Processing helix chain 'B' and resid 2950 through 2984 removed outlier: 6.084A pdb=" N PHE B2956 " --> pdb=" O ILE B2952 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ALA B2957 " --> pdb=" O GLU B2953 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE B2958 " --> pdb=" O LYS B2954 " (cutoff:3.500A) Processing helix chain 'B' and resid 2992 through 3015 removed outlier: 4.278A pdb=" N LEU B3004 " --> pdb=" O ALA B3000 " (cutoff:3.500A) Proline residue: B3005 - end of helix Processing helix chain 'B' and resid 3033 through 3052 Processing helix chain 'B' and resid 3054 through 3059 Processing helix chain 'B' and resid 3060 through 3076 removed outlier: 4.732A pdb=" N ALA B3064 " --> pdb=" O THR B3060 " (cutoff:3.500A) Processing helix chain 'B' and resid 3077 through 3084 removed outlier: 4.409A pdb=" N VAL B3081 " --> pdb=" O ASP B3077 " (cutoff:3.500A) Processing helix chain 'B' and resid 3086 through 3113 Processing helix chain 'B' and resid 3124 through 3152 removed outlier: 5.267A pdb=" N LEU B3138 " --> pdb=" O THR B3134 " (cutoff:3.500A) Proline residue: B3139 - end of helix Processing helix chain 'B' and resid 3160 through 3180 removed outlier: 3.612A pdb=" N SER B3172 " --> pdb=" O ARG B3168 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B3179 " --> pdb=" O SER B3175 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ARG B3180 " --> pdb=" O LEU B3176 " (cutoff:3.500A) Processing helix chain 'B' and resid 3181 through 3202 removed outlier: 3.817A pdb=" N LYS B3186 " --> pdb=" O PRO B3182 " (cutoff:3.500A) Proline residue: B3189 - end of helix Processing helix chain 'B' and resid 3208 through 3216 removed outlier: 4.088A pdb=" N ASN B3212 " --> pdb=" O GLU B3208 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU B3213 " --> pdb=" O PRO B3209 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR B3214 " --> pdb=" O GLU B3210 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN B3215 " --> pdb=" O LEU B3211 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ALA B3216 " --> pdb=" O ASN B3212 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3208 through 3216' Processing helix chain 'B' and resid 3218 through 3223 Processing helix chain 'B' and resid 3224 through 3232 removed outlier: 4.437A pdb=" N ARG B3228 " --> pdb=" O SER B3224 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA B3229 " --> pdb=" O PRO B3225 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE B3230 " --> pdb=" O ARG B3226 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B3231 " --> pdb=" O GLU B3227 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLY B3232 " --> pdb=" O ARG B3228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3224 through 3232' Processing helix chain 'B' and resid 3236 through 3242 removed outlier: 3.532A pdb=" N MET B3240 " --> pdb=" O SER B3236 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N CYS B3241 " --> pdb=" O VAL B3237 " (cutoff:3.500A) Proline residue: B3242 - end of helix No H-bonds generated for 'chain 'B' and resid 3236 through 3242' Processing helix chain 'B' and resid 3246 through 3261 Processing helix chain 'B' and resid 3263 through 3268 removed outlier: 3.835A pdb=" N MET B3267 " --> pdb=" O ARG B3263 " (cutoff:3.500A) Proline residue: B3268 - end of helix No H-bonds generated for 'chain 'B' and resid 3263 through 3268' Processing helix chain 'B' and resid 3269 through 3289 removed outlier: 4.574A pdb=" N LEU B3275 " --> pdb=" O ILE B3271 " (cutoff:3.500A) Proline residue: B3276 - end of helix Proline residue: B3283 - end of helix removed outlier: 3.658A pdb=" N ARG B3288 " --> pdb=" O ARG B3284 " (cutoff:3.500A) Processing helix chain 'B' and resid 3309 through 3328 Processing helix chain 'B' and resid 3333 through 3348 removed outlier: 4.800A pdb=" N LYS B3337 " --> pdb=" O ALA B3333 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B3338 " --> pdb=" O SER B3334 " (cutoff:3.500A) Proline residue: B3345 - end of helix removed outlier: 4.322A pdb=" N SER B3348 " --> pdb=" O GLN B3344 " (cutoff:3.500A) Processing helix chain 'B' and resid 3351 through 3384 removed outlier: 4.707A pdb=" N LEU B3355 " --> pdb=" O ARG B3351 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG B3356 " --> pdb=" O PRO B3352 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE B3360 " --> pdb=" O ARG B3356 " (cutoff:3.500A) Proline residue: B3361 - end of helix removed outlier: 4.405A pdb=" N ALA B3384 " --> pdb=" O LEU B3380 " (cutoff:3.500A) Processing helix chain 'B' and resid 3390 through 3414 removed outlier: 6.730A pdb=" N LEU B3394 " --> pdb=" O GLU B3390 " (cutoff:3.500A) Proline residue: B3411 - end of helix Processing helix chain 'B' and resid 3420 through 3428 Proline residue: B3428 - end of helix Processing helix chain 'B' and resid 3429 through 3449 Processing helix chain 'B' and resid 3450 through 3464 removed outlier: 3.759A pdb=" N ARG B3454 " --> pdb=" O HIS B3450 " (cutoff:3.500A) Processing helix chain 'B' and resid 3466 through 3472 removed outlier: 4.047A pdb=" N PHE B3470 " --> pdb=" O ASN B3466 " (cutoff:3.500A) Processing helix chain 'B' and resid 3509 through 3527 removed outlier: 3.622A pdb=" N LEU B3515 " --> pdb=" O ILE B3511 " (cutoff:3.500A) Proline residue: B3520 - end of helix removed outlier: 3.579A pdb=" N MET B3525 " --> pdb=" O ILE B3521 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ALA B3527 " --> pdb=" O LEU B3523 " (cutoff:3.500A) Processing helix chain 'B' and resid 3528 through 3544 removed outlier: 5.272A pdb=" N ASP B3532 " --> pdb=" O PRO B3528 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU B3533 " --> pdb=" O THR B3529 " (cutoff:3.500A) Processing helix chain 'B' and resid 3546 through 3558 removed outlier: 3.743A pdb=" N LEU B3558 " --> pdb=" O LEU B3554 " (cutoff:3.500A) Processing helix chain 'B' and resid 3563 through 3568 Proline residue: B3568 - end of helix Processing helix chain 'B' and resid 3569 through 3581 Proline residue: B3581 - end of helix Processing helix chain 'B' and resid 3589 through 3613 Proline residue: B3613 - end of helix Processing helix chain 'B' and resid 3634 through 3639 removed outlier: 4.720A pdb=" N MET B3639 " --> pdb=" O ALA B3635 " (cutoff:3.500A) Processing helix chain 'B' and resid 3646 through 3662 Processing helix chain 'B' and resid 3670 through 3681 removed outlier: 5.546A pdb=" N ALA B3681 " --> pdb=" O ASP B3677 " (cutoff:3.500A) Processing helix chain 'B' and resid 3683 through 3688 removed outlier: 3.736A pdb=" N GLU B3687 " --> pdb=" O GLU B3683 " (cutoff:3.500A) Processing helix chain 'B' and resid 3697 through 3712 Processing helix chain 'B' and resid 3720 through 3735 removed outlier: 3.558A pdb=" N ASP B3728 " --> pdb=" O MET B3724 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS B3734 " --> pdb=" O MET B3730 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N HIS B3735 " --> pdb=" O ALA B3731 " (cutoff:3.500A) Processing helix chain 'B' and resid 3755 through 3775 removed outlier: 3.636A pdb=" N LEU B3773 " --> pdb=" O GLN B3769 " (cutoff:3.500A) Processing helix chain 'B' and resid 3777 through 3790 removed outlier: 4.203A pdb=" N LYS B3790 " --> pdb=" O ILE B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3794 through 3809 Processing helix chain 'B' and resid 3812 through 3827 Processing helix chain 'B' and resid 3829 through 3842 Processing helix chain 'B' and resid 3846 through 3860 removed outlier: 4.875A pdb=" N GLY B3860 " --> pdb=" O ALA B3856 " (cutoff:3.500A) Processing helix chain 'B' and resid 3880 through 3896 removed outlier: 3.613A pdb=" N CYS B3895 " --> pdb=" O LEU B3891 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3908 removed outlier: 4.239A pdb=" N ARG B3907 " --> pdb=" O GLN B3903 " (cutoff:3.500A) Processing helix chain 'B' and resid 3917 through 3942 removed outlier: 4.610A pdb=" N GLY B3942 " --> pdb=" O TRP B3938 " (cutoff:3.500A) Processing helix chain 'B' and resid 3947 through 3973 Processing helix chain 'B' and resid 3976 through 3987 removed outlier: 4.729A pdb=" N ARG B3987 " --> pdb=" O LEU B3983 " (cutoff:3.500A) Processing helix chain 'B' and resid 3988 through 4010 removed outlier: 3.712A pdb=" N ASP B4009 " --> pdb=" O LYS B4005 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER B4010 " --> pdb=" O LEU B4006 " (cutoff:3.500A) Processing helix chain 'B' and resid 4012 through 4035 Processing helix chain 'B' and resid 4041 through 4055 Processing helix chain 'B' and resid 4056 through 4074 removed outlier: 4.750A pdb=" N LYS B4072 " --> pdb=" O PHE B4068 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP B4073 " --> pdb=" O LEU B4069 " (cutoff:3.500A) Processing helix chain 'B' and resid 4077 through 4085 removed outlier: 5.135A pdb=" N THR B4085 " --> pdb=" O GLN B4081 " (cutoff:3.500A) Processing helix chain 'B' and resid 4092 through 4104 Processing helix chain 'B' and resid 4107 through 4119 removed outlier: 4.436A pdb=" N GLU B4119 " --> pdb=" O LEU B4115 " (cutoff:3.500A) Processing helix chain 'B' and resid 4127 through 4158 removed outlier: 4.420A pdb=" N PHE B4135 " --> pdb=" O PHE B4131 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN B4136 " --> pdb=" O ALA B4132 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU B4137 " --> pdb=" O ASN B4133 " (cutoff:3.500A) Proline residue: B4138 - end of helix removed outlier: 3.870A pdb=" N ASP B4141 " --> pdb=" O GLU B4137 " (cutoff:3.500A) Proline residue: B4158 - end of helix Processing helix chain 'B' and resid 4160 through 4171 removed outlier: 3.508A pdb=" N LEU B4169 " --> pdb=" O ASN B4165 " (cutoff:3.500A) Processing helix chain 'B' and resid 4172 through 4178 Processing helix chain 'B' and resid 4201 through 4210 Processing helix chain 'B' and resid 4211 through 4227 Processing helix chain 'B' and resid 4232 through 4255 Processing helix chain 'B' and resid 4538 through 4557 Processing helix chain 'B' and resid 4558 through 4578 removed outlier: 4.361A pdb=" N PHE B4577 " --> pdb=" O PHE B4573 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR B4578 " --> pdb=" O ILE B4574 " (cutoff:3.500A) Processing helix chain 'B' and resid 4636 through 4681 removed outlier: 4.109A pdb=" N VAL B4664 " --> pdb=" O ASN B4660 " (cutoff:3.500A) Proline residue: B4665 - end of helix Processing helix chain 'B' and resid 4694 through 4705 removed outlier: 3.848A pdb=" N GLN B4698 " --> pdb=" O ASP B4694 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU B4702 " --> pdb=" O GLN B4698 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B4703 " --> pdb=" O TRP B4699 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B4704 " --> pdb=" O ASP B4700 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASN B4705 " --> pdb=" O ARG B4701 " (cutoff:3.500A) Processing helix chain 'B' and resid 4717 through 4727 Processing helix chain 'B' and resid 4731 through 4740 Processing helix chain 'B' and resid 4742 through 4752 Processing helix chain 'B' and resid 4761 through 4770 removed outlier: 4.338A pdb=" N TRP B4765 " --> pdb=" O GLY B4761 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP B4770 " --> pdb=" O ILE B4766 " (cutoff:3.500A) Processing helix chain 'B' and resid 4771 through 4784 Processing helix chain 'B' and resid 4785 through 4803 removed outlier: 3.789A pdb=" N HIS B4801 " --> pdb=" O SER B4797 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR B4802 " --> pdb=" O LEU B4798 " (cutoff:3.500A) Processing helix chain 'B' and resid 4804 through 4818 removed outlier: 4.548A pdb=" N ALA B4808 " --> pdb=" O ASN B4804 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA B4809 " --> pdb=" O PHE B4805 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N HIS B4810 " --> pdb=" O PHE B4806 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU B4811 " --> pdb=" O PHE B4807 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU B4812 " --> pdb=" O ALA B4808 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP B4813 " --> pdb=" O ALA B4809 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE B4814 " --> pdb=" O HIS B4810 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA B4815 " --> pdb=" O LEU B4811 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET B4816 " --> pdb=" O LEU B4812 " (cutoff:3.500A) Processing helix chain 'B' and resid 4819 through 4830 removed outlier: 3.592A pdb=" N SER B4827 " --> pdb=" O THR B4823 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B4828 " --> pdb=" O ILE B4824 " (cutoff:3.500A) Processing helix chain 'B' and resid 4831 through 4856 Processing helix chain 'B' and resid 4857 through 4862 removed outlier: 4.370A pdb=" N TYR B4861 " --> pdb=" O PHE B4857 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN B4862 " --> pdb=" O ARG B4858 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4857 through 4862' Processing helix chain 'B' and resid 4876 through 4891 removed outlier: 4.180A pdb=" N VAL B4889 " --> pdb=" O MET B4885 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG B4890 " --> pdb=" O TYR B4886 " (cutoff:3.500A) Processing helix chain 'B' and resid 4894 through 4899 removed outlier: 4.211A pdb=" N GLU B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) Processing helix chain 'B' and resid 4907 through 4922 Processing helix chain 'B' and resid 4926 through 4955 Processing helix chain 'B' and resid 4962 through 4968 removed outlier: 3.870A pdb=" N PHE B4966 " --> pdb=" O GLY B4962 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR B4968 " --> pdb=" O ASP B4964 " (cutoff:3.500A) Processing helix chain 'B' and resid 4971 through 4979 Processing helix chain 'B' and resid 4982 through 4997 removed outlier: 5.334A pdb=" N ASP B4997 " --> pdb=" O LEU B4993 " (cutoff:3.500A) Processing helix chain 'B' and resid 5002 through 5015 Processing helix chain 'B' and resid 5025 through 5031 Processing helix chain 'B' and resid 323 through 328 removed outlier: 4.979A pdb=" N VAL B 326 " --> pdb=" O LYS B 323 " (cutoff:3.500A) Proline residue: B 328 - end of helix Processing helix chain 'B' and resid 3582 through 3588 removed outlier: 4.953A pdb=" N GLU B3585 " --> pdb=" O GLY B3582 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASP B3586 " --> pdb=" O ARG B3583 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ALA B3587 " --> pdb=" O GLU B3584 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASP B3588 " --> pdb=" O GLU B3585 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3582 through 3588' Processing helix chain 'B' and resid 5016 through 5021 removed outlier: 4.454A pdb=" N PHE B5019 " --> pdb=" O CYS B5016 " (cutoff:3.500A) Proline residue: B5021 - end of helix Processing helix chain 'B' and resid 4683 through 4688 Processing helix chain 'C' and resid 62 through 67 removed outlier: 4.355A pdb=" N CYS C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 67' Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.777A pdb=" N HIS C 256 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ALA C 257 " --> pdb=" O VAL C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 257' Processing helix chain 'C' and resid 304 through 309 removed outlier: 5.061A pdb=" N HIS C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 395 through 423 removed outlier: 3.776A pdb=" N PHE C 422 " --> pdb=" O GLY C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 454 Processing helix chain 'C' and resid 461 through 483 Processing helix chain 'C' and resid 484 through 498 removed outlier: 4.507A pdb=" N TYR C 498 " --> pdb=" O ARG C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 508 removed outlier: 3.735A pdb=" N PHE C 507 " --> pdb=" O HIS C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 532 removed outlier: 4.317A pdb=" N SER C 515 " --> pdb=" O GLU C 511 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TRP C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS C 517 " --> pdb=" O ALA C 513 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLU C 518 " --> pdb=" O GLU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 545 removed outlier: 3.812A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE C 541 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER C 542 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 553 removed outlier: 4.117A pdb=" N LYS C 551 " --> pdb=" O TRP C 547 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP C 553 " --> pdb=" O VAL C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 572 Processing helix chain 'C' and resid 573 through 579 Processing helix chain 'C' and resid 580 through 594 removed outlier: 3.513A pdb=" N LEU C 591 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 610 removed outlier: 3.592A pdb=" N LEU C 601 " --> pdb=" O ASN C 597 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS C 608 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL C 609 " --> pdb=" O CYS C 605 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N CYS C 610 " --> pdb=" O SER C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 630 Proline residue: C 628 - end of helix Processing helix chain 'C' and resid 811 through 816 removed outlier: 4.509A pdb=" N ALA C 815 " --> pdb=" O PRO C 811 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL C 816 " --> pdb=" O CYS C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 816' Processing helix chain 'C' and resid 848 through 854 removed outlier: 4.093A pdb=" N PHE C 852 " --> pdb=" O SER C 848 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL C 853 " --> pdb=" O HIS C 849 " (cutoff:3.500A) Proline residue: C 854 - end of helix No H-bonds generated for 'chain 'C' and resid 848 through 854' Processing helix chain 'C' and resid 866 through 891 removed outlier: 3.709A pdb=" N ILE C 871 " --> pdb=" O HIS C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 936 Processing helix chain 'C' and resid 944 through 951 removed outlier: 4.517A pdb=" N GLU C 948 " --> pdb=" O ASP C 944 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP C 949 " --> pdb=" O GLU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 962 removed outlier: 4.502A pdb=" N MET C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 1005 Processing helix chain 'C' and resid 1024 through 1029 removed outlier: 3.777A pdb=" N LEU C1028 " --> pdb=" O PRO C1024 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP C1029 " --> pdb=" O TYR C1025 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1024 through 1029' Processing helix chain 'C' and resid 1030 through 1049 removed outlier: 3.540A pdb=" N ALA C1043 " --> pdb=" O SER C1039 " (cutoff:3.500A) Processing helix chain 'C' and resid 1068 through 1074 removed outlier: 4.925A pdb=" N ARG C1074 " --> pdb=" O GLY C1070 " (cutoff:3.500A) Processing helix chain 'C' and resid 1218 through 1223 removed outlier: 7.101A pdb=" N GLU C1222 " --> pdb=" O CYS C1218 " (cutoff:3.500A) Processing helix chain 'C' and resid 1424 through 1431 Processing helix chain 'C' and resid 1445 through 1450 removed outlier: 3.923A pdb=" N VAL C1449 " --> pdb=" O GLU C1445 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TRP C1450 " --> pdb=" O PRO C1446 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1445 through 1450' Processing helix chain 'C' and resid 1497 through 1503 removed outlier: 4.432A pdb=" N PHE C1501 " --> pdb=" O TRP C1497 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C1502 " --> pdb=" O GLY C1498 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N SER C1503 " --> pdb=" O GLY C1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1497 through 1503' Processing helix chain 'C' and resid 1575 through 1581 removed outlier: 3.823A pdb=" N ALA C1579 " --> pdb=" O PRO C1575 " (cutoff:3.500A) Processing helix chain 'C' and resid 1650 through 1657 removed outlier: 4.306A pdb=" N LEU C1654 " --> pdb=" O ASP C1650 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER C1655 " --> pdb=" O ILE C1651 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU C1656 " --> pdb=" O LEU C1652 " (cutoff:3.500A) Processing helix chain 'C' and resid 1658 through 1676 Processing helix chain 'C' and resid 1679 through 1690 removed outlier: 3.876A pdb=" N SER C1688 " --> pdb=" O HIS C1684 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS C1689 " --> pdb=" O ALA C1685 " (cutoff:3.500A) Processing helix chain 'C' and resid 1691 through 1701 Processing helix chain 'C' and resid 1705 through 1720 Processing helix chain 'C' and resid 1721 through 1733 removed outlier: 4.193A pdb=" N SER C1733 " --> pdb=" O ARG C1729 " (cutoff:3.500A) Processing helix chain 'C' and resid 1740 through 1747 removed outlier: 5.706A pdb=" N THR C1747 " --> pdb=" O THR C1743 " (cutoff:3.500A) Processing helix chain 'C' and resid 1805 through 1827 Processing helix chain 'C' and resid 1835 through 1854 Proline residue: C1842 - end of helix Processing helix chain 'C' and resid 1857 through 1869 Processing helix chain 'C' and resid 1926 through 1931 removed outlier: 4.898A pdb=" N LYS C1931 " --> pdb=" O LEU C1927 " (cutoff:3.500A) Processing helix chain 'C' and resid 1933 through 1985 removed outlier: 5.341A pdb=" N PHE C1985 " --> pdb=" O LEU C1981 " (cutoff:3.500A) Processing helix chain 'C' and resid 1988 through 2001 removed outlier: 3.759A pdb=" N ARG C1994 " --> pdb=" O ALA C1990 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU C1998 " --> pdb=" O ARG C1994 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE C1999 " --> pdb=" O ARG C1995 " (cutoff:3.500A) Processing helix chain 'C' and resid 2002 through 2012 Processing helix chain 'C' and resid 2025 through 2044 removed outlier: 3.657A pdb=" N GLU C2031 " --> pdb=" O GLU C2027 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C2032 " --> pdb=" O ILE C2028 " (cutoff:3.500A) Processing helix chain 'C' and resid 2094 through 2110 Processing helix chain 'C' and resid 2114 through 2131 removed outlier: 3.810A pdb=" N GLY C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) Processing helix chain 'C' and resid 2132 through 2142 Proline residue: C2140 - end of helix Processing helix chain 'C' and resid 2146 through 2170 removed outlier: 3.887A pdb=" N VAL C2150 " --> pdb=" O SER C2146 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU C2151 " --> pdb=" O VAL C2147 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP C2152 " --> pdb=" O SER C2148 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C2167 " --> pdb=" O ILE C2163 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE C2168 " --> pdb=" O ARG C2164 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL C2169 " --> pdb=" O SER C2165 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN C2170 " --> pdb=" O LEU C2166 " (cutoff:3.500A) Processing helix chain 'C' and resid 2172 through 2190 removed outlier: 5.492A pdb=" N LYS C2190 " --> pdb=" O ILE C2186 " (cutoff:3.500A) Processing helix chain 'C' and resid 2195 through 2203 Processing helix chain 'C' and resid 2204 through 2220 removed outlier: 5.209A pdb=" N GLY C2219 " --> pdb=" O VAL C2215 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU C2220 " --> pdb=" O LEU C2216 " (cutoff:3.500A) Processing helix chain 'C' and resid 2226 through 2245 removed outlier: 4.084A pdb=" N SER C2244 " --> pdb=" O PHE C2240 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG C2245 " --> pdb=" O CYS C2241 " (cutoff:3.500A) Processing helix chain 'C' and resid 2246 through 2255 removed outlier: 3.644A pdb=" N HIS C2254 " --> pdb=" O SER C2250 " (cutoff:3.500A) Processing helix chain 'C' and resid 2256 through 2263 removed outlier: 4.246A pdb=" N GLY C2263 " --> pdb=" O LEU C2259 " (cutoff:3.500A) Processing helix chain 'C' and resid 2272 through 2282 removed outlier: 3.523A pdb=" N VAL C2281 " --> pdb=" O ALA C2277 " (cutoff:3.500A) Processing helix chain 'C' and resid 2284 through 2291 Processing helix chain 'C' and resid 2292 through 2309 Processing helix chain 'C' and resid 2311 through 2318 Processing helix chain 'C' and resid 2325 through 2341 removed outlier: 3.756A pdb=" N ARG C2331 " --> pdb=" O CYS C2327 " (cutoff:3.500A) Processing helix chain 'C' and resid 2347 through 2362 Proline residue: C2362 - end of helix Processing helix chain 'C' and resid 2376 through 2391 Proline residue: C2391 - end of helix Processing helix chain 'C' and resid 2418 through 2438 Processing helix chain 'C' and resid 2440 through 2447 Processing helix chain 'C' and resid 2448 through 2463 Proline residue: C2463 - end of helix Processing helix chain 'C' and resid 2464 through 2473 Processing helix chain 'C' and resid 2496 through 2510 removed outlier: 3.865A pdb=" N LYS C2500 " --> pdb=" O VAL C2496 " (cutoff:3.500A) Processing helix chain 'C' and resid 2515 through 2526 Processing helix chain 'C' and resid 2527 through 2539 removed outlier: 3.607A pdb=" N ASP C2538 " --> pdb=" O ALA C2534 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N THR C2539 " --> pdb=" O ALA C2535 " (cutoff:3.500A) Processing helix chain 'C' and resid 2545 through 2567 removed outlier: 5.048A pdb=" N LEU C2560 " --> pdb=" O CYS C2556 " (cutoff:3.500A) Proline residue: C2561 - end of helix Processing helix chain 'C' and resid 2576 through 2594 removed outlier: 3.947A pdb=" N GLY C2593 " --> pdb=" O ARG C2589 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ARG C2594 " --> pdb=" O LEU C2590 " (cutoff:3.500A) Processing helix chain 'C' and resid 2597 through 2615 removed outlier: 3.685A pdb=" N TYR C2614 " --> pdb=" O ALA C2610 " (cutoff:3.500A) Processing helix chain 'C' and resid 2616 through 2631 removed outlier: 3.906A pdb=" N LEU C2620 " --> pdb=" O ARG C2616 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN C2621 " --> pdb=" O PRO C2617 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N HIS C2622 " --> pdb=" O SER C2618 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU C2623 " --> pdb=" O MET C2619 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C2629 " --> pdb=" O ARG C2625 " (cutoff:3.500A) Processing helix chain 'C' and resid 2637 through 2653 Proline residue: C2641 - end of helix Processing helix chain 'C' and resid 2669 through 2690 Processing helix chain 'C' and resid 2693 through 2712 Proline residue: C2702 - end of helix Proline residue: C2712 - end of helix Processing helix chain 'C' and resid 2742 through 2747 removed outlier: 5.125A pdb=" N ILE C2747 " --> pdb=" O THR C2743 " (cutoff:3.500A) Processing helix chain 'C' and resid 2749 through 2775 Processing helix chain 'C' and resid 2799 through 2821 Proline residue: C2809 - end of helix Processing helix chain 'C' and resid 2869 through 2899 Processing helix chain 'C' and resid 2908 through 2913 removed outlier: 5.395A pdb=" N THR C2913 " --> pdb=" O TYR C2909 " (cutoff:3.500A) Processing helix chain 'C' and resid 2916 through 2935 removed outlier: 4.657A pdb=" N ASP C2920 " --> pdb=" O GLU C2916 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS C2923 " --> pdb=" O ARG C2919 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU C2927 " --> pdb=" O LYS C2923 " (cutoff:3.500A) Processing helix chain 'C' and resid 2941 through 2948 removed outlier: 3.821A pdb=" N MET C2945 " --> pdb=" O GLY C2941 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASP C2948 " --> pdb=" O ASP C2944 " (cutoff:3.500A) Processing helix chain 'C' and resid 2950 through 2984 removed outlier: 6.084A pdb=" N PHE C2956 " --> pdb=" O ILE C2952 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ALA C2957 " --> pdb=" O GLU C2953 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE C2958 " --> pdb=" O LYS C2954 " (cutoff:3.500A) Processing helix chain 'C' and resid 2992 through 3015 removed outlier: 4.279A pdb=" N LEU C3004 " --> pdb=" O ALA C3000 " (cutoff:3.500A) Proline residue: C3005 - end of helix Processing helix chain 'C' and resid 3033 through 3052 Processing helix chain 'C' and resid 3054 through 3059 Processing helix chain 'C' and resid 3060 through 3076 removed outlier: 4.732A pdb=" N ALA C3064 " --> pdb=" O THR C3060 " (cutoff:3.500A) Processing helix chain 'C' and resid 3077 through 3084 removed outlier: 4.410A pdb=" N VAL C3081 " --> pdb=" O ASP C3077 " (cutoff:3.500A) Processing helix chain 'C' and resid 3086 through 3113 Processing helix chain 'C' and resid 3124 through 3152 removed outlier: 5.266A pdb=" N LEU C3138 " --> pdb=" O THR C3134 " (cutoff:3.500A) Proline residue: C3139 - end of helix Processing helix chain 'C' and resid 3160 through 3180 removed outlier: 3.612A pdb=" N SER C3172 " --> pdb=" O ARG C3168 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C3179 " --> pdb=" O SER C3175 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ARG C3180 " --> pdb=" O LEU C3176 " (cutoff:3.500A) Processing helix chain 'C' and resid 3181 through 3202 removed outlier: 3.817A pdb=" N LYS C3186 " --> pdb=" O PRO C3182 " (cutoff:3.500A) Proline residue: C3189 - end of helix Processing helix chain 'C' and resid 3208 through 3216 removed outlier: 4.087A pdb=" N ASN C3212 " --> pdb=" O GLU C3208 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU C3213 " --> pdb=" O PRO C3209 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TYR C3214 " --> pdb=" O GLU C3210 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN C3215 " --> pdb=" O LEU C3211 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ALA C3216 " --> pdb=" O ASN C3212 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3208 through 3216' Processing helix chain 'C' and resid 3218 through 3223 Processing helix chain 'C' and resid 3224 through 3232 removed outlier: 4.437A pdb=" N ARG C3228 " --> pdb=" O SER C3224 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA C3229 " --> pdb=" O PRO C3225 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE C3230 " --> pdb=" O ARG C3226 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU C3231 " --> pdb=" O GLU C3227 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLY C3232 " --> pdb=" O ARG C3228 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3224 through 3232' Processing helix chain 'C' and resid 3236 through 3242 removed outlier: 3.531A pdb=" N MET C3240 " --> pdb=" O SER C3236 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N CYS C3241 " --> pdb=" O VAL C3237 " (cutoff:3.500A) Proline residue: C3242 - end of helix No H-bonds generated for 'chain 'C' and resid 3236 through 3242' Processing helix chain 'C' and resid 3246 through 3261 Processing helix chain 'C' and resid 3263 through 3268 removed outlier: 3.835A pdb=" N MET C3267 " --> pdb=" O ARG C3263 " (cutoff:3.500A) Proline residue: C3268 - end of helix No H-bonds generated for 'chain 'C' and resid 3263 through 3268' Processing helix chain 'C' and resid 3269 through 3289 removed outlier: 4.574A pdb=" N LEU C3275 " --> pdb=" O ILE C3271 " (cutoff:3.500A) Proline residue: C3276 - end of helix Proline residue: C3283 - end of helix removed outlier: 3.658A pdb=" N ARG C3288 " --> pdb=" O ARG C3284 " (cutoff:3.500A) Processing helix chain 'C' and resid 3309 through 3328 Processing helix chain 'C' and resid 3333 through 3348 removed outlier: 4.800A pdb=" N LYS C3337 " --> pdb=" O ALA C3333 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG C3338 " --> pdb=" O SER C3334 " (cutoff:3.500A) Proline residue: C3345 - end of helix removed outlier: 4.323A pdb=" N SER C3348 " --> pdb=" O GLN C3344 " (cutoff:3.500A) Processing helix chain 'C' and resid 3351 through 3384 removed outlier: 4.708A pdb=" N LEU C3355 " --> pdb=" O ARG C3351 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ARG C3356 " --> pdb=" O PRO C3352 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE C3360 " --> pdb=" O ARG C3356 " (cutoff:3.500A) Proline residue: C3361 - end of helix removed outlier: 4.406A pdb=" N ALA C3384 " --> pdb=" O LEU C3380 " (cutoff:3.500A) Processing helix chain 'C' and resid 3390 through 3414 removed outlier: 6.730A pdb=" N LEU C3394 " --> pdb=" O GLU C3390 " (cutoff:3.500A) Proline residue: C3411 - end of helix Processing helix chain 'C' and resid 3420 through 3428 Proline residue: C3428 - end of helix Processing helix chain 'C' and resid 3429 through 3449 Processing helix chain 'C' and resid 3450 through 3464 removed outlier: 3.759A pdb=" N ARG C3454 " --> pdb=" O HIS C3450 " (cutoff:3.500A) Processing helix chain 'C' and resid 3466 through 3472 removed outlier: 4.046A pdb=" N PHE C3470 " --> pdb=" O ASN C3466 " (cutoff:3.500A) Processing helix chain 'C' and resid 3509 through 3527 removed outlier: 3.622A pdb=" N LEU C3515 " --> pdb=" O ILE C3511 " (cutoff:3.500A) Proline residue: C3520 - end of helix removed outlier: 3.579A pdb=" N MET C3525 " --> pdb=" O ILE C3521 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ALA C3527 " --> pdb=" O LEU C3523 " (cutoff:3.500A) Processing helix chain 'C' and resid 3528 through 3544 removed outlier: 5.272A pdb=" N ASP C3532 " --> pdb=" O PRO C3528 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU C3533 " --> pdb=" O THR C3529 " (cutoff:3.500A) Processing helix chain 'C' and resid 3546 through 3558 removed outlier: 3.744A pdb=" N LEU C3558 " --> pdb=" O LEU C3554 " (cutoff:3.500A) Processing helix chain 'C' and resid 3563 through 3568 Proline residue: C3568 - end of helix Processing helix chain 'C' and resid 3569 through 3581 Proline residue: C3581 - end of helix Processing helix chain 'C' and resid 3589 through 3613 Proline residue: C3613 - end of helix Processing helix chain 'C' and resid 3634 through 3639 removed outlier: 4.720A pdb=" N MET C3639 " --> pdb=" O ALA C3635 " (cutoff:3.500A) Processing helix chain 'C' and resid 3646 through 3662 Processing helix chain 'C' and resid 3670 through 3681 removed outlier: 5.546A pdb=" N ALA C3681 " --> pdb=" O ASP C3677 " (cutoff:3.500A) Processing helix chain 'C' and resid 3683 through 3688 removed outlier: 3.737A pdb=" N GLU C3687 " --> pdb=" O GLU C3683 " (cutoff:3.500A) Processing helix chain 'C' and resid 3697 through 3712 Processing helix chain 'C' and resid 3720 through 3735 removed outlier: 3.557A pdb=" N ASP C3728 " --> pdb=" O MET C3724 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS C3734 " --> pdb=" O MET C3730 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N HIS C3735 " --> pdb=" O ALA C3731 " (cutoff:3.500A) Processing helix chain 'C' and resid 3755 through 3775 removed outlier: 3.636A pdb=" N LEU C3773 " --> pdb=" O GLN C3769 " (cutoff:3.500A) Processing helix chain 'C' and resid 3777 through 3790 removed outlier: 4.204A pdb=" N LYS C3790 " --> pdb=" O ILE C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3794 through 3809 Processing helix chain 'C' and resid 3812 through 3827 Processing helix chain 'C' and resid 3829 through 3842 Processing helix chain 'C' and resid 3846 through 3860 removed outlier: 4.875A pdb=" N GLY C3860 " --> pdb=" O ALA C3856 " (cutoff:3.500A) Processing helix chain 'C' and resid 3880 through 3896 removed outlier: 3.612A pdb=" N CYS C3895 " --> pdb=" O LEU C3891 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3908 removed outlier: 4.240A pdb=" N ARG C3907 " --> pdb=" O GLN C3903 " (cutoff:3.500A) Processing helix chain 'C' and resid 3917 through 3942 removed outlier: 4.610A pdb=" N GLY C3942 " --> pdb=" O TRP C3938 " (cutoff:3.500A) Processing helix chain 'C' and resid 3947 through 3973 Processing helix chain 'C' and resid 3976 through 3987 removed outlier: 4.729A pdb=" N ARG C3987 " --> pdb=" O LEU C3983 " (cutoff:3.500A) Processing helix chain 'C' and resid 3988 through 4010 removed outlier: 3.713A pdb=" N ASP C4009 " --> pdb=" O LYS C4005 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER C4010 " --> pdb=" O LEU C4006 " (cutoff:3.500A) Processing helix chain 'C' and resid 4012 through 4035 Processing helix chain 'C' and resid 4041 through 4055 Processing helix chain 'C' and resid 4056 through 4074 removed outlier: 4.750A pdb=" N LYS C4072 " --> pdb=" O PHE C4068 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP C4073 " --> pdb=" O LEU C4069 " (cutoff:3.500A) Processing helix chain 'C' and resid 4077 through 4085 removed outlier: 5.135A pdb=" N THR C4085 " --> pdb=" O GLN C4081 " (cutoff:3.500A) Processing helix chain 'C' and resid 4092 through 4104 Processing helix chain 'C' and resid 4107 through 4119 removed outlier: 4.437A pdb=" N GLU C4119 " --> pdb=" O LEU C4115 " (cutoff:3.500A) Processing helix chain 'C' and resid 4127 through 4158 removed outlier: 4.420A pdb=" N PHE C4135 " --> pdb=" O PHE C4131 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN C4136 " --> pdb=" O ALA C4132 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU C4137 " --> pdb=" O ASN C4133 " (cutoff:3.500A) Proline residue: C4138 - end of helix removed outlier: 3.870A pdb=" N ASP C4141 " --> pdb=" O GLU C4137 " (cutoff:3.500A) Proline residue: C4158 - end of helix Processing helix chain 'C' and resid 4160 through 4171 removed outlier: 3.508A pdb=" N LEU C4169 " --> pdb=" O ASN C4165 " (cutoff:3.500A) Processing helix chain 'C' and resid 4172 through 4178 Processing helix chain 'C' and resid 4201 through 4210 Processing helix chain 'C' and resid 4211 through 4227 Processing helix chain 'C' and resid 4232 through 4255 Processing helix chain 'C' and resid 4538 through 4557 Processing helix chain 'C' and resid 4558 through 4578 removed outlier: 4.362A pdb=" N PHE C4577 " --> pdb=" O PHE C4573 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR C4578 " --> pdb=" O ILE C4574 " (cutoff:3.500A) Processing helix chain 'C' and resid 4636 through 4681 removed outlier: 4.109A pdb=" N VAL C4664 " --> pdb=" O ASN C4660 " (cutoff:3.500A) Proline residue: C4665 - end of helix Processing helix chain 'C' and resid 4694 through 4705 removed outlier: 3.848A pdb=" N GLN C4698 " --> pdb=" O ASP C4694 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU C4702 " --> pdb=" O GLN C4698 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL C4703 " --> pdb=" O TRP C4699 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C4704 " --> pdb=" O ASP C4700 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASN C4705 " --> pdb=" O ARG C4701 " (cutoff:3.500A) Processing helix chain 'C' and resid 4717 through 4727 Processing helix chain 'C' and resid 4731 through 4740 Processing helix chain 'C' and resid 4742 through 4752 Processing helix chain 'C' and resid 4761 through 4770 removed outlier: 4.338A pdb=" N TRP C4765 " --> pdb=" O GLY C4761 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP C4770 " --> pdb=" O ILE C4766 " (cutoff:3.500A) Processing helix chain 'C' and resid 4771 through 4784 Processing helix chain 'C' and resid 4785 through 4803 removed outlier: 3.789A pdb=" N HIS C4801 " --> pdb=" O SER C4797 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR C4802 " --> pdb=" O LEU C4798 " (cutoff:3.500A) Processing helix chain 'C' and resid 4804 through 4818 removed outlier: 4.549A pdb=" N ALA C4808 " --> pdb=" O ASN C4804 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA C4809 " --> pdb=" O PHE C4805 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N HIS C4810 " --> pdb=" O PHE C4806 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU C4811 " --> pdb=" O PHE C4807 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU C4812 " --> pdb=" O ALA C4808 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP C4813 " --> pdb=" O ALA C4809 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE C4814 " --> pdb=" O HIS C4810 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA C4815 " --> pdb=" O LEU C4811 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET C4816 " --> pdb=" O LEU C4812 " (cutoff:3.500A) Processing helix chain 'C' and resid 4819 through 4830 removed outlier: 3.592A pdb=" N SER C4827 " --> pdb=" O THR C4823 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C4828 " --> pdb=" O ILE C4824 " (cutoff:3.500A) Processing helix chain 'C' and resid 4831 through 4856 Processing helix chain 'C' and resid 4857 through 4862 removed outlier: 4.369A pdb=" N TYR C4861 " --> pdb=" O PHE C4857 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN C4862 " --> pdb=" O ARG C4858 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4857 through 4862' Processing helix chain 'C' and resid 4876 through 4891 removed outlier: 4.180A pdb=" N VAL C4889 " --> pdb=" O MET C4885 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG C4890 " --> pdb=" O TYR C4886 " (cutoff:3.500A) Processing helix chain 'C' and resid 4894 through 4899 removed outlier: 4.211A pdb=" N GLU C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) Processing helix chain 'C' and resid 4907 through 4922 Processing helix chain 'C' and resid 4926 through 4955 Processing helix chain 'C' and resid 4962 through 4968 removed outlier: 3.871A pdb=" N PHE C4966 " --> pdb=" O GLY C4962 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C4968 " --> pdb=" O ASP C4964 " (cutoff:3.500A) Processing helix chain 'C' and resid 4971 through 4979 Processing helix chain 'C' and resid 4982 through 4997 removed outlier: 5.334A pdb=" N ASP C4997 " --> pdb=" O LEU C4993 " (cutoff:3.500A) Processing helix chain 'C' and resid 5002 through 5015 Processing helix chain 'C' and resid 5025 through 5031 Processing helix chain 'C' and resid 323 through 328 removed outlier: 4.979A pdb=" N VAL C 326 " --> pdb=" O LYS C 323 " (cutoff:3.500A) Proline residue: C 328 - end of helix Processing helix chain 'C' and resid 3582 through 3588 removed outlier: 4.953A pdb=" N GLU C3585 " --> pdb=" O GLY C3582 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASP C3586 " --> pdb=" O ARG C3583 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ALA C3587 " --> pdb=" O GLU C3584 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASP C3588 " --> pdb=" O GLU C3585 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3582 through 3588' Processing helix chain 'C' and resid 5016 through 5021 removed outlier: 4.453A pdb=" N PHE C5019 " --> pdb=" O CYS C5016 " (cutoff:3.500A) Proline residue: C5021 - end of helix Processing helix chain 'C' and resid 4683 through 4688 Processing helix chain 'E' and resid 39 through 44 removed outlier: 4.065A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 3.899A pdb=" N ALA E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N SER E 68 " --> pdb=" O VAL E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.930A pdb=" N TYR E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 removed outlier: 4.051A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 4.001A pdb=" N ALA H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER H 68 " --> pdb=" O VAL H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 3.944A pdb=" N TYR H 83 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 4.056A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 4.003A pdb=" N ALA F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N SER F 68 " --> pdb=" O VAL F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.944A pdb=" N TYR F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 4.051A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 4.004A pdb=" N ALA G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.944A pdb=" N TYR G 83 " --> pdb=" O SER G 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 24 removed outlier: 4.697A pdb=" N LYS J 22 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU J 23 " --> pdb=" O HIS J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 43 removed outlier: 4.587A pdb=" N ASP J 36 " --> pdb=" O LYS J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 49 Processing helix chain 'J' and resid 51 through 65 removed outlier: 4.338A pdb=" N ASP J 63 " --> pdb=" O MET J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 91 removed outlier: 3.664A pdb=" N LEU J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 24 removed outlier: 4.697A pdb=" N LYS L 22 " --> pdb=" O ALA L 18 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU L 23 " --> pdb=" O HIS L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 43 removed outlier: 4.587A pdb=" N ASP L 36 " --> pdb=" O LYS L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 49 Processing helix chain 'L' and resid 51 through 65 removed outlier: 4.338A pdb=" N ASP L 63 " --> pdb=" O MET L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 91 removed outlier: 3.664A pdb=" N LEU L 82 " --> pdb=" O LEU L 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 24 removed outlier: 4.696A pdb=" N LYS N 22 " --> pdb=" O ALA N 18 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU N 23 " --> pdb=" O HIS N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 43 removed outlier: 4.588A pdb=" N ASP N 36 " --> pdb=" O LYS N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 49 Processing helix chain 'N' and resid 51 through 65 removed outlier: 4.338A pdb=" N ASP N 63 " --> pdb=" O MET N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 91 removed outlier: 3.663A pdb=" N LEU N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 24 removed outlier: 4.697A pdb=" N LYS P 22 " --> pdb=" O ALA P 18 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU P 23 " --> pdb=" O HIS P 19 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 43 removed outlier: 4.586A pdb=" N ASP P 36 " --> pdb=" O LYS P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 49 Processing helix chain 'P' and resid 51 through 65 removed outlier: 4.338A pdb=" N ASP P 63 " --> pdb=" O MET P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 71 through 91 removed outlier: 3.664A pdb=" N LEU P 82 " --> pdb=" O LEU P 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 24 removed outlier: 3.944A pdb=" N HIS I 19 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 43 removed outlier: 4.604A pdb=" N ASP I 36 " --> pdb=" O LYS I 32 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER I 43 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 49 removed outlier: 3.893A pdb=" N VAL I 48 " --> pdb=" O GLY I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 66 removed outlier: 3.778A pdb=" N ASP I 63 " --> pdb=" O MET I 59 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY I 66 " --> pdb=" O LEU I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 88 Processing helix chain 'K' and resid 3 through 24 removed outlier: 3.943A pdb=" N HIS K 19 " --> pdb=" O VAL K 15 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS K 22 " --> pdb=" O ALA K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 43 removed outlier: 4.604A pdb=" N ASP K 36 " --> pdb=" O LYS K 32 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER K 43 " --> pdb=" O GLN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 49 removed outlier: 3.892A pdb=" N VAL K 48 " --> pdb=" O GLY K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 66 removed outlier: 3.778A pdb=" N ASP K 63 " --> pdb=" O MET K 59 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 88 Processing helix chain 'M' and resid 3 through 24 removed outlier: 3.944A pdb=" N HIS M 19 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 43 removed outlier: 4.603A pdb=" N ASP M 36 " --> pdb=" O LYS M 32 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER M 43 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 49 removed outlier: 3.892A pdb=" N VAL M 48 " --> pdb=" O GLY M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 66 removed outlier: 3.778A pdb=" N ASP M 63 " --> pdb=" O MET M 59 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY M 66 " --> pdb=" O LEU M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 88 Processing helix chain 'O' and resid 3 through 24 removed outlier: 3.944A pdb=" N HIS O 19 " --> pdb=" O VAL O 15 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS O 22 " --> pdb=" O ALA O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 43 removed outlier: 4.603A pdb=" N ASP O 36 " --> pdb=" O LYS O 32 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER O 43 " --> pdb=" O GLN O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 49 removed outlier: 3.893A pdb=" N VAL O 48 " --> pdb=" O GLY O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 66 removed outlier: 3.777A pdb=" N ASP O 63 " --> pdb=" O MET O 59 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY O 66 " --> pdb=" O LEU O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 88 Processing sheet with id= 1, first strand: chain 'A' and resid 48 through 53 removed outlier: 6.305A pdb=" N LYS A 35 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU A 23 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N ALA A 40 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 13.178A pdb=" N VAL A 21 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU A 20 " --> pdb=" O ILE A 206 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 68 through 71 removed outlier: 6.589A pdb=" N LEU A 109 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 149 through 153 Processing sheet with id= 4, first strand: chain 'A' and resid 182 through 185 Processing sheet with id= 5, first strand: chain 'A' and resid 246 through 249 removed outlier: 5.348A pdb=" N VAL A 246 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 283 through 286 removed outlier: 4.928A pdb=" N ILE A 283 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A 290 " --> pdb=" O HIS A 285 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 315 through 319 Processing sheet with id= 8, first strand: chain 'A' and resid 727 through 731 removed outlier: 3.613A pdb=" N THR A 724 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU A 720 " --> pdb=" O VAL A 731 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N HIS A 721 " --> pdb=" O ASP A 718 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N HIS A 682 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 754 through 760 removed outlier: 3.751A pdb=" N ASP A 743 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS A 789 " --> pdb=" O ASP A 670 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY A1626 " --> pdb=" O ALA A1621 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 767 through 770 Processing sheet with id= 11, first strand: chain 'A' and resid 830 through 834 removed outlier: 4.954A pdb=" N TYR A 830 " --> pdb=" O VAL A 841 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY A 837 " --> pdb=" O GLY A 834 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU A1203 " --> pdb=" O PRO A 838 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN A1199 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A1200 " --> pdb=" O VAL A1096 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLY A1087 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP A1148 " --> pdb=" O ALA A1095 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 892 through 895 Processing sheet with id= 13, first strand: chain 'A' and resid 937 through 943 removed outlier: 7.982A pdb=" N GLY A 937 " --> pdb=" O PRO A1057 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS A 939 " --> pdb=" O GLU A1055 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA A 943 " --> pdb=" O GLY A1051 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLY A1051 " --> pdb=" O ALA A 943 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1006 through 1009 removed outlier: 3.516A pdb=" N SER A1009 " --> pdb=" O ASN A1019 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 1135 through 1139 removed outlier: 3.814A pdb=" N GLY A1127 " --> pdb=" O MET A1101 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N MET A1101 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU A1100 " --> pdb=" O GLY A1196 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE A1075 " --> pdb=" O SER A1240 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR A1236 " --> pdb=" O GLU A1079 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N THR A1237 " --> pdb=" O MET A1609 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 1268 through 1274 removed outlier: 3.909A pdb=" N VAL A1563 " --> pdb=" O LEU A1273 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL A1562 " --> pdb=" O PHE A1441 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLY A1568 " --> pdb=" O TYR A1435 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TYR A1435 " --> pdb=" O GLY A1568 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR A1432 " --> pdb=" O LEU A1523 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A1527 " --> pdb=" O ASP A1522 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLY A1526 " --> pdb=" O VAL A1543 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 1295 through 1298 removed outlier: 4.583A pdb=" N THR A1547 " --> pdb=" O PHE A1298 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE A1289 " --> pdb=" O LEU A1601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU A1597 " --> pdb=" O SER A1293 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 2823 through 2826 removed outlier: 4.147A pdb=" N THR A2823 " --> pdb=" O THR A2939 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU A2825 " --> pdb=" O ALA A2937 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A2937 " --> pdb=" O GLU A2825 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'A' and resid 4180 through 4187 removed outlier: 4.872A pdb=" N TYR A4180 " --> pdb=" O ILE A4200 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'A' and resid 4579 through 4582 Processing sheet with id= 21, first strand: chain 'D' and resid 48 through 53 removed outlier: 6.306A pdb=" N LYS D 35 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU D 23 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N ALA D 40 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 13.179A pdb=" N VAL D 21 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU D 20 " --> pdb=" O ILE D 206 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'D' and resid 68 through 71 removed outlier: 6.589A pdb=" N LEU D 109 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 149 through 153 Processing sheet with id= 24, first strand: chain 'D' and resid 182 through 185 Processing sheet with id= 25, first strand: chain 'D' and resid 246 through 249 removed outlier: 5.349A pdb=" N VAL D 246 " --> pdb=" O ALA D 377 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'D' and resid 283 through 286 removed outlier: 4.927A pdb=" N ILE D 283 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG D 290 " --> pdb=" O HIS D 285 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'D' and resid 315 through 319 Processing sheet with id= 28, first strand: chain 'D' and resid 727 through 731 removed outlier: 3.612A pdb=" N THR D 724 " --> pdb=" O VAL D 727 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU D 720 " --> pdb=" O VAL D 731 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N HIS D 721 " --> pdb=" O ASP D 718 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N HIS D 682 " --> pdb=" O SER D 785 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'D' and resid 754 through 760 removed outlier: 3.750A pdb=" N ASP D 743 " --> pdb=" O VAL D 669 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS D 789 " --> pdb=" O ASP D 670 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY D1626 " --> pdb=" O ALA D1621 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'D' and resid 767 through 770 Processing sheet with id= 31, first strand: chain 'D' and resid 830 through 834 removed outlier: 4.954A pdb=" N TYR D 830 " --> pdb=" O VAL D 841 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY D 837 " --> pdb=" O GLY D 834 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU D1203 " --> pdb=" O PRO D 838 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN D1199 " --> pdb=" O GLY D 842 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D1200 " --> pdb=" O VAL D1096 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLY D1087 " --> pdb=" O LEU D1156 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP D1148 " --> pdb=" O ALA D1095 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 892 through 895 Processing sheet with id= 33, first strand: chain 'D' and resid 937 through 943 removed outlier: 7.982A pdb=" N GLY D 937 " --> pdb=" O PRO D1057 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS D 939 " --> pdb=" O GLU D1055 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA D 943 " --> pdb=" O GLY D1051 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLY D1051 " --> pdb=" O ALA D 943 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 1006 through 1009 removed outlier: 3.516A pdb=" N SER D1009 " --> pdb=" O ASN D1019 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 1135 through 1139 removed outlier: 3.814A pdb=" N GLY D1127 " --> pdb=" O MET D1101 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N MET D1101 " --> pdb=" O GLY D1127 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU D1100 " --> pdb=" O GLY D1196 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE D1075 " --> pdb=" O SER D1240 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR D1236 " --> pdb=" O GLU D1079 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N THR D1237 " --> pdb=" O MET D1609 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 1268 through 1274 removed outlier: 3.909A pdb=" N VAL D1563 " --> pdb=" O LEU D1273 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL D1562 " --> pdb=" O PHE D1441 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLY D1568 " --> pdb=" O TYR D1435 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TYR D1435 " --> pdb=" O GLY D1568 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR D1432 " --> pdb=" O LEU D1523 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D1527 " --> pdb=" O ASP D1522 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLY D1526 " --> pdb=" O VAL D1543 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'D' and resid 1295 through 1298 removed outlier: 4.583A pdb=" N THR D1547 " --> pdb=" O PHE D1298 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE D1289 " --> pdb=" O LEU D1601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU D1597 " --> pdb=" O SER D1293 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'D' and resid 2823 through 2826 removed outlier: 4.146A pdb=" N THR D2823 " --> pdb=" O THR D2939 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU D2825 " --> pdb=" O ALA D2937 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D2937 " --> pdb=" O GLU D2825 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 4180 through 4187 removed outlier: 4.872A pdb=" N TYR D4180 " --> pdb=" O ILE D4200 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 4579 through 4582 Processing sheet with id= 41, first strand: chain 'B' and resid 48 through 53 removed outlier: 6.305A pdb=" N LYS B 35 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU B 23 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N ALA B 40 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 13.177A pdb=" N VAL B 21 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU B 20 " --> pdb=" O ILE B 206 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'B' and resid 68 through 71 removed outlier: 6.590A pdb=" N LEU B 109 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'B' and resid 149 through 153 Processing sheet with id= 44, first strand: chain 'B' and resid 182 through 185 Processing sheet with id= 45, first strand: chain 'B' and resid 246 through 249 removed outlier: 5.348A pdb=" N VAL B 246 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'B' and resid 283 through 286 removed outlier: 4.927A pdb=" N ILE B 283 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG B 290 " --> pdb=" O HIS B 285 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'B' and resid 315 through 319 Processing sheet with id= 48, first strand: chain 'B' and resid 727 through 731 removed outlier: 3.613A pdb=" N THR B 724 " --> pdb=" O VAL B 727 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU B 720 " --> pdb=" O VAL B 731 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N HIS B 721 " --> pdb=" O ASP B 718 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N HIS B 682 " --> pdb=" O SER B 785 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'B' and resid 754 through 760 removed outlier: 3.751A pdb=" N ASP B 743 " --> pdb=" O VAL B 669 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS B 789 " --> pdb=" O ASP B 670 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY B1626 " --> pdb=" O ALA B1621 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'B' and resid 767 through 770 Processing sheet with id= 51, first strand: chain 'B' and resid 830 through 834 removed outlier: 4.955A pdb=" N TYR B 830 " --> pdb=" O VAL B 841 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY B 837 " --> pdb=" O GLY B 834 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU B1203 " --> pdb=" O PRO B 838 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLN B1199 " --> pdb=" O GLY B 842 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B1200 " --> pdb=" O VAL B1096 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLY B1087 " --> pdb=" O LEU B1156 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP B1148 " --> pdb=" O ALA B1095 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'B' and resid 892 through 895 Processing sheet with id= 53, first strand: chain 'B' and resid 937 through 943 removed outlier: 7.982A pdb=" N GLY B 937 " --> pdb=" O PRO B1057 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS B 939 " --> pdb=" O GLU B1055 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA B 943 " --> pdb=" O GLY B1051 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLY B1051 " --> pdb=" O ALA B 943 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'B' and resid 1006 through 1009 removed outlier: 3.516A pdb=" N SER B1009 " --> pdb=" O ASN B1019 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'B' and resid 1135 through 1139 removed outlier: 3.814A pdb=" N GLY B1127 " --> pdb=" O MET B1101 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N MET B1101 " --> pdb=" O GLY B1127 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU B1100 " --> pdb=" O GLY B1196 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ILE B1075 " --> pdb=" O SER B1240 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR B1236 " --> pdb=" O GLU B1079 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N THR B1237 " --> pdb=" O MET B1609 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'B' and resid 1268 through 1274 removed outlier: 3.910A pdb=" N VAL B1563 " --> pdb=" O LEU B1273 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL B1562 " --> pdb=" O PHE B1441 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLY B1568 " --> pdb=" O TYR B1435 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TYR B1435 " --> pdb=" O GLY B1568 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N THR B1432 " --> pdb=" O LEU B1523 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B1527 " --> pdb=" O ASP B1522 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY B1526 " --> pdb=" O VAL B1543 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'B' and resid 1295 through 1298 removed outlier: 4.584A pdb=" N THR B1547 " --> pdb=" O PHE B1298 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE B1289 " --> pdb=" O LEU B1601 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU B1597 " --> pdb=" O SER B1293 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'B' and resid 2823 through 2826 removed outlier: 4.147A pdb=" N THR B2823 " --> pdb=" O THR B2939 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU B2825 " --> pdb=" O ALA B2937 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B2937 " --> pdb=" O GLU B2825 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'B' and resid 4180 through 4187 removed outlier: 4.873A pdb=" N TYR B4180 " --> pdb=" O ILE B4200 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'B' and resid 4579 through 4582 Processing sheet with id= 61, first strand: chain 'C' and resid 48 through 53 removed outlier: 6.305A pdb=" N LYS C 35 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU C 23 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N ALA C 40 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 13.179A pdb=" N VAL C 21 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU C 20 " --> pdb=" O ILE C 206 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'C' and resid 68 through 71 removed outlier: 6.589A pdb=" N LEU C 109 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'C' and resid 149 through 153 Processing sheet with id= 64, first strand: chain 'C' and resid 182 through 185 Processing sheet with id= 65, first strand: chain 'C' and resid 246 through 249 removed outlier: 5.348A pdb=" N VAL C 246 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'C' and resid 283 through 286 removed outlier: 4.927A pdb=" N ILE C 283 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 290 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'C' and resid 315 through 319 Processing sheet with id= 68, first strand: chain 'C' and resid 727 through 731 removed outlier: 3.613A pdb=" N THR C 724 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU C 720 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N HIS C 721 " --> pdb=" O ASP C 718 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS C 682 " --> pdb=" O SER C 785 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'C' and resid 754 through 760 removed outlier: 3.750A pdb=" N ASP C 743 " --> pdb=" O VAL C 669 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS C 789 " --> pdb=" O ASP C 670 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY C1626 " --> pdb=" O ALA C1621 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'C' and resid 767 through 770 Processing sheet with id= 71, first strand: chain 'C' and resid 830 through 834 removed outlier: 4.955A pdb=" N TYR C 830 " --> pdb=" O VAL C 841 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY C 837 " --> pdb=" O GLY C 834 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU C1203 " --> pdb=" O PRO C 838 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLN C1199 " --> pdb=" O GLY C 842 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL C1200 " --> pdb=" O VAL C1096 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLY C1087 " --> pdb=" O LEU C1156 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP C1148 " --> pdb=" O ALA C1095 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'C' and resid 892 through 895 Processing sheet with id= 73, first strand: chain 'C' and resid 937 through 943 removed outlier: 7.981A pdb=" N GLY C 937 " --> pdb=" O PRO C1057 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS C 939 " --> pdb=" O GLU C1055 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA C 943 " --> pdb=" O GLY C1051 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLY C1051 " --> pdb=" O ALA C 943 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'C' and resid 1006 through 1009 removed outlier: 3.516A pdb=" N SER C1009 " --> pdb=" O ASN C1019 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'C' and resid 1135 through 1139 removed outlier: 3.814A pdb=" N GLY C1127 " --> pdb=" O MET C1101 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N MET C1101 " --> pdb=" O GLY C1127 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU C1100 " --> pdb=" O GLY C1196 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ILE C1075 " --> pdb=" O SER C1240 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR C1236 " --> pdb=" O GLU C1079 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR C1237 " --> pdb=" O MET C1609 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'C' and resid 1268 through 1274 removed outlier: 3.909A pdb=" N VAL C1563 " --> pdb=" O LEU C1273 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL C1562 " --> pdb=" O PHE C1441 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLY C1568 " --> pdb=" O TYR C1435 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TYR C1435 " --> pdb=" O GLY C1568 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N THR C1432 " --> pdb=" O LEU C1523 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C1527 " --> pdb=" O ASP C1522 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLY C1526 " --> pdb=" O VAL C1543 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'C' and resid 1295 through 1298 removed outlier: 4.583A pdb=" N THR C1547 " --> pdb=" O PHE C1298 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE C1289 " --> pdb=" O LEU C1601 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU C1597 " --> pdb=" O SER C1293 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'C' and resid 2823 through 2826 removed outlier: 4.147A pdb=" N THR C2823 " --> pdb=" O THR C2939 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU C2825 " --> pdb=" O ALA C2937 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C2937 " --> pdb=" O GLU C2825 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'C' and resid 4180 through 4187 removed outlier: 4.872A pdb=" N TYR C4180 " --> pdb=" O ILE C4200 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'C' and resid 4579 through 4582 Processing sheet with id= 81, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.711A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL E 24 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.720A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL H 24 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'F' and resid 3 through 8 removed outlier: 6.722A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL F 24 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'G' and resid 3 through 8 removed outlier: 6.715A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL G 24 " --> pdb=" O LEU G 105 " (cutoff:3.500A) 8068 hydrogen bonds defined for protein. 24092 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: 130.18 Time building geometry restraints manager: 51.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 25096 1.31 - 1.44: 39616 1.44 - 1.56: 85807 1.56 - 1.69: 69 1.69 - 1.81: 1564 Bond restraints: 152152 Sorted by residual: bond pdb=" C11 PCW D5103 " pdb=" O3 PCW D5103 " ideal model delta sigma weight residual 1.326 1.419 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C11 PCW A8002 " pdb=" O3 PCW A8002 " ideal model delta sigma weight residual 1.326 1.419 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C11 PCW C5103 " pdb=" O3 PCW C5103 " ideal model delta sigma weight residual 1.326 1.419 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C11 PCW B8002 " pdb=" O3 PCW B8002 " ideal model delta sigma weight residual 1.326 1.419 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C11 PCW D5101 " pdb=" O3 PCW D5101 " ideal model delta sigma weight residual 1.326 1.419 -0.093 2.00e-02 2.50e+03 2.14e+01 ... (remaining 152147 not shown) Histogram of bond angle deviations from ideal: 95.01 - 107.19: 5478 107.19 - 119.38: 124068 119.38 - 131.56: 76122 131.56 - 143.74: 264 143.74 - 155.93: 8 Bond angle restraints: 205940 Sorted by residual: angle pdb=" C5 PCW A8003 " pdb=" N PCW A8003 " pdb=" C7 PCW A8003 " ideal model delta sigma weight residual 107.31 141.30 -33.99 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C5 PCW D5101 " pdb=" N PCW D5101 " pdb=" C7 PCW D5101 " ideal model delta sigma weight residual 107.31 141.29 -33.98 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C5 PCW C5101 " pdb=" N PCW C5101 " pdb=" C7 PCW C5101 " ideal model delta sigma weight residual 107.31 141.27 -33.96 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C5 PCW B8003 " pdb=" N PCW B8003 " pdb=" C7 PCW B8003 " ideal model delta sigma weight residual 107.31 141.27 -33.96 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C5 PCW A8002 " pdb=" N PCW A8002 " pdb=" C7 PCW A8002 " ideal model delta sigma weight residual 107.31 138.72 -31.41 3.00e+00 1.11e-01 1.10e+02 ... (remaining 205935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 83512 17.86 - 35.73: 6693 35.73 - 53.59: 1183 53.59 - 71.46: 348 71.46 - 89.32: 172 Dihedral angle restraints: 91908 sinusoidal: 37764 harmonic: 54144 Sorted by residual: dihedral pdb=" CA MET B3240 " pdb=" C MET B3240 " pdb=" N CYS B3241 " pdb=" CA CYS B3241 " ideal model delta harmonic sigma weight residual 180.00 148.90 31.10 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA MET C3240 " pdb=" C MET C3240 " pdb=" N CYS C3241 " pdb=" CA CYS C3241 " ideal model delta harmonic sigma weight residual 180.00 148.91 31.09 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA MET A3240 " pdb=" C MET A3240 " pdb=" N CYS A3241 " pdb=" CA CYS A3241 " ideal model delta harmonic sigma weight residual 180.00 148.92 31.08 0 5.00e+00 4.00e-02 3.86e+01 ... (remaining 91905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 18151 0.043 - 0.085: 3403 0.085 - 0.128: 986 0.128 - 0.171: 72 0.171 - 0.214: 12 Chirality restraints: 22624 Sorted by residual: chirality pdb=" C2 PCW C5101 " pdb=" C1 PCW C5101 " pdb=" C3 PCW C5101 " pdb=" O2 PCW C5101 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C2 PCW A8003 " pdb=" C1 PCW A8003 " pdb=" C3 PCW A8003 " pdb=" O2 PCW A8003 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C2 PCW B8002 " pdb=" C1 PCW B8002 " pdb=" C3 PCW B8002 " pdb=" O2 PCW B8002 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 22621 not shown) Planarity restraints: 26768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A1055 " 0.023 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C GLU A1055 " -0.077 2.00e-02 2.50e+03 pdb=" O GLU A1055 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO A1056 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D1055 " 0.023 2.00e-02 2.50e+03 4.42e-02 1.96e+01 pdb=" C GLU D1055 " -0.077 2.00e-02 2.50e+03 pdb=" O GLU D1055 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO D1056 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C1055 " -0.023 2.00e-02 2.50e+03 4.42e-02 1.96e+01 pdb=" C GLU C1055 " 0.077 2.00e-02 2.50e+03 pdb=" O GLU C1055 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO C1056 " -0.026 2.00e-02 2.50e+03 ... (remaining 26765 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 162 2.25 - 2.91: 61469 2.91 - 3.58: 226433 3.58 - 4.24: 352260 4.24 - 4.90: 603773 Nonbonded interactions: 1244097 Sorted by model distance: nonbonded pdb=" OD1 ASP M 56 " pdb=" NH2 ARG C3638 " model vdw 1.591 2.520 nonbonded pdb=" OD1 ASP O 56 " pdb=" NH2 ARG D3638 " model vdw 1.603 2.520 nonbonded pdb=" OD1 ASP K 56 " pdb=" NH2 ARG B3638 " model vdw 1.632 2.520 nonbonded pdb=" NH2 ARG A3638 " pdb=" OD1 ASP I 56 " model vdw 1.635 2.520 nonbonded pdb=" O GLY P 44 " pdb=" OD1 ASP P 47 " model vdw 1.644 3.040 ... (remaining 1244092 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 11 through 919 or resid 921 through 5035 or resid 8003)) selection = (chain 'B' and (resid 11 through 919 or resid 921 through 5035 or resid 8003)) selection = (chain 'C' and (resid 11 through 919 or resid 921 through 5035 or resid 5103)) selection = (chain 'D' and (resid 11 through 919 or resid 921 through 5035 or resid 5103)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and resid 2 through 94) selection = chain 'J' selection = (chain 'K' and resid 2 through 94) selection = chain 'L' selection = (chain 'M' and resid 2 through 94) selection = chain 'N' selection = (chain 'O' and resid 2 through 94) selection = chain 'P' } 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=0.44 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 32.580 Check model and map are aligned: 1.700 Set scattering table: 1.090 Process input model: 516.260 Find NCS groups from input model: 12.950 Set up NCS constraints: 1.250 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: 0.040 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 574.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 152152 Z= 0.216 Angle : 0.725 33.987 205940 Z= 0.375 Chirality : 0.037 0.214 22624 Planarity : 0.005 0.077 26768 Dihedral : 13.997 89.321 56924 Min Nonbonded Distance : 1.591 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.22 % Favored : 97.76 % Rotamer: Outliers : 0.05 % Allowed : 0.09 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.48 (0.06), residues: 18540 helix: 1.95 (0.05), residues: 9924 sheet: 0.14 (0.13), residues: 1644 loop : -0.16 (0.07), residues: 6972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP D1144 HIS 0.010 0.001 HIS B 219 PHE 0.019 0.001 PHE B3399 TYR 0.020 0.001 TYR A1978 ARG 0.017 0.001 ARG B1810 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2433 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2425 time to evaluate : 13.069 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: A 35 LYS cc_start: 0.8757 (mtpt) cc_final: 0.8352 (mtpp) REVERT: A 228 MET cc_start: 0.7653 (mpp) cc_final: 0.7230 (mpp) REVERT: A 925 MET cc_start: 0.9148 (mmp) cc_final: 0.8572 (mmm) REVERT: A 1042 GLN cc_start: 0.9368 (mm110) cc_final: 0.9026 (mm-40) REVERT: A 1871 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7624 (mm-30) REVERT: A 2313 MET cc_start: 0.7603 (mpp) cc_final: 0.7333 (mpp) REVERT: A 3451 ASN cc_start: 0.8953 (m110) cc_final: 0.8697 (m110) REVERT: A 3453 LYS cc_start: 0.8899 (mttp) cc_final: 0.8614 (mttp) REVERT: A 3595 ARG cc_start: 0.8771 (tpp80) cc_final: 0.8432 (tpp80) REVERT: A 3853 GLN cc_start: 0.8565 (tt0) cc_final: 0.8185 (tt0) REVERT: A 4107 THR cc_start: 0.7091 (m) cc_final: 0.6850 (t) REVERT: A 4674 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7625 (mm-30) REVERT: A 4897 ASP cc_start: 0.8336 (m-30) cc_final: 0.8031 (m-30) REVERT: A 5010 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8367 (tttm) REVERT: E 15 THR cc_start: 0.8754 (m) cc_final: 0.8290 (p) REVERT: E 78 SER cc_start: 0.8616 (m) cc_final: 0.8386 (p) REVERT: I 39 GLN cc_start: 0.8624 (pp30) cc_final: 0.8328 (pp30) REVERT: I 65 ASN cc_start: 0.7176 (t0) cc_final: 0.6938 (t0) REVERT: H 15 THR cc_start: 0.8791 (m) cc_final: 0.8304 (p) REVERT: H 78 SER cc_start: 0.8632 (m) cc_final: 0.8403 (p) REVERT: F 15 THR cc_start: 0.8809 (m) cc_final: 0.8324 (p) REVERT: F 78 SER cc_start: 0.8630 (m) cc_final: 0.8411 (p) REVERT: G 15 THR cc_start: 0.8794 (m) cc_final: 0.8301 (p) REVERT: G 78 SER cc_start: 0.8640 (m) cc_final: 0.8414 (p) REVERT: M 65 ASN cc_start: 0.7271 (t0) cc_final: 0.7058 (t0) REVERT: L 62 LEU cc_start: 0.7295 (pp) cc_final: 0.6993 (tp) REVERT: P 34 LEU cc_start: 0.8382 (tp) cc_final: 0.6993 (tp) REVERT: P 75 TYR cc_start: 0.8867 (t80) cc_final: 0.8622 (t80) REVERT: D 35 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8352 (mtpp) REVERT: D 228 MET cc_start: 0.7623 (mpp) cc_final: 0.7212 (mpp) REVERT: D 620 ASP cc_start: 0.8104 (m-30) cc_final: 0.7857 (m-30) REVERT: D 924 GLN cc_start: 0.8897 (pm20) cc_final: 0.8688 (pm20) REVERT: D 925 MET cc_start: 0.9143 (mmp) cc_final: 0.8518 (mmm) REVERT: D 1042 GLN cc_start: 0.9352 (mm110) cc_final: 0.9110 (mm-40) REVERT: D 1445 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8448 (mm-30) REVERT: D 1871 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7598 (mm-30) REVERT: D 3451 ASN cc_start: 0.8940 (m110) cc_final: 0.8683 (m110) REVERT: D 3453 LYS cc_start: 0.8884 (mttp) cc_final: 0.8604 (mttp) REVERT: D 3595 ARG cc_start: 0.8753 (tpp80) cc_final: 0.8422 (tpp80) REVERT: D 3853 GLN cc_start: 0.8560 (tt0) cc_final: 0.8156 (tt0) REVERT: D 4107 THR cc_start: 0.7073 (m) cc_final: 0.6851 (t) REVERT: D 4674 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7618 (mm-30) REVERT: D 4837 MET cc_start: 0.8386 (mmp) cc_final: 0.8156 (mmm) REVERT: D 4897 ASP cc_start: 0.8345 (m-30) cc_final: 0.8046 (m-30) REVERT: D 5010 LYS cc_start: 0.8603 (ttmm) cc_final: 0.8355 (tttm) REVERT: B 35 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8353 (mtpp) REVERT: B 228 MET cc_start: 0.7617 (mpp) cc_final: 0.7205 (mpp) REVERT: B 620 ASP cc_start: 0.8087 (m-30) cc_final: 0.7855 (m-30) REVERT: B 924 GLN cc_start: 0.8919 (pm20) cc_final: 0.8699 (pm20) REVERT: B 925 MET cc_start: 0.9127 (mmp) cc_final: 0.8504 (mmm) REVERT: B 1042 GLN cc_start: 0.9352 (mm110) cc_final: 0.9115 (mm-40) REVERT: B 1445 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8441 (mm-30) REVERT: B 1871 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7630 (mm-30) REVERT: B 3451 ASN cc_start: 0.8944 (m110) cc_final: 0.8690 (m110) REVERT: B 3453 LYS cc_start: 0.8888 (mttp) cc_final: 0.8608 (mttp) REVERT: B 3595 ARG cc_start: 0.8757 (tpp80) cc_final: 0.8424 (tpp80) REVERT: B 3853 GLN cc_start: 0.8587 (tt0) cc_final: 0.8187 (tt0) REVERT: B 4107 THR cc_start: 0.7045 (m) cc_final: 0.6811 (t) REVERT: B 4674 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7621 (mm-30) REVERT: B 4837 MET cc_start: 0.8389 (mmp) cc_final: 0.8153 (mmm) REVERT: B 4897 ASP cc_start: 0.8348 (m-30) cc_final: 0.8060 (m-30) REVERT: B 5010 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8361 (tttm) REVERT: C 35 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8356 (mtpp) REVERT: C 197 MET cc_start: 0.7512 (mtt) cc_final: 0.7255 (mtm) REVERT: C 228 MET cc_start: 0.7645 (mpp) cc_final: 0.7234 (mpp) REVERT: C 620 ASP cc_start: 0.8096 (m-30) cc_final: 0.7860 (m-30) REVERT: C 924 GLN cc_start: 0.8894 (pm20) cc_final: 0.8688 (pm20) REVERT: C 925 MET cc_start: 0.9127 (mmp) cc_final: 0.8523 (mmm) REVERT: C 1042 GLN cc_start: 0.9347 (mm110) cc_final: 0.9111 (mm-40) REVERT: C 1445 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8447 (mm-30) REVERT: C 1871 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7628 (mm-30) REVERT: C 3451 ASN cc_start: 0.8940 (m110) cc_final: 0.8685 (m110) REVERT: C 3453 LYS cc_start: 0.8897 (mttp) cc_final: 0.8619 (mttp) REVERT: C 3595 ARG cc_start: 0.8753 (tpp80) cc_final: 0.8424 (tpp80) REVERT: C 3853 GLN cc_start: 0.8583 (tt0) cc_final: 0.8184 (tt0) REVERT: C 4107 THR cc_start: 0.7047 (m) cc_final: 0.6822 (t) REVERT: C 4674 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7624 (mm-30) REVERT: C 4837 MET cc_start: 0.8394 (mmp) cc_final: 0.8159 (mmm) REVERT: C 4897 ASP cc_start: 0.8345 (m-30) cc_final: 0.8059 (m-30) REVERT: C 5010 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8360 (tttm) outliers start: 8 outliers final: 0 residues processed: 2432 average time/residue: 1.3573 time to fit residues: 5730.2178 Evaluate side-chains 1887 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1887 time to evaluate : 12.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 1570 optimal weight: 0.8980 chunk 1409 optimal weight: 0.9980 chunk 782 optimal weight: 0.0370 chunk 481 optimal weight: 9.9990 chunk 950 optimal weight: 7.9990 chunk 753 optimal weight: 10.0000 chunk 1457 optimal weight: 6.9990 chunk 564 optimal weight: 5.9990 chunk 886 optimal weight: 4.9990 chunk 1085 optimal weight: 6.9990 chunk 1689 optimal weight: 50.0000 overall best weight: 2.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 HIS ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 GLN ** A2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3431 ASN A3458 ASN A3463 ASN A3606 HIS ** A3872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3930 GLN A4145 ASN ** A4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4945 GLN ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** K 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 HIS ** D 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1012 GLN D1973 ASN ** D2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3431 ASN D3458 ASN D3463 ASN D3606 HIS ** D3872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3930 GLN ** D4145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4945 GLN B 721 HIS ** B 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1012 GLN B1973 ASN ** B2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3458 ASN B3463 ASN B3606 HIS ** B3872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3930 GLN B4145 ASN ** B4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4945 GLN C 721 HIS ** C 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3431 ASN C3458 ASN C3463 ASN C3606 HIS ** C3872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3930 GLN C4145 ASN ** C4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4945 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 152152 Z= 0.316 Angle : 0.622 14.869 205940 Z= 0.319 Chirality : 0.043 0.319 22624 Planarity : 0.005 0.066 26768 Dihedral : 5.904 78.569 20604 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.11 % Favored : 97.87 % Rotamer: Outliers : 0.86 % Allowed : 5.69 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.57 (0.06), residues: 18540 helix: 2.00 (0.05), residues: 9976 sheet: 0.17 (0.13), residues: 1612 loop : -0.09 (0.08), residues: 6952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C1144 HIS 0.013 0.001 HIS J 17 PHE 0.064 0.002 PHE B4096 TYR 0.041 0.002 TYR A1052 ARG 0.010 0.001 ARG D3349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2173 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 2034 time to evaluate : 13.093 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: A 35 LYS cc_start: 0.8819 (mtpt) cc_final: 0.8507 (mtpp) REVERT: A 82 MET cc_start: 0.8704 (ttp) cc_final: 0.8472 (ptm) REVERT: A 939 HIS cc_start: 0.7690 (m-70) cc_final: 0.6458 (m90) REVERT: A 1623 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7338 (mm-30) REVERT: A 1987 MET cc_start: 0.7227 (mmt) cc_final: 0.5780 (mpp) REVERT: A 2210 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7442 (tp30) REVERT: A 2933 MET cc_start: 0.7106 (ttp) cc_final: 0.6806 (ppp) REVERT: A 3857 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7510 (mm-30) REVERT: A 4674 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7591 (mm-30) REVERT: A 5010 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8414 (tttm) REVERT: E 15 THR cc_start: 0.8788 (m) cc_final: 0.8346 (p) REVERT: E 54 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8744 (mp10) REVERT: E 78 SER cc_start: 0.8593 (m) cc_final: 0.8361 (p) REVERT: H 15 THR cc_start: 0.8796 (m) cc_final: 0.8304 (p) REVERT: H 78 SER cc_start: 0.8601 (m) cc_final: 0.8391 (p) REVERT: F 15 THR cc_start: 0.8811 (m) cc_final: 0.8336 (p) REVERT: F 78 SER cc_start: 0.8582 (m) cc_final: 0.8379 (p) REVERT: G 15 THR cc_start: 0.8797 (m) cc_final: 0.8343 (p) REVERT: G 78 SER cc_start: 0.8606 (m) cc_final: 0.8400 (p) REVERT: K 62 LEU cc_start: 0.8898 (pp) cc_final: 0.8581 (mm) REVERT: O 62 LEU cc_start: 0.8864 (pp) cc_final: 0.8612 (mm) REVERT: L 59 MET cc_start: 0.8929 (mmm) cc_final: 0.8581 (mmm) REVERT: N 59 MET cc_start: 0.8963 (mmm) cc_final: 0.8677 (mmm) REVERT: P 34 LEU cc_start: 0.8372 (tp) cc_final: 0.7725 (tp) REVERT: P 59 MET cc_start: 0.8905 (mmm) cc_final: 0.8613 (mmm) REVERT: P 75 TYR cc_start: 0.8964 (t80) cc_final: 0.8634 (t80) REVERT: D 35 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8513 (mtpp) REVERT: D 82 MET cc_start: 0.8707 (ttp) cc_final: 0.8503 (ptm) REVERT: D 620 ASP cc_start: 0.8115 (m-30) cc_final: 0.7820 (m-30) REVERT: D 924 GLN cc_start: 0.8973 (pm20) cc_final: 0.8654 (pm20) REVERT: D 1445 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8433 (mm-30) REVERT: D 1987 MET cc_start: 0.7370 (mmt) cc_final: 0.5986 (mpp) REVERT: D 2210 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7434 (tp30) REVERT: D 2503 MET cc_start: 0.8971 (mmt) cc_final: 0.8756 (mmt) REVERT: D 2933 MET cc_start: 0.7139 (ttp) cc_final: 0.6832 (ppp) REVERT: D 3857 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7483 (mm-30) REVERT: D 4674 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7611 (mm-30) REVERT: D 4837 MET cc_start: 0.8438 (mmp) cc_final: 0.8193 (mmm) REVERT: D 4897 ASP cc_start: 0.8476 (m-30) cc_final: 0.8125 (m-30) REVERT: D 5010 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8421 (tttm) REVERT: B 35 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8543 (mtpp) REVERT: B 82 MET cc_start: 0.8711 (ttp) cc_final: 0.8485 (ptm) REVERT: B 620 ASP cc_start: 0.8119 (m-30) cc_final: 0.7826 (m-30) REVERT: B 924 GLN cc_start: 0.8968 (pm20) cc_final: 0.8643 (pm20) REVERT: B 1445 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8440 (mm-30) REVERT: B 1987 MET cc_start: 0.7378 (mmt) cc_final: 0.5985 (mpp) REVERT: B 2210 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7442 (tp30) REVERT: B 2933 MET cc_start: 0.7157 (ttp) cc_final: 0.6851 (ppp) REVERT: B 3857 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7533 (mm-30) REVERT: B 4674 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7613 (mm-30) REVERT: B 4729 ILE cc_start: 0.8896 (mm) cc_final: 0.8684 (mm) REVERT: B 4897 ASP cc_start: 0.8479 (m-30) cc_final: 0.8127 (m-30) REVERT: B 5010 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8415 (tttm) REVERT: C 35 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8522 (mtpp) REVERT: C 620 ASP cc_start: 0.8114 (m-30) cc_final: 0.7827 (m-30) REVERT: C 924 GLN cc_start: 0.8966 (pm20) cc_final: 0.8669 (pm20) REVERT: C 928 GLU cc_start: 0.8790 (pt0) cc_final: 0.8590 (pt0) REVERT: C 1445 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8438 (mm-30) REVERT: C 1987 MET cc_start: 0.7379 (mmt) cc_final: 0.5995 (mpp) REVERT: C 2210 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7439 (tp30) REVERT: C 2503 MET cc_start: 0.8970 (mmt) cc_final: 0.8752 (mmt) REVERT: C 2933 MET cc_start: 0.7138 (ttp) cc_final: 0.6827 (ppp) REVERT: C 3694 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8310 (mtpp) REVERT: C 3857 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7523 (mm-30) REVERT: C 4674 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7618 (mm-30) REVERT: C 4729 ILE cc_start: 0.8894 (mm) cc_final: 0.8682 (mm) REVERT: C 5010 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8418 (tttm) outliers start: 139 outliers final: 100 residues processed: 2089 average time/residue: 1.2633 time to fit residues: 4652.9856 Evaluate side-chains 1909 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1808 time to evaluate : 12.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 2001 SER Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2007 ILE Chi-restraints excluded: chain A residue 2624 LEU Chi-restraints excluded: chain A residue 2971 SER Chi-restraints excluded: chain A residue 3088 ILE Chi-restraints excluded: chain A residue 3156 ASP Chi-restraints excluded: chain A residue 3160 ASP Chi-restraints excluded: chain A residue 3161 ASP Chi-restraints excluded: chain A residue 3253 GLU Chi-restraints excluded: chain A residue 3559 ASN Chi-restraints excluded: chain A residue 3599 GLU Chi-restraints excluded: chain A residue 3876 LYS Chi-restraints excluded: chain A residue 4866 ASP Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain O residue 19 HIS Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain P residue 36 ASP Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 846 CYS Chi-restraints excluded: chain D residue 858 ASP Chi-restraints excluded: chain D residue 1047 LEU Chi-restraints excluded: chain D residue 1265 VAL Chi-restraints excluded: chain D residue 1422 ARG Chi-restraints excluded: chain D residue 1424 ASP Chi-restraints excluded: chain D residue 2001 SER Chi-restraints excluded: chain D residue 2005 GLU Chi-restraints excluded: chain D residue 2007 ILE Chi-restraints excluded: chain D residue 2624 LEU Chi-restraints excluded: chain D residue 2971 SER Chi-restraints excluded: chain D residue 3088 ILE Chi-restraints excluded: chain D residue 3156 ASP Chi-restraints excluded: chain D residue 3160 ASP Chi-restraints excluded: chain D residue 3253 GLU Chi-restraints excluded: chain D residue 3559 ASN Chi-restraints excluded: chain D residue 3599 GLU Chi-restraints excluded: chain D residue 4866 ASP Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 846 CYS Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1265 VAL Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 2001 SER Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2007 ILE Chi-restraints excluded: chain B residue 2624 LEU Chi-restraints excluded: chain B residue 2971 SER Chi-restraints excluded: chain B residue 3088 ILE Chi-restraints excluded: chain B residue 3156 ASP Chi-restraints excluded: chain B residue 3160 ASP Chi-restraints excluded: chain B residue 3253 GLU Chi-restraints excluded: chain B residue 3559 ASN Chi-restraints excluded: chain B residue 3599 GLU Chi-restraints excluded: chain B residue 3876 LYS Chi-restraints excluded: chain B residue 4866 ASP Chi-restraints excluded: chain B residue 4964 ASP Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 846 CYS Chi-restraints excluded: chain C residue 858 ASP Chi-restraints excluded: chain C residue 1422 ARG Chi-restraints excluded: chain C residue 1424 ASP Chi-restraints excluded: chain C residue 2001 SER Chi-restraints excluded: chain C residue 2005 GLU Chi-restraints excluded: chain C residue 2007 ILE Chi-restraints excluded: chain C residue 2624 LEU Chi-restraints excluded: chain C residue 2971 SER Chi-restraints excluded: chain C residue 3088 ILE Chi-restraints excluded: chain C residue 3156 ASP Chi-restraints excluded: chain C residue 3160 ASP Chi-restraints excluded: chain C residue 3161 ASP Chi-restraints excluded: chain C residue 3253 GLU Chi-restraints excluded: chain C residue 3559 ASN Chi-restraints excluded: chain C residue 3599 GLU Chi-restraints excluded: chain C residue 3876 LYS Chi-restraints excluded: chain C residue 4866 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 938 optimal weight: 6.9990 chunk 524 optimal weight: 8.9990 chunk 1405 optimal weight: 3.9990 chunk 1150 optimal weight: 2.9990 chunk 465 optimal weight: 5.9990 chunk 1692 optimal weight: 0.9980 chunk 1827 optimal weight: 2.9990 chunk 1507 optimal weight: 20.0000 chunk 1678 optimal weight: 50.0000 chunk 576 optimal weight: 0.3980 chunk 1357 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN A 939 HIS A1507 GLN A1973 ASN A2037 GLN ** A2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3458 ASN ** A3870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN ** K 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 659 GLN D 939 HIS ** D2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 939 HIS ** B2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3431 ASN ** B3870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS C 659 GLN C 939 HIS C1012 GLN C1973 ASN ** C2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 152152 Z= 0.279 Angle : 0.597 16.709 205940 Z= 0.303 Chirality : 0.041 0.336 22624 Planarity : 0.005 0.064 26768 Dihedral : 5.639 67.989 20604 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.00 % Favored : 97.98 % Rotamer: Outliers : 1.12 % Allowed : 6.53 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.62 (0.06), residues: 18540 helix: 2.03 (0.05), residues: 9948 sheet: 0.23 (0.13), residues: 1620 loop : -0.04 (0.08), residues: 6972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP J 91 HIS 0.011 0.001 HIS C 219 PHE 0.054 0.002 PHE A4096 TYR 0.038 0.002 TYR B1052 ARG 0.013 0.001 ARG D2416 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2089 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1908 time to evaluate : 13.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8458 (mtpp) REVERT: A 939 HIS cc_start: 0.7223 (m90) cc_final: 0.6957 (m90) REVERT: A 962 MET cc_start: 0.3962 (tpp) cc_final: 0.3686 (tpp) REVERT: A 1623 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7328 (mm-30) REVERT: A 1987 MET cc_start: 0.6894 (mmt) cc_final: 0.5738 (mpp) REVERT: A 2210 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7397 (tp30) REVERT: A 2679 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8941 (tt) REVERT: A 2933 MET cc_start: 0.7331 (ttp) cc_final: 0.7064 (ppp) REVERT: A 3857 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7525 (mm-30) REVERT: A 4674 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7592 (mm-30) REVERT: A 5010 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8415 (tttm) REVERT: E 15 THR cc_start: 0.8806 (m) cc_final: 0.8362 (p) REVERT: E 54 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8738 (mp10) REVERT: J 48 VAL cc_start: 0.9008 (m) cc_final: 0.8791 (p) REVERT: I 61 GLU cc_start: 0.8740 (tp30) cc_final: 0.8121 (tp30) REVERT: I 62 LEU cc_start: 0.8558 (pp) cc_final: 0.8275 (pp) REVERT: H 15 THR cc_start: 0.8813 (m) cc_final: 0.8361 (p) REVERT: F 15 THR cc_start: 0.8824 (m) cc_final: 0.8385 (p) REVERT: F 54 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8745 (mp10) REVERT: G 15 THR cc_start: 0.8823 (m) cc_final: 0.8378 (p) REVERT: G 54 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8737 (mp10) REVERT: P 34 LEU cc_start: 0.8593 (tp) cc_final: 0.8215 (tp) REVERT: P 75 TYR cc_start: 0.8987 (t80) cc_final: 0.8711 (t80) REVERT: D 14 PHE cc_start: 0.8595 (m-80) cc_final: 0.8223 (m-80) REVERT: D 35 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8453 (mtpp) REVERT: D 620 ASP cc_start: 0.8111 (m-30) cc_final: 0.7808 (m-30) REVERT: D 921 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.7844 (p90) REVERT: D 939 HIS cc_start: 0.7137 (m90) cc_final: 0.6866 (m90) REVERT: D 962 MET cc_start: 0.3864 (tpp) cc_final: 0.3491 (tpp) REVERT: D 1445 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8435 (mm-30) REVERT: D 1623 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7346 (mm-30) REVERT: D 1987 MET cc_start: 0.7030 (mmt) cc_final: 0.6159 (mpp) REVERT: D 2210 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7384 (tp30) REVERT: D 2679 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8954 (tt) REVERT: D 2933 MET cc_start: 0.7351 (ttp) cc_final: 0.7034 (ppp) REVERT: D 3857 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7522 (mm-30) REVERT: D 4674 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7607 (mm-30) REVERT: D 5010 LYS cc_start: 0.8640 (ttmm) cc_final: 0.8395 (tttm) REVERT: B 14 PHE cc_start: 0.8598 (m-80) cc_final: 0.8228 (m-80) REVERT: B 35 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8457 (mtpp) REVERT: B 620 ASP cc_start: 0.8113 (m-30) cc_final: 0.7811 (m-30) REVERT: B 921 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7847 (p90) REVERT: B 939 HIS cc_start: 0.7133 (m90) cc_final: 0.6865 (m90) REVERT: B 962 MET cc_start: 0.3845 (tpp) cc_final: 0.3471 (tpp) REVERT: B 1038 ASP cc_start: 0.8748 (t0) cc_final: 0.8353 (t0) REVERT: B 1041 CYS cc_start: 0.9272 (t) cc_final: 0.8456 (p) REVERT: B 1445 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8417 (mm-30) REVERT: B 1623 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7329 (mm-30) REVERT: B 1987 MET cc_start: 0.7032 (mmt) cc_final: 0.5755 (mpp) REVERT: B 2210 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7398 (tp30) REVERT: B 2679 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8960 (tt) REVERT: B 2933 MET cc_start: 0.7357 (ttp) cc_final: 0.7052 (ppp) REVERT: B 3857 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7542 (mm-30) REVERT: B 4674 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7597 (mm-30) REVERT: B 4729 ILE cc_start: 0.8926 (mm) cc_final: 0.8722 (mm) REVERT: B 5010 LYS cc_start: 0.8643 (ttmm) cc_final: 0.8400 (tttm) REVERT: C 14 PHE cc_start: 0.8600 (m-80) cc_final: 0.8216 (m-80) REVERT: C 35 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8456 (mtpp) REVERT: C 620 ASP cc_start: 0.8114 (m-30) cc_final: 0.7815 (m-30) REVERT: C 921 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7837 (p90) REVERT: C 928 GLU cc_start: 0.8727 (pt0) cc_final: 0.8522 (pt0) REVERT: C 939 HIS cc_start: 0.7147 (m90) cc_final: 0.6877 (m90) REVERT: C 962 MET cc_start: 0.3858 (tpp) cc_final: 0.3488 (tpp) REVERT: C 1038 ASP cc_start: 0.8754 (t0) cc_final: 0.8354 (t0) REVERT: C 1041 CYS cc_start: 0.9274 (t) cc_final: 0.8413 (p) REVERT: C 1445 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8436 (mm-30) REVERT: C 1623 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7352 (mm-30) REVERT: C 1987 MET cc_start: 0.7035 (mmt) cc_final: 0.6160 (mpp) REVERT: C 2210 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7387 (tp30) REVERT: C 2679 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8956 (tt) REVERT: C 2933 MET cc_start: 0.7341 (ttp) cc_final: 0.7033 (ppp) REVERT: C 3217 CYS cc_start: 0.7977 (p) cc_final: 0.7687 (p) REVERT: C 3857 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7531 (mm-30) REVERT: C 4674 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7600 (mm-30) REVERT: C 4729 ILE cc_start: 0.8922 (mm) cc_final: 0.8719 (mm) REVERT: C 5010 LYS cc_start: 0.8640 (ttmm) cc_final: 0.8395 (tttm) outliers start: 181 outliers final: 133 residues processed: 1975 average time/residue: 1.2822 time to fit residues: 4484.5287 Evaluate side-chains 1949 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1805 time to evaluate : 12.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 2001 SER Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2007 ILE Chi-restraints excluded: chain A residue 2679 LEU Chi-restraints excluded: chain A residue 2971 SER Chi-restraints excluded: chain A residue 3088 ILE Chi-restraints excluded: chain A residue 3156 ASP Chi-restraints excluded: chain A residue 3160 ASP Chi-restraints excluded: chain A residue 3161 ASP Chi-restraints excluded: chain A residue 3226 ARG Chi-restraints excluded: chain A residue 3253 GLU Chi-restraints excluded: chain A residue 3394 LEU Chi-restraints excluded: chain A residue 3536 LEU Chi-restraints excluded: chain A residue 3559 ASN Chi-restraints excluded: chain A residue 3599 GLU Chi-restraints excluded: chain A residue 3876 LYS Chi-restraints excluded: chain A residue 4816 MET Chi-restraints excluded: chain A residue 4866 ASP Chi-restraints excluded: chain A residue 4931 GLN Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain O residue 19 HIS Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 846 CYS Chi-restraints excluded: chain D residue 858 ASP Chi-restraints excluded: chain D residue 921 TYR Chi-restraints excluded: chain D residue 1422 ARG Chi-restraints excluded: chain D residue 1424 ASP Chi-restraints excluded: chain D residue 1623 GLU Chi-restraints excluded: chain D residue 2001 SER Chi-restraints excluded: chain D residue 2005 GLU Chi-restraints excluded: chain D residue 2007 ILE Chi-restraints excluded: chain D residue 2679 LEU Chi-restraints excluded: chain D residue 2971 SER Chi-restraints excluded: chain D residue 3088 ILE Chi-restraints excluded: chain D residue 3156 ASP Chi-restraints excluded: chain D residue 3160 ASP Chi-restraints excluded: chain D residue 3226 ARG Chi-restraints excluded: chain D residue 3253 GLU Chi-restraints excluded: chain D residue 3394 LEU Chi-restraints excluded: chain D residue 3559 ASN Chi-restraints excluded: chain D residue 3599 GLU Chi-restraints excluded: chain D residue 4816 MET Chi-restraints excluded: chain D residue 4866 ASP Chi-restraints excluded: chain D residue 4931 GLN Chi-restraints excluded: chain D residue 4964 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 846 CYS Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1623 GLU Chi-restraints excluded: chain B residue 2001 SER Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2007 ILE Chi-restraints excluded: chain B residue 2679 LEU Chi-restraints excluded: chain B residue 2971 SER Chi-restraints excluded: chain B residue 3088 ILE Chi-restraints excluded: chain B residue 3156 ASP Chi-restraints excluded: chain B residue 3160 ASP Chi-restraints excluded: chain B residue 3161 ASP Chi-restraints excluded: chain B residue 3226 ARG Chi-restraints excluded: chain B residue 3253 GLU Chi-restraints excluded: chain B residue 3394 LEU Chi-restraints excluded: chain B residue 3559 ASN Chi-restraints excluded: chain B residue 3599 GLU Chi-restraints excluded: chain B residue 3876 LYS Chi-restraints excluded: chain B residue 4816 MET Chi-restraints excluded: chain B residue 4866 ASP Chi-restraints excluded: chain B residue 4931 GLN Chi-restraints excluded: chain B residue 4964 ASP Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 846 CYS Chi-restraints excluded: chain C residue 858 ASP Chi-restraints excluded: chain C residue 921 TYR Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1422 ARG Chi-restraints excluded: chain C residue 1424 ASP Chi-restraints excluded: chain C residue 1623 GLU Chi-restraints excluded: chain C residue 2001 SER Chi-restraints excluded: chain C residue 2005 GLU Chi-restraints excluded: chain C residue 2007 ILE Chi-restraints excluded: chain C residue 2679 LEU Chi-restraints excluded: chain C residue 2971 SER Chi-restraints excluded: chain C residue 3088 ILE Chi-restraints excluded: chain C residue 3156 ASP Chi-restraints excluded: chain C residue 3160 ASP Chi-restraints excluded: chain C residue 3161 ASP Chi-restraints excluded: chain C residue 3226 ARG Chi-restraints excluded: chain C residue 3253 GLU Chi-restraints excluded: chain C residue 3394 LEU Chi-restraints excluded: chain C residue 3559 ASN Chi-restraints excluded: chain C residue 3599 GLU Chi-restraints excluded: chain C residue 3876 LYS Chi-restraints excluded: chain C residue 4816 MET Chi-restraints excluded: chain C residue 4866 ASP Chi-restraints excluded: chain C residue 4931 GLN Chi-restraints excluded: chain C residue 4964 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 1671 optimal weight: 30.0000 chunk 1272 optimal weight: 0.8980 chunk 878 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 807 optimal weight: 30.0000 chunk 1136 optimal weight: 2.9990 chunk 1698 optimal weight: 5.9990 chunk 1797 optimal weight: 8.9990 chunk 887 optimal weight: 9.9990 chunk 1609 optimal weight: 8.9990 chunk 484 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1570 GLN A2037 GLN ** A2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3872 GLN ** A4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1507 GLN D1570 GLN ** D2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3458 ASN ** D3870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3872 GLN ** D4145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1507 GLN B1570 GLN ** B2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3458 ASN ** B3870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3872 GLN ** B4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1507 GLN C1570 GLN ** C2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3458 ASN C3870 ASN C3872 GLN ** C4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 152152 Z= 0.357 Angle : 0.609 15.053 205940 Z= 0.311 Chirality : 0.043 0.313 22624 Planarity : 0.005 0.066 26768 Dihedral : 5.548 67.945 20604 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.26 % Favored : 97.72 % Rotamer: Outliers : 1.42 % Allowed : 7.34 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.58 (0.06), residues: 18540 helix: 1.99 (0.05), residues: 9940 sheet: 0.13 (0.13), residues: 1624 loop : -0.03 (0.08), residues: 6976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D3286 HIS 0.013 0.001 HIS D 219 PHE 0.053 0.002 PHE B4096 TYR 0.035 0.002 TYR B3605 ARG 0.011 0.001 ARG A1822 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2087 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1857 time to evaluate : 13.166 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: A 35 LYS cc_start: 0.8828 (mtpt) cc_final: 0.8408 (mtpp) REVERT: A 939 HIS cc_start: 0.7024 (m90) cc_final: 0.6747 (m90) REVERT: A 1037 ARG cc_start: 0.8317 (mtm110) cc_final: 0.8023 (mtm110) REVERT: A 1038 ASP cc_start: 0.8755 (t0) cc_final: 0.8425 (t0) REVERT: A 1041 CYS cc_start: 0.9224 (t) cc_final: 0.8413 (p) REVERT: A 1623 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7332 (mm-30) REVERT: A 1987 MET cc_start: 0.6812 (mmt) cc_final: 0.5555 (mpp) REVERT: A 2210 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7408 (tp30) REVERT: A 2679 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9007 (tt) REVERT: A 2701 MET cc_start: 0.8247 (tmm) cc_final: 0.8019 (tmm) REVERT: A 2933 MET cc_start: 0.7291 (ttp) cc_final: 0.7037 (ppp) REVERT: A 3694 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8345 (mmtt) REVERT: A 4674 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7615 (mm-30) REVERT: A 5010 LYS cc_start: 0.8681 (ttmm) cc_final: 0.8442 (tttm) REVERT: E 54 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8718 (mp10) REVERT: I 39 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8939 (pp30) REVERT: I 45 PHE cc_start: 0.6205 (OUTLIER) cc_final: 0.5927 (t80) REVERT: H 54 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8701 (mp10) REVERT: F 15 THR cc_start: 0.8853 (m) cc_final: 0.8349 (p) REVERT: F 54 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8750 (mp10) REVERT: G 15 THR cc_start: 0.8836 (m) cc_final: 0.8336 (p) REVERT: G 54 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8727 (mp10) REVERT: K 39 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8933 (pp30) REVERT: M 39 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8929 (pp30) REVERT: O 34 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7756 (mm) REVERT: L 59 MET cc_start: 0.9085 (mmm) cc_final: 0.8675 (mmm) REVERT: P 34 LEU cc_start: 0.8550 (tp) cc_final: 0.7671 (tp) REVERT: P 75 TYR cc_start: 0.9029 (t80) cc_final: 0.8687 (t80) REVERT: D 35 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8419 (mtpp) REVERT: D 620 ASP cc_start: 0.8140 (m-30) cc_final: 0.7824 (m-30) REVERT: D 921 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.8089 (p90) REVERT: D 925 MET cc_start: 0.8965 (mmm) cc_final: 0.8749 (mpp) REVERT: D 939 HIS cc_start: 0.7059 (m90) cc_final: 0.6761 (m90) REVERT: D 962 MET cc_start: 0.3838 (tpp) cc_final: 0.3422 (tpp) REVERT: D 1038 ASP cc_start: 0.8735 (t0) cc_final: 0.8390 (t0) REVERT: D 1041 CYS cc_start: 0.9249 (t) cc_final: 0.8444 (p) REVERT: D 1445 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8431 (mm-30) REVERT: D 1623 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7382 (mm-30) REVERT: D 1987 MET cc_start: 0.6863 (mmt) cc_final: 0.5749 (mpp) REVERT: D 2210 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7424 (tp30) REVERT: D 2313 MET cc_start: 0.7833 (mpp) cc_final: 0.7428 (mpp) REVERT: D 2679 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9010 (tt) REVERT: D 3694 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8351 (mmtt) REVERT: D 4674 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7602 (mm-30) REVERT: D 5010 LYS cc_start: 0.8681 (ttmm) cc_final: 0.8440 (tttm) REVERT: B 20 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8205 (mm-30) REVERT: B 35 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8421 (mtpp) REVERT: B 620 ASP cc_start: 0.8137 (m-30) cc_final: 0.7823 (m-30) REVERT: B 855 CYS cc_start: 0.8881 (m) cc_final: 0.8677 (m) REVERT: B 921 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.8157 (p90) REVERT: B 939 HIS cc_start: 0.7062 (m90) cc_final: 0.6768 (m90) REVERT: B 962 MET cc_start: 0.3827 (tpp) cc_final: 0.3410 (tpp) REVERT: B 1038 ASP cc_start: 0.8708 (t0) cc_final: 0.8430 (t0) REVERT: B 1041 CYS cc_start: 0.9261 (t) cc_final: 0.8432 (p) REVERT: B 1445 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8403 (mm-30) REVERT: B 1623 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7350 (mm-30) REVERT: B 1987 MET cc_start: 0.6855 (mmt) cc_final: 0.5610 (mpp) REVERT: B 2210 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7440 (tp30) REVERT: B 2313 MET cc_start: 0.7831 (mpp) cc_final: 0.7433 (mpp) REVERT: B 2679 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9019 (tt) REVERT: B 2701 MET cc_start: 0.8217 (tmm) cc_final: 0.7957 (tmm) REVERT: B 2933 MET cc_start: 0.7303 (ttp) cc_final: 0.7040 (ppp) REVERT: B 3287 GLU cc_start: 0.8505 (tp30) cc_final: 0.8176 (mm-30) REVERT: B 3694 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8346 (mmtt) REVERT: B 3857 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7580 (mm-30) REVERT: B 4107 THR cc_start: 0.7152 (m) cc_final: 0.6817 (t) REVERT: B 4674 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7616 (mm-30) REVERT: B 4729 ILE cc_start: 0.8980 (mm) cc_final: 0.8710 (mt) REVERT: B 5010 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8440 (tttm) REVERT: C 35 LYS cc_start: 0.8842 (mtpt) cc_final: 0.8431 (mtpp) REVERT: C 620 ASP cc_start: 0.8136 (m-30) cc_final: 0.7825 (m-30) REVERT: C 921 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7858 (p90) REVERT: C 928 GLU cc_start: 0.8772 (pt0) cc_final: 0.8353 (pt0) REVERT: C 939 HIS cc_start: 0.7077 (m90) cc_final: 0.6779 (m90) REVERT: C 962 MET cc_start: 0.3868 (tpp) cc_final: 0.3468 (tpp) REVERT: C 1038 ASP cc_start: 0.8704 (t0) cc_final: 0.8417 (t0) REVERT: C 1041 CYS cc_start: 0.9270 (t) cc_final: 0.8454 (p) REVERT: C 1445 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8424 (mm-30) REVERT: C 1623 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: C 1987 MET cc_start: 0.6868 (mmt) cc_final: 0.5754 (mpp) REVERT: C 2210 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7429 (tp30) REVERT: C 2313 MET cc_start: 0.7827 (mpp) cc_final: 0.7442 (mpp) REVERT: C 2679 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9016 (tt) REVERT: C 2701 MET cc_start: 0.8213 (tmm) cc_final: 0.7955 (tmm) REVERT: C 2933 MET cc_start: 0.7283 (ttp) cc_final: 0.7018 (ppp) REVERT: C 3217 CYS cc_start: 0.8048 (p) cc_final: 0.7771 (p) REVERT: C 3287 GLU cc_start: 0.8477 (tp30) cc_final: 0.8138 (mm-30) REVERT: C 3857 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7570 (mm-30) REVERT: C 4107 THR cc_start: 0.7147 (m) cc_final: 0.6819 (t) REVERT: C 4674 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7621 (mm-30) REVERT: C 4729 ILE cc_start: 0.8977 (mm) cc_final: 0.8711 (mt) REVERT: C 5010 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8445 (tttm) outliers start: 230 outliers final: 153 residues processed: 1958 average time/residue: 1.2678 time to fit residues: 4395.2154 Evaluate side-chains 1930 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1761 time to evaluate : 12.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 2001 SER Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2007 ILE Chi-restraints excluded: chain A residue 2679 LEU Chi-restraints excluded: chain A residue 2971 SER Chi-restraints excluded: chain A residue 3088 ILE Chi-restraints excluded: chain A residue 3156 ASP Chi-restraints excluded: chain A residue 3160 ASP Chi-restraints excluded: chain A residue 3161 ASP Chi-restraints excluded: chain A residue 3226 ARG Chi-restraints excluded: chain A residue 3394 LEU Chi-restraints excluded: chain A residue 3451 ASN Chi-restraints excluded: chain A residue 3462 GLN Chi-restraints excluded: chain A residue 3559 ASN Chi-restraints excluded: chain A residue 3599 GLU Chi-restraints excluded: chain A residue 3694 LYS Chi-restraints excluded: chain A residue 3876 LYS Chi-restraints excluded: chain A residue 4720 ARG Chi-restraints excluded: chain A residue 4816 MET Chi-restraints excluded: chain A residue 4866 ASP Chi-restraints excluded: chain A residue 4931 GLN Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 846 CYS Chi-restraints excluded: chain D residue 858 ASP Chi-restraints excluded: chain D residue 921 TYR Chi-restraints excluded: chain D residue 932 THR Chi-restraints excluded: chain D residue 1047 LEU Chi-restraints excluded: chain D residue 1265 VAL Chi-restraints excluded: chain D residue 1422 ARG Chi-restraints excluded: chain D residue 1424 ASP Chi-restraints excluded: chain D residue 1623 GLU Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2001 SER Chi-restraints excluded: chain D residue 2005 GLU Chi-restraints excluded: chain D residue 2007 ILE Chi-restraints excluded: chain D residue 2272 THR Chi-restraints excluded: chain D residue 2679 LEU Chi-restraints excluded: chain D residue 2971 SER Chi-restraints excluded: chain D residue 3088 ILE Chi-restraints excluded: chain D residue 3156 ASP Chi-restraints excluded: chain D residue 3160 ASP Chi-restraints excluded: chain D residue 3161 ASP Chi-restraints excluded: chain D residue 3394 LEU Chi-restraints excluded: chain D residue 3451 ASN Chi-restraints excluded: chain D residue 3462 GLN Chi-restraints excluded: chain D residue 3559 ASN Chi-restraints excluded: chain D residue 3599 GLU Chi-restraints excluded: chain D residue 3694 LYS Chi-restraints excluded: chain D residue 4720 ARG Chi-restraints excluded: chain D residue 4816 MET Chi-restraints excluded: chain D residue 4866 ASP Chi-restraints excluded: chain D residue 4931 GLN Chi-restraints excluded: chain D residue 4964 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 846 CYS Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1265 VAL Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1623 GLU Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2001 SER Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2007 ILE Chi-restraints excluded: chain B residue 2272 THR Chi-restraints excluded: chain B residue 2679 LEU Chi-restraints excluded: chain B residue 2971 SER Chi-restraints excluded: chain B residue 3088 ILE Chi-restraints excluded: chain B residue 3156 ASP Chi-restraints excluded: chain B residue 3160 ASP Chi-restraints excluded: chain B residue 3161 ASP Chi-restraints excluded: chain B residue 3226 ARG Chi-restraints excluded: chain B residue 3324 ILE Chi-restraints excluded: chain B residue 3394 LEU Chi-restraints excluded: chain B residue 3451 ASN Chi-restraints excluded: chain B residue 3462 GLN Chi-restraints excluded: chain B residue 3559 ASN Chi-restraints excluded: chain B residue 3599 GLU Chi-restraints excluded: chain B residue 3694 LYS Chi-restraints excluded: chain B residue 3876 LYS Chi-restraints excluded: chain B residue 4720 ARG Chi-restraints excluded: chain B residue 4816 MET Chi-restraints excluded: chain B residue 4866 ASP Chi-restraints excluded: chain B residue 4931 GLN Chi-restraints excluded: chain B residue 4964 ASP Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 846 CYS Chi-restraints excluded: chain C residue 858 ASP Chi-restraints excluded: chain C residue 921 TYR Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1071 ASP Chi-restraints excluded: chain C residue 1422 ARG Chi-restraints excluded: chain C residue 1424 ASP Chi-restraints excluded: chain C residue 1623 GLU Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2001 SER Chi-restraints excluded: chain C residue 2005 GLU Chi-restraints excluded: chain C residue 2007 ILE Chi-restraints excluded: chain C residue 2679 LEU Chi-restraints excluded: chain C residue 2971 SER Chi-restraints excluded: chain C residue 3088 ILE Chi-restraints excluded: chain C residue 3156 ASP Chi-restraints excluded: chain C residue 3160 ASP Chi-restraints excluded: chain C residue 3161 ASP Chi-restraints excluded: chain C residue 3394 LEU Chi-restraints excluded: chain C residue 3451 ASN Chi-restraints excluded: chain C residue 3462 GLN Chi-restraints excluded: chain C residue 3559 ASN Chi-restraints excluded: chain C residue 3599 GLU Chi-restraints excluded: chain C residue 3694 LYS Chi-restraints excluded: chain C residue 3876 LYS Chi-restraints excluded: chain C residue 4720 ARG Chi-restraints excluded: chain C residue 4816 MET Chi-restraints excluded: chain C residue 4866 ASP Chi-restraints excluded: chain C residue 4931 GLN Chi-restraints excluded: chain C residue 4964 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 1497 optimal weight: 0.6980 chunk 1020 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 1338 optimal weight: 0.1980 chunk 741 optimal weight: 6.9990 chunk 1534 optimal weight: 5.9990 chunk 1242 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 918 optimal weight: 6.9990 chunk 1613 optimal weight: 4.9990 chunk 453 optimal weight: 20.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 HIS A2037 GLN ** A2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3870 ASN ** A4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 HIS ** D1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2037 GLN ** D2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3870 ASN ** D4145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 HIS ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2037 GLN ** B2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3870 ASN ** B4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 HIS C2037 GLN ** C2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 152152 Z= 0.250 Angle : 0.580 15.230 205940 Z= 0.295 Chirality : 0.041 0.328 22624 Planarity : 0.004 0.068 26768 Dihedral : 5.394 66.145 20604 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.42 % Allowed : 8.17 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.65 (0.06), residues: 18540 helix: 2.09 (0.05), residues: 9884 sheet: 0.15 (0.13), residues: 1616 loop : -0.04 (0.08), residues: 7040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 91 HIS 0.010 0.001 HIS P 17 PHE 0.058 0.002 PHE D4096 TYR 0.040 0.001 TYR B3605 ARG 0.015 0.000 ARG A2889 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2088 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1857 time to evaluate : 13.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 PHE cc_start: 0.8605 (m-80) cc_final: 0.8256 (m-80) REVERT: A 20 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8166 (mm-30) REVERT: A 35 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8407 (mtpp) REVERT: A 939 HIS cc_start: 0.7207 (m90) cc_final: 0.6900 (m90) REVERT: A 961 MET cc_start: 0.3942 (tpp) cc_final: 0.3524 (tpt) REVERT: A 982 GLN cc_start: 0.8587 (mp10) cc_final: 0.8239 (mp10) REVERT: A 1037 ARG cc_start: 0.8333 (mtm110) cc_final: 0.8028 (mtm110) REVERT: A 1038 ASP cc_start: 0.8702 (t0) cc_final: 0.8418 (t0) REVERT: A 1041 CYS cc_start: 0.9230 (t) cc_final: 0.8399 (p) REVERT: A 1623 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7340 (mm-30) REVERT: A 1987 MET cc_start: 0.6783 (mmt) cc_final: 0.5542 (mpp) REVERT: A 2210 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7369 (tp30) REVERT: A 2313 MET cc_start: 0.7839 (mpp) cc_final: 0.7633 (mpp) REVERT: A 2701 MET cc_start: 0.8261 (tmm) cc_final: 0.8000 (tmm) REVERT: A 2933 MET cc_start: 0.7256 (ttp) cc_final: 0.6997 (ppp) REVERT: A 2949 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7786 (p) REVERT: A 3185 GLU cc_start: 0.7811 (mp0) cc_final: 0.7569 (mp0) REVERT: A 3694 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8327 (mmtt) REVERT: A 4674 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7595 (mm-30) REVERT: A 5010 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8420 (tttm) REVERT: E 54 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8722 (mp10) REVERT: J 74 GLU cc_start: 0.8848 (mp0) cc_final: 0.8591 (pm20) REVERT: I 34 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7948 (mm) REVERT: H 54 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8690 (mp10) REVERT: F 15 THR cc_start: 0.8851 (m) cc_final: 0.8358 (p) REVERT: F 54 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8746 (mp10) REVERT: G 15 THR cc_start: 0.8847 (m) cc_final: 0.8383 (p) REVERT: G 54 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8702 (mp10) REVERT: K 34 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8026 (mm) REVERT: K 59 MET cc_start: 0.8680 (ppp) cc_final: 0.8474 (ppp) REVERT: M 34 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7895 (mm) REVERT: O 34 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7800 (mm) REVERT: O 61 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7436 (pp20) REVERT: P 34 LEU cc_start: 0.8534 (tp) cc_final: 0.8034 (tp) REVERT: P 75 TYR cc_start: 0.9019 (t80) cc_final: 0.8768 (t80) REVERT: D 14 PHE cc_start: 0.8613 (m-80) cc_final: 0.8260 (m-80) REVERT: D 20 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8163 (mm-30) REVERT: D 35 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8427 (mtpp) REVERT: D 620 ASP cc_start: 0.8121 (m-30) cc_final: 0.7810 (m-30) REVERT: D 921 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8103 (p90) REVERT: D 939 HIS cc_start: 0.7038 (m90) cc_final: 0.6731 (m90) REVERT: D 982 GLN cc_start: 0.8599 (mp10) cc_final: 0.8258 (mp10) REVERT: D 1037 ARG cc_start: 0.8350 (mtm110) cc_final: 0.8069 (mtm110) REVERT: D 1038 ASP cc_start: 0.8692 (t0) cc_final: 0.8424 (t0) REVERT: D 1041 CYS cc_start: 0.9234 (t) cc_final: 0.8457 (p) REVERT: D 1042 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8887 (mm-40) REVERT: D 1445 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8421 (mm-30) REVERT: D 1623 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7370 (mm-30) REVERT: D 1987 MET cc_start: 0.6762 (mmt) cc_final: 0.5524 (mpp) REVERT: D 2210 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7419 (tp30) REVERT: D 2212 MET cc_start: 0.8284 (ttp) cc_final: 0.7993 (ttm) REVERT: D 2313 MET cc_start: 0.7792 (mpp) cc_final: 0.7352 (mpp) REVERT: D 2370 ARG cc_start: 0.7881 (tmm160) cc_final: 0.5793 (tmm-80) REVERT: D 2625 ARG cc_start: 0.8454 (ttp-170) cc_final: 0.8149 (ttp80) REVERT: D 2701 MET cc_start: 0.8248 (tmm) cc_final: 0.8035 (tmm) REVERT: D 2933 MET cc_start: 0.7240 (ttp) cc_final: 0.6869 (ppp) REVERT: D 2949 THR cc_start: 0.7959 (OUTLIER) cc_final: 0.7700 (p) REVERT: D 3185 GLU cc_start: 0.7859 (mp0) cc_final: 0.7616 (mp0) REVERT: D 3694 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8331 (mmtt) REVERT: D 4674 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7596 (mm-30) REVERT: D 5010 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8415 (tttm) REVERT: B 14 PHE cc_start: 0.8622 (m-80) cc_final: 0.8277 (m-80) REVERT: B 20 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8167 (mm-30) REVERT: B 35 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8423 (mtpp) REVERT: B 620 ASP cc_start: 0.8111 (m-30) cc_final: 0.7804 (m-30) REVERT: B 921 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.7901 (p90) REVERT: B 939 HIS cc_start: 0.7021 (m90) cc_final: 0.6715 (m90) REVERT: B 982 GLN cc_start: 0.8579 (mp10) cc_final: 0.8240 (mp10) REVERT: B 1037 ARG cc_start: 0.8309 (mtm110) cc_final: 0.8010 (mtm110) REVERT: B 1038 ASP cc_start: 0.8645 (t0) cc_final: 0.8424 (t0) REVERT: B 1041 CYS cc_start: 0.9251 (t) cc_final: 0.8449 (p) REVERT: B 1042 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8878 (mm-40) REVERT: B 1445 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8408 (mm-30) REVERT: B 1623 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: B 1987 MET cc_start: 0.6765 (mmt) cc_final: 0.5525 (mpp) REVERT: B 2210 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7444 (tp30) REVERT: B 2212 MET cc_start: 0.8289 (ttp) cc_final: 0.7998 (ttm) REVERT: B 2313 MET cc_start: 0.7805 (mpp) cc_final: 0.7377 (mpp) REVERT: B 2625 ARG cc_start: 0.8431 (ttp-170) cc_final: 0.8122 (ttp80) REVERT: B 2701 MET cc_start: 0.8232 (tmm) cc_final: 0.7929 (tmm) REVERT: B 2933 MET cc_start: 0.7353 (ttp) cc_final: 0.7044 (ppp) REVERT: B 2949 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7699 (p) REVERT: B 3694 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8333 (mmtt) REVERT: B 4674 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7602 (mm-30) REVERT: B 5010 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8422 (tttm) REVERT: C 35 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8431 (mtpp) REVERT: C 620 ASP cc_start: 0.8114 (m-30) cc_final: 0.7809 (m-30) REVERT: C 921 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8065 (p90) REVERT: C 928 GLU cc_start: 0.8615 (pt0) cc_final: 0.8152 (pt0) REVERT: C 939 HIS cc_start: 0.7065 (m90) cc_final: 0.6758 (m90) REVERT: C 982 GLN cc_start: 0.8596 (mp10) cc_final: 0.8256 (mp10) REVERT: C 1037 ARG cc_start: 0.8331 (mtm110) cc_final: 0.8035 (mtm110) REVERT: C 1038 ASP cc_start: 0.8628 (t0) cc_final: 0.8403 (t0) REVERT: C 1041 CYS cc_start: 0.9251 (t) cc_final: 0.8423 (p) REVERT: C 1042 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8869 (mm-40) REVERT: C 1445 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8409 (mm-30) REVERT: C 1623 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7376 (mm-30) REVERT: C 1987 MET cc_start: 0.6747 (mmt) cc_final: 0.5510 (mpp) REVERT: C 2210 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7424 (tp30) REVERT: C 2313 MET cc_start: 0.7803 (mpp) cc_final: 0.7387 (mpp) REVERT: C 2370 ARG cc_start: 0.7881 (tmm160) cc_final: 0.5800 (tmm-80) REVERT: C 2625 ARG cc_start: 0.8432 (ttp-170) cc_final: 0.8128 (ttp80) REVERT: C 2933 MET cc_start: 0.7331 (ttp) cc_final: 0.7032 (ppp) REVERT: C 2949 THR cc_start: 0.7939 (OUTLIER) cc_final: 0.7685 (p) REVERT: C 3185 GLU cc_start: 0.7853 (mp0) cc_final: 0.7610 (mp0) REVERT: C 3217 CYS cc_start: 0.8039 (p) cc_final: 0.7759 (p) REVERT: C 3694 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8372 (mmtt) REVERT: C 4674 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7604 (mm-30) REVERT: C 5010 LYS cc_start: 0.8658 (ttmm) cc_final: 0.8412 (tttm) outliers start: 231 outliers final: 168 residues processed: 1959 average time/residue: 1.2669 time to fit residues: 4380.4625 Evaluate side-chains 1972 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1784 time to evaluate : 12.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 2001 SER Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2007 ILE Chi-restraints excluded: chain A residue 2949 THR Chi-restraints excluded: chain A residue 2971 SER Chi-restraints excluded: chain A residue 3088 ILE Chi-restraints excluded: chain A residue 3109 GLU Chi-restraints excluded: chain A residue 3160 ASP Chi-restraints excluded: chain A residue 3161 ASP Chi-restraints excluded: chain A residue 3226 ARG Chi-restraints excluded: chain A residue 3394 LEU Chi-restraints excluded: chain A residue 3451 ASN Chi-restraints excluded: chain A residue 3462 GLN Chi-restraints excluded: chain A residue 3559 ASN Chi-restraints excluded: chain A residue 3599 GLU Chi-restraints excluded: chain A residue 3694 LYS Chi-restraints excluded: chain A residue 3876 LYS Chi-restraints excluded: chain A residue 3902 PHE Chi-restraints excluded: chain A residue 4166 PHE Chi-restraints excluded: chain A residue 4816 MET Chi-restraints excluded: chain A residue 4866 ASP Chi-restraints excluded: chain A residue 4931 GLN Chi-restraints excluded: chain A residue 4990 LEU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain N residue 36 ASP Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 846 CYS Chi-restraints excluded: chain D residue 858 ASP Chi-restraints excluded: chain D residue 921 TYR Chi-restraints excluded: chain D residue 932 THR Chi-restraints excluded: chain D residue 1071 ASP Chi-restraints excluded: chain D residue 1265 VAL Chi-restraints excluded: chain D residue 1422 ARG Chi-restraints excluded: chain D residue 1424 ASP Chi-restraints excluded: chain D residue 1488 LEU Chi-restraints excluded: chain D residue 1623 GLU Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2001 SER Chi-restraints excluded: chain D residue 2005 GLU Chi-restraints excluded: chain D residue 2007 ILE Chi-restraints excluded: chain D residue 2272 THR Chi-restraints excluded: chain D residue 2949 THR Chi-restraints excluded: chain D residue 2971 SER Chi-restraints excluded: chain D residue 3088 ILE Chi-restraints excluded: chain D residue 3109 GLU Chi-restraints excluded: chain D residue 3160 ASP Chi-restraints excluded: chain D residue 3161 ASP Chi-restraints excluded: chain D residue 3226 ARG Chi-restraints excluded: chain D residue 3394 LEU Chi-restraints excluded: chain D residue 3451 ASN Chi-restraints excluded: chain D residue 3462 GLN Chi-restraints excluded: chain D residue 3559 ASN Chi-restraints excluded: chain D residue 3599 GLU Chi-restraints excluded: chain D residue 3694 LYS Chi-restraints excluded: chain D residue 3902 PHE Chi-restraints excluded: chain D residue 4166 PHE Chi-restraints excluded: chain D residue 4720 ARG Chi-restraints excluded: chain D residue 4816 MET Chi-restraints excluded: chain D residue 4866 ASP Chi-restraints excluded: chain D residue 4931 GLN Chi-restraints excluded: chain D residue 4964 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 846 CYS Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 1071 ASP Chi-restraints excluded: chain B residue 1265 VAL Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1623 GLU Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2001 SER Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2007 ILE Chi-restraints excluded: chain B residue 2272 THR Chi-restraints excluded: chain B residue 2949 THR Chi-restraints excluded: chain B residue 2971 SER Chi-restraints excluded: chain B residue 3088 ILE Chi-restraints excluded: chain B residue 3109 GLU Chi-restraints excluded: chain B residue 3156 ASP Chi-restraints excluded: chain B residue 3160 ASP Chi-restraints excluded: chain B residue 3161 ASP Chi-restraints excluded: chain B residue 3394 LEU Chi-restraints excluded: chain B residue 3451 ASN Chi-restraints excluded: chain B residue 3462 GLN Chi-restraints excluded: chain B residue 3559 ASN Chi-restraints excluded: chain B residue 3599 GLU Chi-restraints excluded: chain B residue 3694 LYS Chi-restraints excluded: chain B residue 3876 LYS Chi-restraints excluded: chain B residue 3902 PHE Chi-restraints excluded: chain B residue 4816 MET Chi-restraints excluded: chain B residue 4866 ASP Chi-restraints excluded: chain B residue 4931 GLN Chi-restraints excluded: chain B residue 4964 ASP Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 846 CYS Chi-restraints excluded: chain C residue 858 ASP Chi-restraints excluded: chain C residue 921 TYR Chi-restraints excluded: chain C residue 932 THR Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1422 ARG Chi-restraints excluded: chain C residue 1424 ASP Chi-restraints excluded: chain C residue 1623 GLU Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2001 SER Chi-restraints excluded: chain C residue 2005 GLU Chi-restraints excluded: chain C residue 2007 ILE Chi-restraints excluded: chain C residue 2949 THR Chi-restraints excluded: chain C residue 2971 SER Chi-restraints excluded: chain C residue 3088 ILE Chi-restraints excluded: chain C residue 3109 GLU Chi-restraints excluded: chain C residue 3156 ASP Chi-restraints excluded: chain C residue 3160 ASP Chi-restraints excluded: chain C residue 3161 ASP Chi-restraints excluded: chain C residue 3226 ARG Chi-restraints excluded: chain C residue 3394 LEU Chi-restraints excluded: chain C residue 3451 ASN Chi-restraints excluded: chain C residue 3462 GLN Chi-restraints excluded: chain C residue 3559 ASN Chi-restraints excluded: chain C residue 3599 GLU Chi-restraints excluded: chain C residue 3694 LYS Chi-restraints excluded: chain C residue 3876 LYS Chi-restraints excluded: chain C residue 3902 PHE Chi-restraints excluded: chain C residue 4166 PHE Chi-restraints excluded: chain C residue 4816 MET Chi-restraints excluded: chain C residue 4866 ASP Chi-restraints excluded: chain C residue 4931 GLN Chi-restraints excluded: chain C residue 4964 ASP Chi-restraints excluded: chain C residue 4990 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 604 optimal weight: 3.9990 chunk 1619 optimal weight: 5.9990 chunk 355 optimal weight: 5.9990 chunk 1055 optimal weight: 6.9990 chunk 443 optimal weight: 10.0000 chunk 1799 optimal weight: 2.9990 chunk 1493 optimal weight: 0.8980 chunk 833 optimal weight: 20.0000 chunk 149 optimal weight: 0.4980 chunk 595 optimal weight: 5.9990 chunk 944 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 GLN ** A2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3817 GLN ** A4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 HIS ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 ASN ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2037 GLN ** D2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2037 GLN ** B2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2037 GLN ** C2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3817 GLN ** C4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 152152 Z= 0.330 Angle : 0.604 15.071 205940 Z= 0.308 Chirality : 0.042 0.324 22624 Planarity : 0.005 0.061 26768 Dihedral : 5.378 65.808 20604 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.54 % Allowed : 8.67 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.56 (0.06), residues: 18540 helix: 2.01 (0.05), residues: 9900 sheet: 0.10 (0.13), residues: 1632 loop : -0.09 (0.08), residues: 7008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D3286 HIS 0.011 0.001 HIS D 219 PHE 0.055 0.002 PHE C4096 TYR 0.042 0.002 TYR A3605 ARG 0.013 0.001 ARG B1822 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2065 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1815 time to evaluate : 13.382 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: A 20 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8185 (mm-30) REVERT: A 35 LYS cc_start: 0.8824 (mtpt) cc_final: 0.8386 (mtpp) REVERT: A 939 HIS cc_start: 0.7194 (m90) cc_final: 0.6887 (m90) REVERT: A 961 MET cc_start: 0.4634 (tpp) cc_final: 0.4227 (tpt) REVERT: A 1037 ARG cc_start: 0.8386 (mtm110) cc_final: 0.8071 (mtm110) REVERT: A 1038 ASP cc_start: 0.8678 (t0) cc_final: 0.8441 (t0) REVERT: A 1041 CYS cc_start: 0.9218 (t) cc_final: 0.8414 (p) REVERT: A 1042 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8908 (mm-40) REVERT: A 1623 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7359 (mm-30) REVERT: A 1987 MET cc_start: 0.6798 (mmt) cc_final: 0.5595 (mpp) REVERT: A 2210 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7419 (tp30) REVERT: A 2313 MET cc_start: 0.7844 (mpp) cc_final: 0.7344 (mpp) REVERT: A 2701 MET cc_start: 0.8293 (tmm) cc_final: 0.8012 (tmm) REVERT: A 3153 PHE cc_start: 0.9237 (m-10) cc_final: 0.9024 (m-10) REVERT: A 3287 GLU cc_start: 0.8493 (tp30) cc_final: 0.8247 (mm-30) REVERT: A 3578 ARG cc_start: 0.8484 (mmm160) cc_final: 0.8087 (mmm160) REVERT: A 3694 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8339 (mmtt) REVERT: A 4674 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7601 (mm-30) REVERT: A 5010 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8433 (tttm) REVERT: E 54 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8722 (mp10) REVERT: J 35 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8683 (ptmm) REVERT: J 70 VAL cc_start: 0.4892 (OUTLIER) cc_final: 0.4592 (m) REVERT: J 74 GLU cc_start: 0.8929 (mp0) cc_final: 0.8721 (mp0) REVERT: I 29 LEU cc_start: 0.6432 (tp) cc_final: 0.5981 (tp) REVERT: I 45 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.6322 (t80) REVERT: H 54 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8697 (mp10) REVERT: F 15 THR cc_start: 0.8863 (m) cc_final: 0.8345 (p) REVERT: F 54 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8744 (mp10) REVERT: G 54 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8722 (mp10) REVERT: M 34 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7937 (mm) REVERT: M 61 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7395 (pp20) REVERT: O 61 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7276 (pp20) REVERT: P 34 LEU cc_start: 0.8499 (tp) cc_final: 0.7595 (tp) REVERT: P 75 TYR cc_start: 0.9040 (t80) cc_final: 0.8719 (t80) REVERT: D 20 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8182 (mm-30) REVERT: D 35 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8396 (mtpp) REVERT: D 128 MET cc_start: 0.7394 (mmm) cc_final: 0.6905 (mmm) REVERT: D 855 CYS cc_start: 0.8888 (m) cc_final: 0.8677 (m) REVERT: D 921 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.7877 (p90) REVERT: D 939 HIS cc_start: 0.7012 (m90) cc_final: 0.6705 (m90) REVERT: D 961 MET cc_start: 0.4024 (tpp) cc_final: 0.3351 (tpt) REVERT: D 962 MET cc_start: 0.3343 (tpt) cc_final: 0.2917 (tpp) REVERT: D 1037 ARG cc_start: 0.8378 (mtm110) cc_final: 0.8075 (mtm110) REVERT: D 1038 ASP cc_start: 0.8689 (t0) cc_final: 0.8447 (t0) REVERT: D 1041 CYS cc_start: 0.9231 (t) cc_final: 0.8429 (p) REVERT: D 1445 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8411 (mm-30) REVERT: D 1623 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: D 1987 MET cc_start: 0.6752 (mmt) cc_final: 0.5566 (mpp) REVERT: D 2210 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7461 (tp30) REVERT: D 2212 MET cc_start: 0.8374 (ttp) cc_final: 0.8106 (ttp) REVERT: D 2701 MET cc_start: 0.8242 (tmm) cc_final: 0.8002 (tmm) REVERT: D 2817 MET cc_start: 0.8946 (tpt) cc_final: 0.8687 (tpt) REVERT: D 2933 MET cc_start: 0.7257 (ttp) cc_final: 0.6892 (ppp) REVERT: D 3185 GLU cc_start: 0.7833 (mp0) cc_final: 0.7465 (mp0) REVERT: D 3349 ARG cc_start: 0.8146 (mmm-85) cc_final: 0.7703 (mmm-85) REVERT: D 3509 SER cc_start: 0.8469 (m) cc_final: 0.8155 (m) REVERT: D 3694 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8362 (mmtt) REVERT: D 4674 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7607 (mm-30) REVERT: D 5010 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8428 (tttm) REVERT: B 20 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8154 (mm-30) REVERT: B 35 LYS cc_start: 0.8845 (mtpt) cc_final: 0.8425 (mtpp) REVERT: B 151 MET cc_start: 0.8847 (mtm) cc_final: 0.8560 (mtt) REVERT: B 197 MET cc_start: 0.8015 (mtt) cc_final: 0.7730 (mtt) REVERT: B 855 CYS cc_start: 0.8876 (m) cc_final: 0.8655 (m) REVERT: B 921 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7849 (p90) REVERT: B 939 HIS cc_start: 0.6993 (m90) cc_final: 0.6682 (m90) REVERT: B 962 MET cc_start: 0.3311 (tpt) cc_final: 0.2871 (tpp) REVERT: B 1037 ARG cc_start: 0.8356 (mtm110) cc_final: 0.8057 (mtm110) REVERT: B 1038 ASP cc_start: 0.8600 (t0) cc_final: 0.8388 (t0) REVERT: B 1041 CYS cc_start: 0.9247 (t) cc_final: 0.8428 (p) REVERT: B 1445 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8400 (mm-30) REVERT: B 1623 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7348 (mm-30) REVERT: B 1987 MET cc_start: 0.6791 (mmt) cc_final: 0.5596 (mpp) REVERT: B 2210 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7465 (tp30) REVERT: B 2212 MET cc_start: 0.8363 (ttp) cc_final: 0.8094 (ttp) REVERT: B 2416 ARG cc_start: 0.8430 (mmm160) cc_final: 0.7959 (mmp80) REVERT: B 2625 ARG cc_start: 0.8461 (ttp-170) cc_final: 0.8168 (ttp80) REVERT: B 2701 MET cc_start: 0.8264 (tmm) cc_final: 0.7930 (tmm) REVERT: B 3287 GLU cc_start: 0.8497 (tp30) cc_final: 0.8246 (mm-30) REVERT: B 3376 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8361 (mp0) REVERT: B 3694 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8354 (mmtt) REVERT: B 4164 ARG cc_start: 0.8668 (mtp180) cc_final: 0.8334 (mtm180) REVERT: B 4674 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7611 (mm-30) REVERT: B 5010 LYS cc_start: 0.8672 (ttmm) cc_final: 0.8427 (tttm) REVERT: C 20 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8175 (mm-30) REVERT: C 35 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8426 (mtpp) REVERT: C 855 CYS cc_start: 0.8879 (m) cc_final: 0.8662 (m) REVERT: C 921 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7858 (p90) REVERT: C 928 GLU cc_start: 0.8631 (pt0) cc_final: 0.8220 (pt0) REVERT: C 939 HIS cc_start: 0.7025 (m90) cc_final: 0.6720 (m90) REVERT: C 962 MET cc_start: 0.3349 (tpt) cc_final: 0.2915 (tpp) REVERT: C 1037 ARG cc_start: 0.8370 (mtm110) cc_final: 0.8058 (mtm110) REVERT: C 1038 ASP cc_start: 0.8598 (t0) cc_final: 0.8368 (t0) REVERT: C 1041 CYS cc_start: 0.9255 (t) cc_final: 0.8417 (p) REVERT: C 1042 GLN cc_start: 0.9166 (mm-40) cc_final: 0.8867 (mm-40) REVERT: C 1445 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8412 (mm-30) REVERT: C 1623 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7391 (mm-30) REVERT: C 1987 MET cc_start: 0.6765 (mmt) cc_final: 0.5579 (mpp) REVERT: C 2210 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7466 (tp30) REVERT: C 2416 ARG cc_start: 0.8432 (mmm160) cc_final: 0.7962 (mmp80) REVERT: C 2817 MET cc_start: 0.8951 (tpt) cc_final: 0.8692 (tpt) REVERT: C 3185 GLU cc_start: 0.7834 (mp0) cc_final: 0.7474 (mp0) REVERT: C 3217 CYS cc_start: 0.8049 (p) cc_final: 0.7790 (p) REVERT: C 3287 GLU cc_start: 0.8489 (tp30) cc_final: 0.8223 (mm-30) REVERT: C 3349 ARG cc_start: 0.8116 (mmm-85) cc_final: 0.7662 (mmm-85) REVERT: C 3376 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8380 (mp0) REVERT: C 3694 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8502 (mtpp) REVERT: C 4674 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7615 (mm-30) REVERT: C 5010 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8452 (tttm) outliers start: 250 outliers final: 178 residues processed: 1931 average time/residue: 1.3898 time to fit residues: 4795.2194 Evaluate side-chains 1944 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1749 time to evaluate : 13.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 2001 SER Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2007 ILE Chi-restraints excluded: chain A residue 2971 SER Chi-restraints excluded: chain A residue 3088 ILE Chi-restraints excluded: chain A residue 3109 GLU Chi-restraints excluded: chain A residue 3156 ASP Chi-restraints excluded: chain A residue 3160 ASP Chi-restraints excluded: chain A residue 3161 ASP Chi-restraints excluded: chain A residue 3394 LEU Chi-restraints excluded: chain A residue 3451 ASN Chi-restraints excluded: chain A residue 3462 GLN Chi-restraints excluded: chain A residue 3559 ASN Chi-restraints excluded: chain A residue 3599 GLU Chi-restraints excluded: chain A residue 3694 LYS Chi-restraints excluded: chain A residue 3876 LYS Chi-restraints excluded: chain A residue 3902 PHE Chi-restraints excluded: chain A residue 4166 PHE Chi-restraints excluded: chain A residue 4720 ARG Chi-restraints excluded: chain A residue 4816 MET Chi-restraints excluded: chain A residue 4866 ASP Chi-restraints excluded: chain A residue 4931 GLN Chi-restraints excluded: chain A residue 4990 LEU Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 45 PHE Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 846 CYS Chi-restraints excluded: chain D residue 858 ASP Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 921 TYR Chi-restraints excluded: chain D residue 932 THR Chi-restraints excluded: chain D residue 1071 ASP Chi-restraints excluded: chain D residue 1265 VAL Chi-restraints excluded: chain D residue 1422 ARG Chi-restraints excluded: chain D residue 1424 ASP Chi-restraints excluded: chain D residue 1488 LEU Chi-restraints excluded: chain D residue 1623 GLU Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2001 SER Chi-restraints excluded: chain D residue 2005 GLU Chi-restraints excluded: chain D residue 2007 ILE Chi-restraints excluded: chain D residue 2272 THR Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2882 ASN Chi-restraints excluded: chain D residue 2971 SER Chi-restraints excluded: chain D residue 3088 ILE Chi-restraints excluded: chain D residue 3109 GLU Chi-restraints excluded: chain D residue 3156 ASP Chi-restraints excluded: chain D residue 3160 ASP Chi-restraints excluded: chain D residue 3161 ASP Chi-restraints excluded: chain D residue 3226 ARG Chi-restraints excluded: chain D residue 3394 LEU Chi-restraints excluded: chain D residue 3451 ASN Chi-restraints excluded: chain D residue 3462 GLN Chi-restraints excluded: chain D residue 3559 ASN Chi-restraints excluded: chain D residue 3599 GLU Chi-restraints excluded: chain D residue 3694 LYS Chi-restraints excluded: chain D residue 3902 PHE Chi-restraints excluded: chain D residue 4166 PHE Chi-restraints excluded: chain D residue 4720 ARG Chi-restraints excluded: chain D residue 4816 MET Chi-restraints excluded: chain D residue 4866 ASP Chi-restraints excluded: chain D residue 4931 GLN Chi-restraints excluded: chain D residue 4964 ASP Chi-restraints excluded: chain D residue 4990 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 846 CYS Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 1071 ASP Chi-restraints excluded: chain B residue 1265 VAL Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1623 GLU Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2001 SER Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2007 ILE Chi-restraints excluded: chain B residue 2272 THR Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2971 SER Chi-restraints excluded: chain B residue 3088 ILE Chi-restraints excluded: chain B residue 3109 GLU Chi-restraints excluded: chain B residue 3156 ASP Chi-restraints excluded: chain B residue 3160 ASP Chi-restraints excluded: chain B residue 3161 ASP Chi-restraints excluded: chain B residue 3226 ARG Chi-restraints excluded: chain B residue 3324 ILE Chi-restraints excluded: chain B residue 3394 LEU Chi-restraints excluded: chain B residue 3451 ASN Chi-restraints excluded: chain B residue 3462 GLN Chi-restraints excluded: chain B residue 3559 ASN Chi-restraints excluded: chain B residue 3599 GLU Chi-restraints excluded: chain B residue 3694 LYS Chi-restraints excluded: chain B residue 3876 LYS Chi-restraints excluded: chain B residue 3902 PHE Chi-restraints excluded: chain B residue 4166 PHE Chi-restraints excluded: chain B residue 4720 ARG Chi-restraints excluded: chain B residue 4816 MET Chi-restraints excluded: chain B residue 4866 ASP Chi-restraints excluded: chain B residue 4931 GLN Chi-restraints excluded: chain B residue 4964 ASP Chi-restraints excluded: chain B residue 4990 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 846 CYS Chi-restraints excluded: chain C residue 858 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 921 TYR Chi-restraints excluded: chain C residue 932 THR Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1422 ARG Chi-restraints excluded: chain C residue 1424 ASP Chi-restraints excluded: chain C residue 1623 GLU Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2001 SER Chi-restraints excluded: chain C residue 2005 GLU Chi-restraints excluded: chain C residue 2007 ILE Chi-restraints excluded: chain C residue 2971 SER Chi-restraints excluded: chain C residue 3088 ILE Chi-restraints excluded: chain C residue 3156 ASP Chi-restraints excluded: chain C residue 3160 ASP Chi-restraints excluded: chain C residue 3161 ASP Chi-restraints excluded: chain C residue 3226 ARG Chi-restraints excluded: chain C residue 3394 LEU Chi-restraints excluded: chain C residue 3451 ASN Chi-restraints excluded: chain C residue 3462 GLN Chi-restraints excluded: chain C residue 3559 ASN Chi-restraints excluded: chain C residue 3599 GLU Chi-restraints excluded: chain C residue 3694 LYS Chi-restraints excluded: chain C residue 3876 LYS Chi-restraints excluded: chain C residue 3902 PHE Chi-restraints excluded: chain C residue 4166 PHE Chi-restraints excluded: chain C residue 4720 ARG Chi-restraints excluded: chain C residue 4816 MET Chi-restraints excluded: chain C residue 4866 ASP Chi-restraints excluded: chain C residue 4931 GLN Chi-restraints excluded: chain C residue 4964 ASP Chi-restraints excluded: chain C residue 4990 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 1735 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 1025 optimal weight: 0.0050 chunk 1314 optimal weight: 0.9990 chunk 1018 optimal weight: 8.9990 chunk 1514 optimal weight: 8.9990 chunk 1004 optimal weight: 5.9990 chunk 1792 optimal weight: 5.9990 chunk 1121 optimal weight: 5.9990 chunk 1092 optimal weight: 0.7980 chunk 827 optimal weight: 9.9990 overall best weight: 2.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 GLN ** A2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 ASN O 19 HIS ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2037 GLN ** D2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3817 GLN ** D4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5001 HIS ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2037 GLN ** B2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3817 GLN B4112 GLN ** B4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2037 GLN ** C2128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4112 GLN ** C4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5001 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 152152 Z= 0.298 Angle : 0.598 15.449 205940 Z= 0.304 Chirality : 0.042 0.340 22624 Planarity : 0.004 0.060 26768 Dihedral : 5.323 65.481 20604 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.45 % Allowed : 9.08 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.58 (0.06), residues: 18540 helix: 2.03 (0.05), residues: 9896 sheet: 0.09 (0.13), residues: 1632 loop : -0.08 (0.08), residues: 7012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP L 91 HIS 0.010 0.001 HIS A 219 PHE 0.054 0.002 PHE N 90 TYR 0.045 0.002 TYR A3605 ARG 0.014 0.000 ARG A1822 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2038 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1802 time to evaluate : 13.279 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: A 35 LYS cc_start: 0.8823 (mtpt) cc_final: 0.8400 (mtpp) REVERT: A 855 CYS cc_start: 0.8847 (m) cc_final: 0.8611 (m) REVERT: A 921 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7967 (p90) REVERT: A 924 GLN cc_start: 0.9050 (pm20) cc_final: 0.8750 (pm20) REVERT: A 939 HIS cc_start: 0.7167 (m90) cc_final: 0.6855 (m90) REVERT: A 961 MET cc_start: 0.4614 (tpp) cc_final: 0.4325 (tpt) REVERT: A 1037 ARG cc_start: 0.8415 (mtm110) cc_final: 0.8106 (mtm110) REVERT: A 1038 ASP cc_start: 0.8656 (t0) cc_final: 0.8424 (t0) REVERT: A 1041 CYS cc_start: 0.9237 (t) cc_final: 0.8406 (p) REVERT: A 1042 GLN cc_start: 0.9151 (mm-40) cc_final: 0.8884 (mm-40) REVERT: A 1623 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7353 (mm-30) REVERT: A 2210 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7403 (tp30) REVERT: A 2212 MET cc_start: 0.8329 (ttp) cc_final: 0.7989 (ttm) REVERT: A 2313 MET cc_start: 0.7856 (mpp) cc_final: 0.7467 (mpp) REVERT: A 2701 MET cc_start: 0.8298 (tmm) cc_final: 0.8007 (tmm) REVERT: A 2933 MET cc_start: 0.7302 (ttp) cc_final: 0.6951 (ppp) REVERT: A 3287 GLU cc_start: 0.8485 (tp30) cc_final: 0.8244 (mm-30) REVERT: A 3694 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8344 (mmtt) REVERT: A 4164 ARG cc_start: 0.8665 (mtp180) cc_final: 0.8341 (mtm180) REVERT: A 4674 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7606 (mm-30) REVERT: A 5010 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8429 (tttm) REVERT: E 54 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8734 (mp10) REVERT: J 35 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8637 (ptmm) REVERT: J 70 VAL cc_start: 0.5045 (OUTLIER) cc_final: 0.4735 (m) REVERT: J 74 GLU cc_start: 0.8961 (mp0) cc_final: 0.8710 (mp0) REVERT: I 49 GLN cc_start: 0.8366 (tp40) cc_final: 0.8112 (tp40) REVERT: H 54 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8711 (mp10) REVERT: F 54 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8735 (mp10) REVERT: G 54 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8733 (mp10) REVERT: K 61 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7514 (pp20) REVERT: M 61 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7214 (pp20) REVERT: O 61 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7298 (pp20) REVERT: P 34 LEU cc_start: 0.8488 (tp) cc_final: 0.7540 (tp) REVERT: P 75 TYR cc_start: 0.9028 (t80) cc_final: 0.8700 (t80) REVERT: D 35 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8418 (mtpp) REVERT: D 855 CYS cc_start: 0.8878 (m) cc_final: 0.8628 (m) REVERT: D 921 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7846 (p90) REVERT: D 939 HIS cc_start: 0.6979 (m90) cc_final: 0.6668 (m90) REVERT: D 962 MET cc_start: 0.3383 (OUTLIER) cc_final: 0.2534 (tpp) REVERT: D 1037 ARG cc_start: 0.8375 (mtm110) cc_final: 0.8068 (mtm110) REVERT: D 1038 ASP cc_start: 0.8635 (t0) cc_final: 0.8415 (t0) REVERT: D 1041 CYS cc_start: 0.9227 (t) cc_final: 0.8415 (p) REVERT: D 1042 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8893 (mm-40) REVERT: D 1445 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8398 (mm-30) REVERT: D 1623 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7390 (mm-30) REVERT: D 1987 MET cc_start: 0.6778 (mmt) cc_final: 0.5624 (mpp) REVERT: D 2210 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7471 (tp30) REVERT: D 2212 MET cc_start: 0.8387 (ttp) cc_final: 0.8152 (ttp) REVERT: D 2701 MET cc_start: 0.8260 (tmm) cc_final: 0.8007 (tmm) REVERT: D 2817 MET cc_start: 0.8930 (tpt) cc_final: 0.8666 (tpt) REVERT: D 2933 MET cc_start: 0.7231 (ttp) cc_final: 0.6890 (ppp) REVERT: D 3185 GLU cc_start: 0.7869 (mp0) cc_final: 0.7498 (mp0) REVERT: D 3509 SER cc_start: 0.8474 (m) cc_final: 0.8170 (m) REVERT: D 3694 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8347 (mmtt) REVERT: D 4674 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7599 (mm-30) REVERT: D 5010 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8423 (tttm) REVERT: B 20 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8143 (mm-30) REVERT: B 35 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8414 (mtpp) REVERT: B 197 MET cc_start: 0.7991 (mtt) cc_final: 0.7691 (mtt) REVERT: B 855 CYS cc_start: 0.8855 (m) cc_final: 0.8639 (m) REVERT: B 921 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7831 (p90) REVERT: B 939 HIS cc_start: 0.6966 (m90) cc_final: 0.6652 (m90) REVERT: B 961 MET cc_start: 0.4402 (tpp) cc_final: 0.4027 (tpt) REVERT: B 962 MET cc_start: 0.3430 (OUTLIER) cc_final: 0.2881 (tpp) REVERT: B 1026 ARG cc_start: 0.8599 (mtp-110) cc_final: 0.8379 (mtp-110) REVERT: B 1037 ARG cc_start: 0.8365 (mtm110) cc_final: 0.8055 (mtm110) REVERT: B 1038 ASP cc_start: 0.8597 (t0) cc_final: 0.8384 (t0) REVERT: B 1041 CYS cc_start: 0.9239 (t) cc_final: 0.8405 (p) REVERT: B 1042 GLN cc_start: 0.9145 (mm-40) cc_final: 0.8883 (mm-40) REVERT: B 1623 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: B 1987 MET cc_start: 0.6799 (mmt) cc_final: 0.5636 (mpp) REVERT: B 2210 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7469 (tp30) REVERT: B 2212 MET cc_start: 0.8389 (ttp) cc_final: 0.8142 (ttp) REVERT: B 2416 ARG cc_start: 0.8363 (mmm160) cc_final: 0.7906 (mmp80) REVERT: B 2701 MET cc_start: 0.8289 (tmm) cc_final: 0.7971 (tmm) REVERT: B 2933 MET cc_start: 0.7201 (ttp) cc_final: 0.6857 (ppp) REVERT: B 3287 GLU cc_start: 0.8495 (tp30) cc_final: 0.8250 (mm-30) REVERT: B 3509 SER cc_start: 0.8486 (m) cc_final: 0.8181 (m) REVERT: B 3694 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8347 (mmtt) REVERT: B 4164 ARG cc_start: 0.8597 (mtp180) cc_final: 0.8323 (mtm180) REVERT: B 4674 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7613 (mm-30) REVERT: B 5010 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8437 (tttm) REVERT: C 20 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8178 (mm-30) REVERT: C 35 LYS cc_start: 0.8833 (mtpt) cc_final: 0.8414 (mtpp) REVERT: C 855 CYS cc_start: 0.8875 (m) cc_final: 0.8669 (m) REVERT: C 921 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7785 (p90) REVERT: C 928 GLU cc_start: 0.8556 (pt0) cc_final: 0.8152 (pt0) REVERT: C 939 HIS cc_start: 0.6995 (m90) cc_final: 0.6685 (m90) REVERT: C 961 MET cc_start: 0.4362 (tpp) cc_final: 0.4023 (tpt) REVERT: C 962 MET cc_start: 0.3475 (OUTLIER) cc_final: 0.2506 (tpp) REVERT: C 1445 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8404 (mm-30) REVERT: C 1623 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7380 (mm-30) REVERT: C 1987 MET cc_start: 0.6787 (mmt) cc_final: 0.5630 (mpp) REVERT: C 2210 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7487 (tp30) REVERT: C 2416 ARG cc_start: 0.8364 (mmm160) cc_final: 0.7907 (mmp80) REVERT: C 2817 MET cc_start: 0.8939 (tpt) cc_final: 0.8677 (tpt) REVERT: C 2933 MET cc_start: 0.7193 (ttp) cc_final: 0.6840 (ppp) REVERT: C 3217 CYS cc_start: 0.8050 (p) cc_final: 0.7783 (p) REVERT: C 3349 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7683 (mmm-85) REVERT: C 3694 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8495 (mtpp) REVERT: C 4164 ARG cc_start: 0.8666 (mtp180) cc_final: 0.8382 (mtm180) REVERT: C 4674 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7616 (mm-30) REVERT: C 5010 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8434 (tttm) outliers start: 236 outliers final: 183 residues processed: 1908 average time/residue: 1.2558 time to fit residues: 4225.9069 Evaluate side-chains 1944 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1741 time to evaluate : 12.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 2001 SER Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2007 ILE Chi-restraints excluded: chain A residue 2171 MET Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2624 LEU Chi-restraints excluded: chain A residue 2971 SER Chi-restraints excluded: chain A residue 3088 ILE Chi-restraints excluded: chain A residue 3109 GLU Chi-restraints excluded: chain A residue 3156 ASP Chi-restraints excluded: chain A residue 3160 ASP Chi-restraints excluded: chain A residue 3161 ASP Chi-restraints excluded: chain A residue 3226 ARG Chi-restraints excluded: chain A residue 3394 LEU Chi-restraints excluded: chain A residue 3451 ASN Chi-restraints excluded: chain A residue 3462 GLN Chi-restraints excluded: chain A residue 3559 ASN Chi-restraints excluded: chain A residue 3599 GLU Chi-restraints excluded: chain A residue 3694 LYS Chi-restraints excluded: chain A residue 3876 LYS Chi-restraints excluded: chain A residue 3902 PHE Chi-restraints excluded: chain A residue 4166 PHE Chi-restraints excluded: chain A residue 4720 ARG Chi-restraints excluded: chain A residue 4816 MET Chi-restraints excluded: chain A residue 4866 ASP Chi-restraints excluded: chain A residue 4931 GLN Chi-restraints excluded: chain A residue 4990 LEU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 9 MET Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 19 HIS Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 846 CYS Chi-restraints excluded: chain D residue 858 ASP Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 921 TYR Chi-restraints excluded: chain D residue 932 THR Chi-restraints excluded: chain D residue 962 MET Chi-restraints excluded: chain D residue 1071 ASP Chi-restraints excluded: chain D residue 1265 VAL Chi-restraints excluded: chain D residue 1422 ARG Chi-restraints excluded: chain D residue 1424 ASP Chi-restraints excluded: chain D residue 1488 LEU Chi-restraints excluded: chain D residue 1623 GLU Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2001 SER Chi-restraints excluded: chain D residue 2005 GLU Chi-restraints excluded: chain D residue 2007 ILE Chi-restraints excluded: chain D residue 2272 THR Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2624 LEU Chi-restraints excluded: chain D residue 2971 SER Chi-restraints excluded: chain D residue 3088 ILE Chi-restraints excluded: chain D residue 3109 GLU Chi-restraints excluded: chain D residue 3156 ASP Chi-restraints excluded: chain D residue 3160 ASP Chi-restraints excluded: chain D residue 3161 ASP Chi-restraints excluded: chain D residue 3226 ARG Chi-restraints excluded: chain D residue 3394 LEU Chi-restraints excluded: chain D residue 3451 ASN Chi-restraints excluded: chain D residue 3462 GLN Chi-restraints excluded: chain D residue 3559 ASN Chi-restraints excluded: chain D residue 3599 GLU Chi-restraints excluded: chain D residue 3694 LYS Chi-restraints excluded: chain D residue 3902 PHE Chi-restraints excluded: chain D residue 4166 PHE Chi-restraints excluded: chain D residue 4720 ARG Chi-restraints excluded: chain D residue 4816 MET Chi-restraints excluded: chain D residue 4866 ASP Chi-restraints excluded: chain D residue 4931 GLN Chi-restraints excluded: chain D residue 4964 ASP Chi-restraints excluded: chain D residue 4990 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 846 CYS Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 1071 ASP Chi-restraints excluded: chain B residue 1265 VAL Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1623 GLU Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2001 SER Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2007 ILE Chi-restraints excluded: chain B residue 2272 THR Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2971 SER Chi-restraints excluded: chain B residue 3088 ILE Chi-restraints excluded: chain B residue 3109 GLU Chi-restraints excluded: chain B residue 3156 ASP Chi-restraints excluded: chain B residue 3160 ASP Chi-restraints excluded: chain B residue 3226 ARG Chi-restraints excluded: chain B residue 3394 LEU Chi-restraints excluded: chain B residue 3451 ASN Chi-restraints excluded: chain B residue 3462 GLN Chi-restraints excluded: chain B residue 3559 ASN Chi-restraints excluded: chain B residue 3599 GLU Chi-restraints excluded: chain B residue 3694 LYS Chi-restraints excluded: chain B residue 3876 LYS Chi-restraints excluded: chain B residue 3902 PHE Chi-restraints excluded: chain B residue 4166 PHE Chi-restraints excluded: chain B residue 4720 ARG Chi-restraints excluded: chain B residue 4816 MET Chi-restraints excluded: chain B residue 4866 ASP Chi-restraints excluded: chain B residue 4931 GLN Chi-restraints excluded: chain B residue 4964 ASP Chi-restraints excluded: chain B residue 4990 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 846 CYS Chi-restraints excluded: chain C residue 858 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 921 TYR Chi-restraints excluded: chain C residue 932 THR Chi-restraints excluded: chain C residue 962 MET Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1422 ARG Chi-restraints excluded: chain C residue 1424 ASP Chi-restraints excluded: chain C residue 1623 GLU Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2001 SER Chi-restraints excluded: chain C residue 2005 GLU Chi-restraints excluded: chain C residue 2007 ILE Chi-restraints excluded: chain C residue 2624 LEU Chi-restraints excluded: chain C residue 2971 SER Chi-restraints excluded: chain C residue 3088 ILE Chi-restraints excluded: chain C residue 3156 ASP Chi-restraints excluded: chain C residue 3160 ASP Chi-restraints excluded: chain C residue 3161 ASP Chi-restraints excluded: chain C residue 3226 ARG Chi-restraints excluded: chain C residue 3394 LEU Chi-restraints excluded: chain C residue 3451 ASN Chi-restraints excluded: chain C residue 3462 GLN Chi-restraints excluded: chain C residue 3559 ASN Chi-restraints excluded: chain C residue 3599 GLU Chi-restraints excluded: chain C residue 3694 LYS Chi-restraints excluded: chain C residue 3876 LYS Chi-restraints excluded: chain C residue 3902 PHE Chi-restraints excluded: chain C residue 4166 PHE Chi-restraints excluded: chain C residue 4720 ARG Chi-restraints excluded: chain C residue 4816 MET Chi-restraints excluded: chain C residue 4866 ASP Chi-restraints excluded: chain C residue 4931 GLN Chi-restraints excluded: chain C residue 4964 ASP Chi-restraints excluded: chain C residue 4990 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 1109 optimal weight: 10.0000 chunk 715 optimal weight: 1.9990 chunk 1070 optimal weight: 6.9990 chunk 540 optimal weight: 5.9990 chunk 352 optimal weight: 20.0000 chunk 347 optimal weight: 4.9990 chunk 1139 optimal weight: 3.9990 chunk 1221 optimal weight: 4.9990 chunk 886 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 1409 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 GLN A2128 GLN A2903 HIS ** A4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2037 GLN D2128 GLN ** D3344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2037 GLN B2128 GLN B2893 GLN ** B3344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4112 GLN ** B4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2037 GLN C2128 GLN ** C3344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4112 GLN ** C4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 152152 Z= 0.431 Angle : 0.649 16.637 205940 Z= 0.330 Chirality : 0.044 0.370 22624 Planarity : 0.005 0.063 26768 Dihedral : 5.413 66.508 20604 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.45 % Allowed : 9.40 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.42 (0.06), residues: 18540 helix: 1.91 (0.05), residues: 9880 sheet: -0.00 (0.13), residues: 1632 loop : -0.16 (0.07), residues: 7028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 91 HIS 0.013 0.001 HIS C 219 PHE 0.054 0.002 PHE J 90 TYR 0.048 0.002 TYR C3605 ARG 0.014 0.001 ARG B1822 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2026 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1790 time to evaluate : 13.157 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: A 35 LYS cc_start: 0.8831 (mtpt) cc_final: 0.8380 (mtpp) REVERT: A 855 CYS cc_start: 0.8861 (m) cc_final: 0.8638 (m) REVERT: A 921 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.8002 (p90) REVERT: A 924 GLN cc_start: 0.9064 (pm20) cc_final: 0.8781 (pm20) REVERT: A 939 HIS cc_start: 0.7061 (m90) cc_final: 0.6762 (m90) REVERT: A 961 MET cc_start: 0.4836 (tpp) cc_final: 0.4582 (tpt) REVERT: A 982 GLN cc_start: 0.8751 (mp10) cc_final: 0.8257 (mp10) REVERT: A 1623 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7327 (mm-30) REVERT: A 2210 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7458 (tp30) REVERT: A 2212 MET cc_start: 0.8393 (ttp) cc_final: 0.8004 (ttm) REVERT: A 2313 MET cc_start: 0.7895 (mpp) cc_final: 0.7481 (mpp) REVERT: A 2933 MET cc_start: 0.7270 (ttp) cc_final: 0.6848 (ppp) REVERT: A 3112 ARG cc_start: 0.8485 (ttm110) cc_final: 0.8216 (ttm110) REVERT: A 3287 GLU cc_start: 0.8510 (tp30) cc_final: 0.8260 (mm-30) REVERT: A 3595 ARG cc_start: 0.8827 (tpp80) cc_final: 0.8383 (tpp80) REVERT: A 3694 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8494 (mtpp) REVERT: A 4125 MET cc_start: 0.5727 (mmp) cc_final: 0.5453 (mmp) REVERT: A 4164 ARG cc_start: 0.8627 (mtp180) cc_final: 0.8341 (mtm180) REVERT: A 4674 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7619 (mm-30) REVERT: A 5010 LYS cc_start: 0.8701 (ttmm) cc_final: 0.8464 (tttm) REVERT: E 54 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8740 (mp10) REVERT: J 35 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8617 (ptmm) REVERT: J 70 VAL cc_start: 0.5276 (OUTLIER) cc_final: 0.5068 (m) REVERT: J 74 GLU cc_start: 0.8989 (mp0) cc_final: 0.8741 (mp0) REVERT: I 61 GLU cc_start: 0.8674 (tp30) cc_final: 0.8122 (tp30) REVERT: H 54 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8720 (mp10) REVERT: F 54 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8741 (mp10) REVERT: G 54 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8723 (mp10) REVERT: K 61 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7282 (pp20) REVERT: M 61 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7215 (pp20) REVERT: M 64 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7962 (tm-30) REVERT: M 65 ASN cc_start: 0.6964 (t0) cc_final: 0.6381 (t0) REVERT: N 57 LYS cc_start: 0.8361 (mmtp) cc_final: 0.8149 (mmtt) REVERT: P 34 LEU cc_start: 0.8535 (tp) cc_final: 0.7581 (tp) REVERT: P 75 TYR cc_start: 0.9068 (t80) cc_final: 0.8724 (t80) REVERT: D 35 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8391 (mtpp) REVERT: D 855 CYS cc_start: 0.8890 (m) cc_final: 0.8674 (m) REVERT: D 921 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7696 (p90) REVERT: D 939 HIS cc_start: 0.6955 (m90) cc_final: 0.6645 (m90) REVERT: D 961 MET cc_start: 0.4478 (tpp) cc_final: 0.4080 (tpt) REVERT: D 962 MET cc_start: 0.3622 (OUTLIER) cc_final: 0.3109 (tpp) REVERT: D 982 GLN cc_start: 0.8745 (mp10) cc_final: 0.8252 (mp10) REVERT: D 1623 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: D 2210 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7490 (tp30) REVERT: D 2701 MET cc_start: 0.8261 (tmm) cc_final: 0.7986 (tmm) REVERT: D 2817 MET cc_start: 0.8947 (tpt) cc_final: 0.8676 (tpt) REVERT: D 2933 MET cc_start: 0.7231 (ttp) cc_final: 0.6883 (ppp) REVERT: D 3112 ARG cc_start: 0.8454 (ttm110) cc_final: 0.8199 (ttm110) REVERT: D 3509 SER cc_start: 0.8493 (m) cc_final: 0.8186 (m) REVERT: D 3595 ARG cc_start: 0.8836 (tpp80) cc_final: 0.8395 (tpp80) REVERT: D 4674 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7616 (mm-30) REVERT: D 5010 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8455 (tttm) REVERT: B 20 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8138 (mm-30) REVERT: B 35 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8386 (mtpp) REVERT: B 197 MET cc_start: 0.8062 (mtt) cc_final: 0.7730 (mtt) REVERT: B 855 CYS cc_start: 0.8870 (m) cc_final: 0.8655 (m) REVERT: B 921 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7804 (p90) REVERT: B 939 HIS cc_start: 0.6978 (m90) cc_final: 0.6669 (m90) REVERT: B 961 MET cc_start: 0.4509 (tpp) cc_final: 0.4215 (tpt) REVERT: B 962 MET cc_start: 0.3544 (OUTLIER) cc_final: 0.2606 (tpp) REVERT: B 982 GLN cc_start: 0.8740 (mp10) cc_final: 0.8267 (mp10) REVERT: B 1623 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7339 (mm-30) REVERT: B 2210 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7507 (tp30) REVERT: B 2933 MET cc_start: 0.7268 (ttp) cc_final: 0.6830 (ppp) REVERT: B 3112 ARG cc_start: 0.8480 (ttm110) cc_final: 0.8229 (ttm110) REVERT: B 3287 GLU cc_start: 0.8518 (tp30) cc_final: 0.8259 (mm-30) REVERT: B 3509 SER cc_start: 0.8536 (m) cc_final: 0.8245 (m) REVERT: B 3595 ARG cc_start: 0.8842 (tpp80) cc_final: 0.8396 (tpp80) REVERT: B 4674 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7618 (mm-30) REVERT: B 5010 LYS cc_start: 0.8701 (ttmm) cc_final: 0.8470 (tttm) REVERT: C 20 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8174 (mm-30) REVERT: C 35 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8388 (mtpp) REVERT: C 855 CYS cc_start: 0.8876 (m) cc_final: 0.8667 (m) REVERT: C 921 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.7621 (p90) REVERT: C 925 MET cc_start: 0.8509 (mpp) cc_final: 0.8103 (mpp) REVERT: C 928 GLU cc_start: 0.8600 (pt0) cc_final: 0.8056 (pt0) REVERT: C 939 HIS cc_start: 0.6968 (m90) cc_final: 0.6660 (m90) REVERT: C 961 MET cc_start: 0.4497 (tpp) cc_final: 0.4201 (tpt) REVERT: C 962 MET cc_start: 0.3609 (OUTLIER) cc_final: 0.2712 (tpp) REVERT: C 982 GLN cc_start: 0.8770 (mp10) cc_final: 0.8285 (mp10) REVERT: C 1037 ARG cc_start: 0.8588 (mtm110) cc_final: 0.8257 (mtm110) REVERT: C 1623 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7368 (mm-30) REVERT: C 2210 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7499 (tp30) REVERT: C 2817 MET cc_start: 0.8928 (tpt) cc_final: 0.8653 (tpt) REVERT: C 2933 MET cc_start: 0.7244 (ttp) cc_final: 0.6807 (ppp) REVERT: C 3217 CYS cc_start: 0.8067 (p) cc_final: 0.7818 (p) REVERT: C 3287 GLU cc_start: 0.8485 (tp30) cc_final: 0.8281 (mm-30) REVERT: C 3509 SER cc_start: 0.8503 (m) cc_final: 0.8196 (m) REVERT: C 3595 ARG cc_start: 0.8829 (tpp80) cc_final: 0.8380 (tpp80) REVERT: C 4164 ARG cc_start: 0.8655 (mtp180) cc_final: 0.8372 (mtm180) REVERT: C 4674 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7622 (mm-30) REVERT: C 5010 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8463 (tttm) outliers start: 236 outliers final: 188 residues processed: 1895 average time/residue: 1.2873 time to fit residues: 4307.7380 Evaluate side-chains 1946 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1742 time to evaluate : 12.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 2001 SER Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2007 ILE Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2624 LEU Chi-restraints excluded: chain A residue 2971 SER Chi-restraints excluded: chain A residue 3088 ILE Chi-restraints excluded: chain A residue 3109 GLU Chi-restraints excluded: chain A residue 3156 ASP Chi-restraints excluded: chain A residue 3160 ASP Chi-restraints excluded: chain A residue 3161 ASP Chi-restraints excluded: chain A residue 3226 ARG Chi-restraints excluded: chain A residue 3394 LEU Chi-restraints excluded: chain A residue 3451 ASN Chi-restraints excluded: chain A residue 3462 GLN Chi-restraints excluded: chain A residue 3559 ASN Chi-restraints excluded: chain A residue 3599 GLU Chi-restraints excluded: chain A residue 3694 LYS Chi-restraints excluded: chain A residue 3876 LYS Chi-restraints excluded: chain A residue 3902 PHE Chi-restraints excluded: chain A residue 4166 PHE Chi-restraints excluded: chain A residue 4720 ARG Chi-restraints excluded: chain A residue 4816 MET Chi-restraints excluded: chain A residue 4866 ASP Chi-restraints excluded: chain A residue 4931 GLN Chi-restraints excluded: chain A residue 4990 LEU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 19 HIS Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain O residue 19 HIS Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain N residue 36 ASP Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 846 CYS Chi-restraints excluded: chain D residue 858 ASP Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 921 TYR Chi-restraints excluded: chain D residue 962 MET Chi-restraints excluded: chain D residue 1047 LEU Chi-restraints excluded: chain D residue 1422 ARG Chi-restraints excluded: chain D residue 1424 ASP Chi-restraints excluded: chain D residue 1488 LEU Chi-restraints excluded: chain D residue 1623 GLU Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2001 SER Chi-restraints excluded: chain D residue 2005 GLU Chi-restraints excluded: chain D residue 2007 ILE Chi-restraints excluded: chain D residue 2272 THR Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2624 LEU Chi-restraints excluded: chain D residue 2971 SER Chi-restraints excluded: chain D residue 3088 ILE Chi-restraints excluded: chain D residue 3109 GLU Chi-restraints excluded: chain D residue 3156 ASP Chi-restraints excluded: chain D residue 3160 ASP Chi-restraints excluded: chain D residue 3161 ASP Chi-restraints excluded: chain D residue 3394 LEU Chi-restraints excluded: chain D residue 3451 ASN Chi-restraints excluded: chain D residue 3462 GLN Chi-restraints excluded: chain D residue 3559 ASN Chi-restraints excluded: chain D residue 3599 GLU Chi-restraints excluded: chain D residue 3694 LYS Chi-restraints excluded: chain D residue 3902 PHE Chi-restraints excluded: chain D residue 4166 PHE Chi-restraints excluded: chain D residue 4720 ARG Chi-restraints excluded: chain D residue 4816 MET Chi-restraints excluded: chain D residue 4866 ASP Chi-restraints excluded: chain D residue 4931 GLN Chi-restraints excluded: chain D residue 4964 ASP Chi-restraints excluded: chain D residue 4990 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 846 CYS Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1623 GLU Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2001 SER Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2007 ILE Chi-restraints excluded: chain B residue 2272 THR Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2624 LEU Chi-restraints excluded: chain B residue 2893 GLN Chi-restraints excluded: chain B residue 2971 SER Chi-restraints excluded: chain B residue 3088 ILE Chi-restraints excluded: chain B residue 3109 GLU Chi-restraints excluded: chain B residue 3156 ASP Chi-restraints excluded: chain B residue 3160 ASP Chi-restraints excluded: chain B residue 3161 ASP Chi-restraints excluded: chain B residue 3226 ARG Chi-restraints excluded: chain B residue 3394 LEU Chi-restraints excluded: chain B residue 3451 ASN Chi-restraints excluded: chain B residue 3462 GLN Chi-restraints excluded: chain B residue 3559 ASN Chi-restraints excluded: chain B residue 3599 GLU Chi-restraints excluded: chain B residue 3694 LYS Chi-restraints excluded: chain B residue 3876 LYS Chi-restraints excluded: chain B residue 3902 PHE Chi-restraints excluded: chain B residue 4166 PHE Chi-restraints excluded: chain B residue 4720 ARG Chi-restraints excluded: chain B residue 4816 MET Chi-restraints excluded: chain B residue 4866 ASP Chi-restraints excluded: chain B residue 4931 GLN Chi-restraints excluded: chain B residue 4964 ASP Chi-restraints excluded: chain B residue 4990 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 846 CYS Chi-restraints excluded: chain C residue 858 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 921 TYR Chi-restraints excluded: chain C residue 932 THR Chi-restraints excluded: chain C residue 962 MET Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1422 ARG Chi-restraints excluded: chain C residue 1424 ASP Chi-restraints excluded: chain C residue 1623 GLU Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2001 SER Chi-restraints excluded: chain C residue 2005 GLU Chi-restraints excluded: chain C residue 2007 ILE Chi-restraints excluded: chain C residue 2272 THR Chi-restraints excluded: chain C residue 2624 LEU Chi-restraints excluded: chain C residue 2971 SER Chi-restraints excluded: chain C residue 3088 ILE Chi-restraints excluded: chain C residue 3156 ASP Chi-restraints excluded: chain C residue 3160 ASP Chi-restraints excluded: chain C residue 3161 ASP Chi-restraints excluded: chain C residue 3394 LEU Chi-restraints excluded: chain C residue 3451 ASN Chi-restraints excluded: chain C residue 3462 GLN Chi-restraints excluded: chain C residue 3559 ASN Chi-restraints excluded: chain C residue 3599 GLU Chi-restraints excluded: chain C residue 3694 LYS Chi-restraints excluded: chain C residue 3876 LYS Chi-restraints excluded: chain C residue 3902 PHE Chi-restraints excluded: chain C residue 4720 ARG Chi-restraints excluded: chain C residue 4816 MET Chi-restraints excluded: chain C residue 4866 ASP Chi-restraints excluded: chain C residue 4931 GLN Chi-restraints excluded: chain C residue 4964 ASP Chi-restraints excluded: chain C residue 4990 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 1630 optimal weight: 3.9990 chunk 1717 optimal weight: 4.9990 chunk 1566 optimal weight: 0.9990 chunk 1670 optimal weight: 2.9990 chunk 1716 optimal weight: 3.9990 chunk 1005 optimal weight: 2.9990 chunk 727 optimal weight: 0.7980 chunk 1311 optimal weight: 1.9990 chunk 512 optimal weight: 9.9990 chunk 1509 optimal weight: 9.9990 chunk 1580 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 GLN ** A4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4648 HIS ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 ASN ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2037 GLN ** D4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4648 HIS ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2037 GLN B3458 ASN ** B4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4648 HIS ** C1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2037 GLN C3458 ASN C4112 GLN ** C4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4648 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 152152 Z= 0.220 Angle : 0.602 19.132 205940 Z= 0.304 Chirality : 0.041 0.376 22624 Planarity : 0.004 0.059 26768 Dihedral : 5.264 64.855 20604 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.18 % Allowed : 9.89 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.55 (0.06), residues: 18540 helix: 2.02 (0.05), residues: 9900 sheet: 0.06 (0.13), residues: 1656 loop : -0.11 (0.08), residues: 6984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP L 91 HIS 0.013 0.001 HIS P 19 PHE 0.055 0.001 PHE J 90 TYR 0.046 0.001 TYR C3605 ARG 0.015 0.000 ARG D1822 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1975 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1783 time to evaluate : 13.110 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: A 35 LYS cc_start: 0.8823 (mtpt) cc_final: 0.8408 (mtpp) REVERT: A 921 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7987 (p90) REVERT: A 924 GLN cc_start: 0.9058 (pm20) cc_final: 0.8845 (pm20) REVERT: A 939 HIS cc_start: 0.7097 (m90) cc_final: 0.6777 (m90) REVERT: A 961 MET cc_start: 0.4880 (tpp) cc_final: 0.4632 (tpt) REVERT: A 1623 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7286 (mm-30) REVERT: A 1987 MET cc_start: 0.7591 (mmp) cc_final: 0.6652 (mpp) REVERT: A 2210 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7388 (tp30) REVERT: A 2212 MET cc_start: 0.8350 (ttp) cc_final: 0.8129 (ttp) REVERT: A 2313 MET cc_start: 0.7877 (mpp) cc_final: 0.7465 (mpp) REVERT: A 2933 MET cc_start: 0.7306 (ttp) cc_final: 0.6883 (ppp) REVERT: A 3112 ARG cc_start: 0.8471 (ttm110) cc_final: 0.8206 (ttm110) REVERT: A 3287 GLU cc_start: 0.8458 (tp30) cc_final: 0.8223 (mm-30) REVERT: A 3605 TYR cc_start: 0.8644 (t80) cc_final: 0.8443 (t80) REVERT: A 3694 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8353 (mmtt) REVERT: A 4164 ARG cc_start: 0.8576 (mtp180) cc_final: 0.8297 (mtm180) REVERT: A 4674 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7603 (mm-30) REVERT: A 5010 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8431 (tttm) REVERT: E 54 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8725 (mp10) REVERT: J 35 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8630 (ptmm) REVERT: J 70 VAL cc_start: 0.4765 (OUTLIER) cc_final: 0.4378 (m) REVERT: J 74 GLU cc_start: 0.8985 (mp0) cc_final: 0.8708 (mp0) REVERT: I 61 GLU cc_start: 0.8606 (tp30) cc_final: 0.8057 (tp30) REVERT: H 54 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8706 (mp10) REVERT: F 54 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8725 (mp10) REVERT: G 54 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8725 (mp10) REVERT: K 45 PHE cc_start: 0.7256 (t80) cc_final: 0.6859 (t80) REVERT: M 61 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7237 (pp20) REVERT: M 64 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7923 (tm-30) REVERT: M 65 ASN cc_start: 0.6735 (t0) cc_final: 0.6195 (t0) REVERT: L 9 MET cc_start: 0.8701 (mmt) cc_final: 0.8127 (ppp) REVERT: N 57 LYS cc_start: 0.8280 (mmtp) cc_final: 0.8061 (mmtt) REVERT: P 34 LEU cc_start: 0.8441 (tp) cc_final: 0.7398 (tp) REVERT: P 75 TYR cc_start: 0.9018 (t80) cc_final: 0.8684 (t80) REVERT: D 35 LYS cc_start: 0.8833 (mtpt) cc_final: 0.8426 (mtpp) REVERT: D 855 CYS cc_start: 0.8836 (m) cc_final: 0.8625 (m) REVERT: D 921 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.7842 (p90) REVERT: D 939 HIS cc_start: 0.6916 (m90) cc_final: 0.6601 (m90) REVERT: D 961 MET cc_start: 0.4536 (tpp) cc_final: 0.4198 (tpt) REVERT: D 962 MET cc_start: 0.3690 (OUTLIER) cc_final: 0.2764 (tpp) REVERT: D 1445 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8380 (mm-30) REVERT: D 1623 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7349 (mm-30) REVERT: D 1987 MET cc_start: 0.7611 (mmp) cc_final: 0.6667 (mpp) REVERT: D 2210 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7450 (tp30) REVERT: D 2701 MET cc_start: 0.8284 (tmm) cc_final: 0.8030 (tmm) REVERT: D 2817 MET cc_start: 0.8919 (tpt) cc_final: 0.8642 (tpt) REVERT: D 2933 MET cc_start: 0.7244 (ttp) cc_final: 0.6907 (ppp) REVERT: D 3112 ARG cc_start: 0.8464 (ttm110) cc_final: 0.8213 (ttm110) REVERT: D 3694 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8354 (mmtt) REVERT: D 4674 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7604 (mm-30) REVERT: D 5010 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8426 (tttm) REVERT: B 20 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8142 (mm-30) REVERT: B 35 LYS cc_start: 0.8827 (mtpt) cc_final: 0.8413 (mtpp) REVERT: B 197 MET cc_start: 0.7964 (mtt) cc_final: 0.7676 (mtt) REVERT: B 855 CYS cc_start: 0.8832 (m) cc_final: 0.8614 (m) REVERT: B 921 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7777 (p90) REVERT: B 939 HIS cc_start: 0.6938 (m90) cc_final: 0.6618 (m90) REVERT: B 961 MET cc_start: 0.4528 (tpp) cc_final: 0.4234 (tpt) REVERT: B 962 MET cc_start: 0.3631 (OUTLIER) cc_final: 0.2724 (tpp) REVERT: B 1623 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7329 (mm-30) REVERT: B 1987 MET cc_start: 0.7600 (mmp) cc_final: 0.6643 (mpp) REVERT: B 2210 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7466 (tp30) REVERT: B 2313 MET cc_start: 0.7929 (mpp) cc_final: 0.7572 (mpp) REVERT: B 2625 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8067 (ttp80) REVERT: B 2933 MET cc_start: 0.7241 (ttp) cc_final: 0.6825 (ppp) REVERT: B 3112 ARG cc_start: 0.8469 (ttm110) cc_final: 0.8219 (ttm110) REVERT: B 3287 GLU cc_start: 0.8465 (tp30) cc_final: 0.8224 (mm-30) REVERT: B 3509 SER cc_start: 0.8500 (m) cc_final: 0.8200 (m) REVERT: B 3694 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8352 (mmtt) REVERT: B 3995 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: B 4164 ARG cc_start: 0.8572 (mtp180) cc_final: 0.8293 (mtm180) REVERT: B 4674 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7620 (mm-30) REVERT: B 5010 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8425 (tttm) REVERT: C 20 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8188 (mm-30) REVERT: C 35 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8426 (mtpp) REVERT: C 855 CYS cc_start: 0.8838 (m) cc_final: 0.8620 (m) REVERT: C 921 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7610 (p90) REVERT: C 928 GLU cc_start: 0.8561 (pt0) cc_final: 0.8118 (pt0) REVERT: C 939 HIS cc_start: 0.6936 (m90) cc_final: 0.6620 (m90) REVERT: C 961 MET cc_start: 0.4512 (tpp) cc_final: 0.4221 (tpt) REVERT: C 962 MET cc_start: 0.3674 (OUTLIER) cc_final: 0.2766 (tpp) REVERT: C 1037 ARG cc_start: 0.8589 (mtm110) cc_final: 0.8289 (mtm110) REVERT: C 1987 MET cc_start: 0.7614 (mmp) cc_final: 0.6686 (mpp) REVERT: C 2210 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7466 (tp30) REVERT: C 2313 MET cc_start: 0.7924 (mpp) cc_final: 0.7569 (mpp) REVERT: C 2817 MET cc_start: 0.8928 (tpt) cc_final: 0.8650 (tpt) REVERT: C 2933 MET cc_start: 0.7217 (ttp) cc_final: 0.6801 (ppp) REVERT: C 3217 CYS cc_start: 0.8052 (p) cc_final: 0.7787 (p) REVERT: C 3694 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8357 (mmtt) REVERT: C 4164 ARG cc_start: 0.8636 (mtp180) cc_final: 0.8318 (mtm180) REVERT: C 4674 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7627 (mm-30) REVERT: C 5010 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8424 (tttm) outliers start: 192 outliers final: 154 residues processed: 1868 average time/residue: 1.2521 time to fit residues: 4127.6532 Evaluate side-chains 1901 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1729 time to evaluate : 12.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 846 CYS Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1422 ARG Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 2001 SER Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2007 ILE Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2624 LEU Chi-restraints excluded: chain A residue 3088 ILE Chi-restraints excluded: chain A residue 3109 GLU Chi-restraints excluded: chain A residue 3156 ASP Chi-restraints excluded: chain A residue 3160 ASP Chi-restraints excluded: chain A residue 3226 ARG Chi-restraints excluded: chain A residue 3394 LEU Chi-restraints excluded: chain A residue 3451 ASN Chi-restraints excluded: chain A residue 3462 GLN Chi-restraints excluded: chain A residue 3559 ASN Chi-restraints excluded: chain A residue 3599 GLU Chi-restraints excluded: chain A residue 3694 LYS Chi-restraints excluded: chain A residue 3876 LYS Chi-restraints excluded: chain A residue 3902 PHE Chi-restraints excluded: chain A residue 4166 PHE Chi-restraints excluded: chain A residue 4816 MET Chi-restraints excluded: chain A residue 4866 ASP Chi-restraints excluded: chain A residue 4931 GLN Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain K residue 19 HIS Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain M residue 4 GLU Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain O residue 19 HIS Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain N residue 27 TYR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain P residue 27 TYR Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain D residue 846 CYS Chi-restraints excluded: chain D residue 858 ASP Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 921 TYR Chi-restraints excluded: chain D residue 932 THR Chi-restraints excluded: chain D residue 962 MET Chi-restraints excluded: chain D residue 1071 ASP Chi-restraints excluded: chain D residue 1422 ARG Chi-restraints excluded: chain D residue 1623 GLU Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2001 SER Chi-restraints excluded: chain D residue 2005 GLU Chi-restraints excluded: chain D residue 2007 ILE Chi-restraints excluded: chain D residue 2272 THR Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2624 LEU Chi-restraints excluded: chain D residue 3088 ILE Chi-restraints excluded: chain D residue 3109 GLU Chi-restraints excluded: chain D residue 3156 ASP Chi-restraints excluded: chain D residue 3160 ASP Chi-restraints excluded: chain D residue 3161 ASP Chi-restraints excluded: chain D residue 3394 LEU Chi-restraints excluded: chain D residue 3451 ASN Chi-restraints excluded: chain D residue 3462 GLN Chi-restraints excluded: chain D residue 3559 ASN Chi-restraints excluded: chain D residue 3599 GLU Chi-restraints excluded: chain D residue 3694 LYS Chi-restraints excluded: chain D residue 3902 PHE Chi-restraints excluded: chain D residue 4166 PHE Chi-restraints excluded: chain D residue 4816 MET Chi-restraints excluded: chain D residue 4866 ASP Chi-restraints excluded: chain D residue 4931 GLN Chi-restraints excluded: chain D residue 4964 ASP Chi-restraints excluded: chain B residue 846 CYS Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 1071 ASP Chi-restraints excluded: chain B residue 1422 ARG Chi-restraints excluded: chain B residue 1623 GLU Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2001 SER Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2007 ILE Chi-restraints excluded: chain B residue 2272 THR Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 3088 ILE Chi-restraints excluded: chain B residue 3109 GLU Chi-restraints excluded: chain B residue 3156 ASP Chi-restraints excluded: chain B residue 3160 ASP Chi-restraints excluded: chain B residue 3161 ASP Chi-restraints excluded: chain B residue 3226 ARG Chi-restraints excluded: chain B residue 3394 LEU Chi-restraints excluded: chain B residue 3451 ASN Chi-restraints excluded: chain B residue 3462 GLN Chi-restraints excluded: chain B residue 3559 ASN Chi-restraints excluded: chain B residue 3599 GLU Chi-restraints excluded: chain B residue 3694 LYS Chi-restraints excluded: chain B residue 3876 LYS Chi-restraints excluded: chain B residue 3902 PHE Chi-restraints excluded: chain B residue 3995 PHE Chi-restraints excluded: chain B residue 4166 PHE Chi-restraints excluded: chain B residue 4816 MET Chi-restraints excluded: chain B residue 4866 ASP Chi-restraints excluded: chain B residue 4931 GLN Chi-restraints excluded: chain B residue 4964 ASP Chi-restraints excluded: chain B residue 4990 LEU Chi-restraints excluded: chain C residue 846 CYS Chi-restraints excluded: chain C residue 858 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 921 TYR Chi-restraints excluded: chain C residue 932 THR Chi-restraints excluded: chain C residue 962 MET Chi-restraints excluded: chain C residue 1071 ASP Chi-restraints excluded: chain C residue 1422 ARG Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2001 SER Chi-restraints excluded: chain C residue 2005 GLU Chi-restraints excluded: chain C residue 2007 ILE Chi-restraints excluded: chain C residue 2166 LEU Chi-restraints excluded: chain C residue 2272 THR Chi-restraints excluded: chain C residue 2624 LEU Chi-restraints excluded: chain C residue 3088 ILE Chi-restraints excluded: chain C residue 3156 ASP Chi-restraints excluded: chain C residue 3160 ASP Chi-restraints excluded: chain C residue 3394 LEU Chi-restraints excluded: chain C residue 3451 ASN Chi-restraints excluded: chain C residue 3462 GLN Chi-restraints excluded: chain C residue 3559 ASN Chi-restraints excluded: chain C residue 3599 GLU Chi-restraints excluded: chain C residue 3694 LYS Chi-restraints excluded: chain C residue 3876 LYS Chi-restraints excluded: chain C residue 3902 PHE Chi-restraints excluded: chain C residue 4816 MET Chi-restraints excluded: chain C residue 4866 ASP Chi-restraints excluded: chain C residue 4931 GLN Chi-restraints excluded: chain C residue 4964 ASP Chi-restraints excluded: chain C residue 4990 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 1664 optimal weight: 5.9990 chunk 1097 optimal weight: 6.9990 chunk 1766 optimal weight: 7.9990 chunk 1078 optimal weight: 0.9980 chunk 838 optimal weight: 0.9990 chunk 1228 optimal weight: 1.9990 chunk 1853 optimal weight: 0.4980 chunk 1705 optimal weight: 2.9990 chunk 1475 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 1139 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 GLN ** A4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5001 HIS ** J 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 ASN ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 ASN ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2037 GLN D2878 GLN ** D4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2037 GLN ** B2325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2893 GLN B3458 ASN B4112 GLN ** B4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5001 HIS ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2037 GLN ** C2325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3458 ASN C4112 GLN ** C4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 152152 Z= 0.220 Angle : 0.604 17.555 205940 Z= 0.304 Chirality : 0.041 0.397 22624 Planarity : 0.004 0.065 26768 Dihedral : 5.180 64.117 20604 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.12 % Allowed : 10.24 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.56 (0.06), residues: 18540 helix: 2.03 (0.05), residues: 9904 sheet: 0.14 (0.13), residues: 1628 loop : -0.14 (0.07), residues: 7008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A2822 HIS 0.009 0.001 HIS L 17 PHE 0.056 0.001 PHE J 90 TYR 0.054 0.001 TYR B3605 ARG 0.015 0.000 ARG C1822 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37080 Ramachandran restraints generated. 18540 Oldfield, 0 Emsley, 18540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1968 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1787 time to evaluate : 13.102 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: A 35 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8415 (mtpp) REVERT: A 921 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.8002 (p90) REVERT: A 924 GLN cc_start: 0.9014 (pm20) cc_final: 0.8691 (pm20) REVERT: A 939 HIS cc_start: 0.7072 (m90) cc_final: 0.6748 (m90) REVERT: A 961 MET cc_start: 0.4879 (tpp) cc_final: 0.4627 (tpt) REVERT: A 1623 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7358 (mm-30) REVERT: A 1987 MET cc_start: 0.7580 (mmp) cc_final: 0.6537 (mpp) REVERT: A 2210 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7400 (tp30) REVERT: A 2313 MET cc_start: 0.7900 (mpp) cc_final: 0.7462 (mpp) REVERT: A 2933 MET cc_start: 0.7308 (ttp) cc_final: 0.6887 (ppp) REVERT: A 3112 ARG cc_start: 0.8452 (ttm110) cc_final: 0.8205 (ttm110) REVERT: A 3250 LEU cc_start: 0.9411 (mt) cc_final: 0.8848 (mt) REVERT: A 3287 GLU cc_start: 0.8458 (tp30) cc_final: 0.8220 (mm-30) REVERT: A 3349 ARG cc_start: 0.8433 (mmm160) cc_final: 0.8162 (mtp85) REVERT: A 3694 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8345 (mmtt) REVERT: A 3861 MET cc_start: 0.4187 (ptp) cc_final: 0.3811 (ptp) REVERT: A 3995 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: A 4164 ARG cc_start: 0.8573 (mtp180) cc_final: 0.8291 (mtm180) REVERT: A 4674 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7597 (mm-30) REVERT: A 5010 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8419 (tttm) REVERT: E 54 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8732 (mp10) REVERT: J 35 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8572 (ptmm) REVERT: J 70 VAL cc_start: 0.4673 (OUTLIER) cc_final: 0.4323 (m) REVERT: J 74 GLU cc_start: 0.8974 (mp0) cc_final: 0.8695 (mp0) REVERT: H 54 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8717 (mp10) REVERT: F 54 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8733 (mp10) REVERT: G 54 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8732 (mp10) REVERT: K 61 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7184 (pp20) REVERT: M 61 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7343 (pp20) REVERT: M 64 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7980 (tm-30) REVERT: M 65 ASN cc_start: 0.6566 (t0) cc_final: 0.6043 (t0) REVERT: N 13 ILE cc_start: 0.8024 (tt) cc_final: 0.7778 (tp) REVERT: N 57 LYS cc_start: 0.8241 (mmtp) cc_final: 0.8025 (mmtt) REVERT: P 57 LYS cc_start: 0.8143 (mmtp) cc_final: 0.7937 (mmtt) REVERT: D 35 LYS cc_start: 0.8826 (mtpt) cc_final: 0.8421 (mtpp) REVERT: D 855 CYS cc_start: 0.8816 (m) cc_final: 0.8597 (m) REVERT: D 921 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7656 (p90) REVERT: D 939 HIS cc_start: 0.6967 (m90) cc_final: 0.6639 (m90) REVERT: D 961 MET cc_start: 0.4688 (tpp) cc_final: 0.4367 (tpt) REVERT: D 962 MET cc_start: 0.3810 (OUTLIER) cc_final: 0.2966 (tpp) REVERT: D 1987 MET cc_start: 0.7597 (mmp) cc_final: 0.6546 (mpp) REVERT: D 2210 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7487 (tp30) REVERT: D 2313 MET cc_start: 0.7917 (mpp) cc_final: 0.7546 (mpp) REVERT: D 2701 MET cc_start: 0.8266 (tmm) cc_final: 0.8010 (tmm) REVERT: D 2933 MET cc_start: 0.7271 (ttp) cc_final: 0.6892 (ppp) REVERT: D 3112 ARG cc_start: 0.8435 (ttm110) cc_final: 0.8189 (ttm110) REVERT: D 3349 ARG cc_start: 0.8436 (mmm160) cc_final: 0.8191 (mtp85) REVERT: D 3433 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8448 (mt-10) REVERT: D 3694 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8341 (mmtt) REVERT: D 3995 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: D 4674 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7600 (mm-30) REVERT: D 5010 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8417 (tttm) REVERT: B 20 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8155 (mm-30) REVERT: B 35 LYS cc_start: 0.8826 (mtpt) cc_final: 0.8417 (mtpp) REVERT: B 197 MET cc_start: 0.7962 (mtt) cc_final: 0.7679 (mtt) REVERT: B 855 CYS cc_start: 0.8825 (m) cc_final: 0.8607 (m) REVERT: B 921 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7781 (p90) REVERT: B 939 HIS cc_start: 0.6998 (m90) cc_final: 0.6670 (m90) REVERT: B 961 MET cc_start: 0.4721 (tpp) cc_final: 0.4435 (tpt) REVERT: B 962 MET cc_start: 0.3937 (OUTLIER) cc_final: 0.3065 (tpp) REVERT: B 1623 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7294 (mm-30) REVERT: B 1987 MET cc_start: 0.7601 (mmp) cc_final: 0.6541 (mpp) REVERT: B 2210 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7496 (tp30) REVERT: B 2313 MET cc_start: 0.7984 (mpp) cc_final: 0.7329 (mpp) REVERT: B 2933 MET cc_start: 0.7245 (ttp) cc_final: 0.6821 (ppp) REVERT: B 3112 ARG cc_start: 0.8441 (ttm110) cc_final: 0.8197 (ttm110) REVERT: B 3287 GLU cc_start: 0.8466 (tp30) cc_final: 0.8229 (mm-30) REVERT: B 3349 ARG cc_start: 0.8427 (mmm160) cc_final: 0.8159 (mtp85) REVERT: B 3433 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8379 (mt-10) REVERT: B 3694 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8346 (mmtt) REVERT: B 3995 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8368 (m-80) REVERT: B 4164 ARG cc_start: 0.8564 (mtp180) cc_final: 0.8280 (mtm180) REVERT: B 4674 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7607 (mm-30) REVERT: B 5010 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8421 (tttm) REVERT: C 35 LYS cc_start: 0.8833 (mtpt) cc_final: 0.8427 (mtpp) REVERT: C 855 CYS cc_start: 0.8802 (m) cc_final: 0.8580 (m) REVERT: C 921 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.7796 (p90) REVERT: C 928 GLU cc_start: 0.8669 (pt0) cc_final: 0.8310 (pt0) REVERT: C 939 HIS cc_start: 0.6945 (m90) cc_final: 0.6624 (m90) REVERT: C 961 MET cc_start: 0.4705 (tpp) cc_final: 0.4421 (tpt) REVERT: C 962 MET cc_start: 0.3858 (OUTLIER) cc_final: 0.2989 (tpp) REVERT: C 1037 ARG cc_start: 0.8581 (mtm110) cc_final: 0.8281 (mtm110) REVERT: C 1987 MET cc_start: 0.7568 (mmp) cc_final: 0.6527 (mpp) REVERT: C 2210 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7465 (tp30) REVERT: C 2313 MET cc_start: 0.7979 (mpp) cc_final: 0.7329 (mpp) REVERT: C 2933 MET cc_start: 0.7222 (ttp) cc_final: 0.6799 (ppp) REVERT: C 3217 CYS cc_start: 0.8043 (p) cc_final: 0.7766 (p) REVERT: C 3287 GLU cc_start: 0.8431 (tp30) cc_final: 0.8216 (mm-30) REVERT: C 3349 ARG cc_start: 0.8427 (mmm160) cc_final: 0.8183 (mtp85) REVERT: C 3433 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8530 (mt-10) REVERT: C 3694 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8355 (mmtt) REVERT: C 4164 ARG cc_start: 0.8582 (mtp180) cc_final: 0.8319 (mtm180) REVERT: C 4674 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7605 (mm-30) REVERT: C 5010 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8423 (tttm) outliers start: 181 outliers final: 147 residues processed: 1872 average time/residue: 1.2597 time to fit residues: 4167.1472 Evaluate side-chains 1894 residues out of total 16252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1727 time to evaluate : 12.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 858 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 921 TYR Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 2001 SER Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2007 ILE Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2624 LEU Chi-restraints excluded: chain A residue 2893 GLN Chi-restraints excluded: chain A residue 3088 ILE Chi-restraints excluded: chain A residue 3109 GLU Chi-restraints excluded: chain A residue 3156 ASP Chi-restraints excluded: chain A residue 3160 ASP Chi-restraints excluded: chain A residue 3226 ARG Chi-restraints excluded: chain A residue 3394 LEU Chi-restraints excluded: chain A residue 3451 ASN Chi-restraints excluded: chain A residue 3462 GLN Chi-restraints excluded: chain A residue 3559 ASN Chi-restraints excluded: chain A residue 3599 GLU Chi-restraints excluded: chain A residue 3694 LYS Chi-restraints excluded: chain A residue 3876 LYS Chi-restraints excluded: chain A residue 3902 PHE Chi-restraints excluded: chain A residue 3995 PHE Chi-restraints excluded: chain A residue 4166 PHE Chi-restraints excluded: chain A residue 4816 MET Chi-restraints excluded: chain A residue 4866 ASP Chi-restraints excluded: chain A residue 4931 GLN Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain J residue 3 SER Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain K residue 19 HIS Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain O residue 19 HIS Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain N residue 27 TYR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain P residue 27 TYR Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 858 ASP Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 921 TYR Chi-restraints excluded: chain D residue 962 MET Chi-restraints excluded: chain D residue 1071 ASP Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2001 SER Chi-restraints excluded: chain D residue 2005 GLU Chi-restraints excluded: chain D residue 2007 ILE Chi-restraints excluded: chain D residue 2272 THR Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 3088 ILE Chi-restraints excluded: chain D residue 3109 GLU Chi-restraints excluded: chain D residue 3156 ASP Chi-restraints excluded: chain D residue 3160 ASP Chi-restraints excluded: chain D residue 3161 ASP Chi-restraints excluded: chain D residue 3394 LEU Chi-restraints excluded: chain D residue 3451 ASN Chi-restraints excluded: chain D residue 3462 GLN Chi-restraints excluded: chain D residue 3559 ASN Chi-restraints excluded: chain D residue 3599 GLU Chi-restraints excluded: chain D residue 3694 LYS Chi-restraints excluded: chain D residue 3902 PHE Chi-restraints excluded: chain D residue 3995 PHE Chi-restraints excluded: chain D residue 4816 MET Chi-restraints excluded: chain D residue 4866 ASP Chi-restraints excluded: chain D residue 4931 GLN Chi-restraints excluded: chain D residue 4964 ASP Chi-restraints excluded: chain B residue 858 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 1071 ASP Chi-restraints excluded: chain B residue 1623 GLU Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2001 SER Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2007 ILE Chi-restraints excluded: chain B residue 2272 THR Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2893 GLN Chi-restraints excluded: chain B residue 3088 ILE Chi-restraints excluded: chain B residue 3109 GLU Chi-restraints excluded: chain B residue 3156 ASP Chi-restraints excluded: chain B residue 3160 ASP Chi-restraints excluded: chain B residue 3161 ASP Chi-restraints excluded: chain B residue 3394 LEU Chi-restraints excluded: chain B residue 3451 ASN Chi-restraints excluded: chain B residue 3462 GLN Chi-restraints excluded: chain B residue 3559 ASN Chi-restraints excluded: chain B residue 3599 GLU Chi-restraints excluded: chain B residue 3694 LYS Chi-restraints excluded: chain B residue 3876 LYS Chi-restraints excluded: chain B residue 3902 PHE Chi-restraints excluded: chain B residue 3995 PHE Chi-restraints excluded: chain B residue 4166 PHE Chi-restraints excluded: chain B residue 4720 ARG Chi-restraints excluded: chain B residue 4816 MET Chi-restraints excluded: chain B residue 4866 ASP Chi-restraints excluded: chain B residue 4931 GLN Chi-restraints excluded: chain B residue 4964 ASP Chi-restraints excluded: chain B residue 4990 LEU Chi-restraints excluded: chain C residue 858 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 921 TYR Chi-restraints excluded: chain C residue 932 THR Chi-restraints excluded: chain C residue 962 MET Chi-restraints excluded: chain C residue 1071 ASP Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2001 SER Chi-restraints excluded: chain C residue 2005 GLU Chi-restraints excluded: chain C residue 2007 ILE Chi-restraints excluded: chain C residue 2166 LEU Chi-restraints excluded: chain C residue 2272 THR Chi-restraints excluded: chain C residue 2624 LEU Chi-restraints excluded: chain C residue 3088 ILE Chi-restraints excluded: chain C residue 3156 ASP Chi-restraints excluded: chain C residue 3160 ASP Chi-restraints excluded: chain C residue 3394 LEU Chi-restraints excluded: chain C residue 3451 ASN Chi-restraints excluded: chain C residue 3462 GLN Chi-restraints excluded: chain C residue 3559 ASN Chi-restraints excluded: chain C residue 3599 GLU Chi-restraints excluded: chain C residue 3694 LYS Chi-restraints excluded: chain C residue 3876 LYS Chi-restraints excluded: chain C residue 3902 PHE Chi-restraints excluded: chain C residue 4166 PHE Chi-restraints excluded: chain C residue 4720 ARG Chi-restraints excluded: chain C residue 4816 MET Chi-restraints excluded: chain C residue 4866 ASP Chi-restraints excluded: chain C residue 4931 GLN Chi-restraints excluded: chain C residue 4964 ASP Chi-restraints excluded: chain C residue 4990 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1860 random chunks: chunk 904 optimal weight: 5.9990 chunk 1172 optimal weight: 0.6980 chunk 1571 optimal weight: 3.9990 chunk 452 optimal weight: 8.9990 chunk 1360 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 chunk 410 optimal weight: 4.9990 chunk 1477 optimal weight: 1.9990 chunk 618 optimal weight: 5.9990 chunk 1517 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 GLN A4112 GLN ** A4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2037 GLN ** D2325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4112 GLN ** D4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2037 GLN ** B2325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4112 GLN ** B4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2878 GLN C3466 ASN C4112 GLN ** C4226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.090753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.060665 restraints weight = 479969.975| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.82 r_work: 0.2615 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 152152 Z= 0.355 Angle : 0.639 21.253 205940 Z= 0.324 Chirality : 0.043 0.379 22624 Planarity : 0.005 0.072 26768 Dihedral : 5.278 64.641 20604 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.18 % Allowed : 10.44 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.46 (0.06), residues: 18540 helix: 1.95 (0.05), residues: 9912 sheet: 0.06 (0.13), residues: 1596 loop : -0.18 (0.07), residues: 7032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A2822 HIS 0.012 0.001 HIS D 219 PHE 0.056 0.002 PHE J 90 TYR 0.049 0.002 TYR B3605 ARG 0.015 0.001 ARG D1822 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 65973.45 seconds wall clock time: 1137 minutes 58.48 seconds (68278.48 seconds total)