Starting phenix.real_space_refine on Sun Mar 24 13:00:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5c_22680/03_2024/7k5c_22680.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5c_22680/03_2024/7k5c_22680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5c_22680/03_2024/7k5c_22680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5c_22680/03_2024/7k5c_22680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5c_22680/03_2024/7k5c_22680.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5c_22680/03_2024/7k5c_22680.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 204 5.16 5 C 25632 2.51 5 N 7242 2.21 5 O 8469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ASP 65": "OD1" <-> "OD2" Residue "H ASP 68": "OD1" <-> "OD2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "H TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 173": "OE1" <-> "OE2" Residue "H ASP 210": "OD1" <-> "OD2" Residue "H ASP 219": "OD1" <-> "OD2" Residue "H PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 307": "OE1" <-> "OE2" Residue "H TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 335": "OE1" <-> "OE2" Residue "H ASP 376": "OD1" <-> "OD2" Residue "H PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 439": "OD1" <-> "OD2" Residue "H ASP 469": "OD1" <-> "OD2" Residue "H ASP 491": "OD1" <-> "OD2" Residue "H ASP 500": "OD1" <-> "OD2" Residue "H ASP 510": "OD1" <-> "OD2" Residue "H ASP 522": "OD1" <-> "OD2" Residue "H GLU 548": "OE1" <-> "OE2" Residue "H ASP 550": "OD1" <-> "OD2" Residue "H GLU 554": "OE1" <-> "OE2" Residue "H GLU 590": "OE1" <-> "OE2" Residue "H GLU 603": "OE1" <-> "OE2" Residue "H PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 614": "OD1" <-> "OD2" Residue "H ASP 616": "OD1" <-> "OD2" Residue "H ASP 668": "OD1" <-> "OD2" Residue "H TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 674": "OD1" <-> "OD2" Residue "H TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 21": "OD1" <-> "OD2" Residue "G TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 31": "NH1" <-> "NH2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 67": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G ASP 100": "OD1" <-> "OD2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G ASP 144": "OD1" <-> "OD2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "G PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 200": "OE1" <-> "OE2" Residue "G PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A ASP 68": "OD1" <-> "OD2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A ASP 219": "OD1" <-> "OD2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 439": "OD1" <-> "OD2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "A ASP 491": "OD1" <-> "OD2" Residue "A ASP 500": "OD1" <-> "OD2" Residue "A ASP 510": "OD1" <-> "OD2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A ASP 550": "OD1" <-> "OD2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A GLU 603": "OE1" <-> "OE2" Residue "A PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A ASP 616": "OD1" <-> "OD2" Residue "A ASP 668": "OD1" <-> "OD2" Residue "A TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 21": "OD1" <-> "OD2" Residue "B TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B ASP 144": "OD1" <-> "OD2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C ASP 68": "OD1" <-> "OD2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C ASP 210": "OD1" <-> "OD2" Residue "C ASP 219": "OD1" <-> "OD2" Residue "C PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C ASP 376": "OD1" <-> "OD2" Residue "C PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 439": "OD1" <-> "OD2" Residue "C ASP 469": "OD1" <-> "OD2" Residue "C ASP 491": "OD1" <-> "OD2" Residue "C ASP 500": "OD1" <-> "OD2" Residue "C ASP 510": "OD1" <-> "OD2" Residue "C ASP 522": "OD1" <-> "OD2" Residue "C GLU 548": "OE1" <-> "OE2" Residue "C ASP 550": "OD1" <-> "OD2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 590": "OE1" <-> "OE2" Residue "C GLU 603": "OE1" <-> "OE2" Residue "C PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C ASP 616": "OD1" <-> "OD2" Residue "C ASP 668": "OD1" <-> "OD2" Residue "C TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 674": "OD1" <-> "OD2" Residue "C TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 21": "OD1" <-> "OD2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D ASP 144": "OD1" <-> "OD2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 65": "OD1" <-> "OD2" Residue "E ASP 68": "OD1" <-> "OD2" Residue "E GLU 102": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E ASP 210": "OD1" <-> "OD2" Residue "E ASP 219": "OD1" <-> "OD2" Residue "E PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 307": "OE1" <-> "OE2" Residue "E TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "E ASP 376": "OD1" <-> "OD2" Residue "E PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 439": "OD1" <-> "OD2" Residue "E ASP 469": "OD1" <-> "OD2" Residue "E ASP 491": "OD1" <-> "OD2" Residue "E ASP 500": "OD1" <-> "OD2" Residue "E ASP 510": "OD1" <-> "OD2" Residue "E ASP 522": "OD1" <-> "OD2" Residue "E GLU 548": "OE1" <-> "OE2" Residue "E ASP 550": "OD1" <-> "OD2" Residue "E GLU 554": "OE1" <-> "OE2" Residue "E GLU 590": "OE1" <-> "OE2" Residue "E GLU 603": "OE1" <-> "OE2" Residue "E PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 614": "OD1" <-> "OD2" Residue "E ASP 616": "OD1" <-> "OD2" Residue "E ASP 668": "OD1" <-> "OD2" Residue "E TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 674": "OD1" <-> "OD2" Residue "E TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 21": "OD1" <-> "OD2" Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 31": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ASP 100": "OD1" <-> "OD2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "F PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 200": "OE1" <-> "OE2" Residue "F PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 65": "OD1" <-> "OD2" Residue "I ASP 68": "OD1" <-> "OD2" Residue "I GLU 102": "OE1" <-> "OE2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 173": "OE1" <-> "OE2" Residue "I ASP 210": "OD1" <-> "OD2" Residue "I ASP 219": "OD1" <-> "OD2" Residue "I PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 307": "OE1" <-> "OE2" Residue "I TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 335": "OE1" <-> "OE2" Residue "I ASP 376": "OD1" <-> "OD2" Residue "I PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 439": "OD1" <-> "OD2" Residue "I ASP 469": "OD1" <-> "OD2" Residue "I ASP 491": "OD1" <-> "OD2" Residue "I ASP 500": "OD1" <-> "OD2" Residue "I ASP 510": "OD1" <-> "OD2" Residue "I ASP 522": "OD1" <-> "OD2" Residue "I GLU 548": "OE1" <-> "OE2" Residue "I ASP 550": "OD1" <-> "OD2" Residue "I GLU 554": "OE1" <-> "OE2" Residue "I GLU 590": "OE1" <-> "OE2" Residue "I GLU 603": "OE1" <-> "OE2" Residue "I PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 614": "OD1" <-> "OD2" Residue "I ASP 616": "OD1" <-> "OD2" Residue "I ASP 668": "OD1" <-> "OD2" Residue "I TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 674": "OD1" <-> "OD2" Residue "I TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 21": "OD1" <-> "OD2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 31": "NH1" <-> "NH2" Residue "J ARG 39": "NH1" <-> "NH2" Residue "J PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 76": "NH1" <-> "NH2" Residue "J ASP 100": "OD1" <-> "OD2" Residue "J GLU 101": "OE1" <-> "OE2" Residue "J TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "J ASP 144": "OD1" <-> "OD2" Residue "J GLU 185": "OE1" <-> "OE2" Residue "J PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 200": "OE1" <-> "OE2" Residue "J PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 65": "OD1" <-> "OD2" Residue "K ASP 68": "OD1" <-> "OD2" Residue "K GLU 102": "OE1" <-> "OE2" Residue "K GLU 126": "OE1" <-> "OE2" Residue "K TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "K ASP 210": "OD1" <-> "OD2" Residue "K ASP 219": "OD1" <-> "OD2" Residue "K PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 307": "OE1" <-> "OE2" Residue "K TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 335": "OE1" <-> "OE2" Residue "K ASP 376": "OD1" <-> "OD2" Residue "K PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 439": "OD1" <-> "OD2" Residue "K ASP 469": "OD1" <-> "OD2" Residue "K ASP 491": "OD1" <-> "OD2" Residue "K ASP 500": "OD1" <-> "OD2" Residue "K ASP 510": "OD1" <-> "OD2" Residue "K ASP 522": "OD1" <-> "OD2" Residue "K GLU 548": "OE1" <-> "OE2" Residue "K ASP 550": "OD1" <-> "OD2" Residue "K GLU 554": "OE1" <-> "OE2" Residue "K GLU 590": "OE1" <-> "OE2" Residue "K GLU 603": "OE1" <-> "OE2" Residue "K PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 614": "OD1" <-> "OD2" Residue "K ASP 616": "OD1" <-> "OD2" Residue "K ASP 668": "OD1" <-> "OD2" Residue "K TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 674": "OD1" <-> "OD2" Residue "K TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 21": "OD1" <-> "OD2" Residue "L TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 39": "NH1" <-> "NH2" Residue "L PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 67": "NH1" <-> "NH2" Residue "L ARG 76": "NH1" <-> "NH2" Residue "L ASP 100": "OD1" <-> "OD2" Residue "L GLU 101": "OE1" <-> "OE2" Residue "L TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "L TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 134": "OE1" <-> "OE2" Residue "L ASP 144": "OD1" <-> "OD2" Residue "L GLU 185": "OE1" <-> "OE2" Residue "L PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 200": "OE1" <-> "OE2" Residue "L PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41547 Number of models: 1 Model: "" Number of chains: 24 Chain: "H" Number of atoms: 5160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5160 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 628} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1728 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 216} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 5160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5160 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 628} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1728 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 216} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 5160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5160 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 628} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1728 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 216} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 5160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5160 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 628} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1728 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 216} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 5160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5160 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 628} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1728 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 216} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 5160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5160 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 628} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1728 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 216} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 19.69, per 1000 atoms: 0.47 Number of scatterers: 41547 At special positions: 0 Unit cell: (146.88, 163.08, 236.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 204 16.00 O 8469 8.00 N 7242 7.00 C 25632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.47 Conformation dependent library (CDL) restraints added in 7.4 seconds 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9840 Finding SS restraints... Secondary structure from input PDB file: 276 helices and 18 sheets defined 72.5% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'H' and resid 57 through 77 removed outlier: 3.547A pdb=" N LYS H 77 " --> pdb=" O GLU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 90 removed outlier: 3.770A pdb=" N ASN H 88 " --> pdb=" O ARG H 84 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 127 removed outlier: 3.721A pdb=" N ASP H 119 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL H 120 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 152 removed outlier: 3.783A pdb=" N ALA H 147 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS H 148 " --> pdb=" O GLN H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 169 Processing helix chain 'H' and resid 170 through 203 removed outlier: 3.618A pdb=" N PHE H 185 " --> pdb=" O ALA H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 213 Processing helix chain 'H' and resid 214 through 232 removed outlier: 3.974A pdb=" N ALA H 218 " --> pdb=" O ARG H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 252 Processing helix chain 'H' and resid 256 through 265 Processing helix chain 'H' and resid 278 through 282 Processing helix chain 'H' and resid 283 through 297 Processing helix chain 'H' and resid 298 through 300 No H-bonds generated for 'chain 'H' and resid 298 through 300' Processing helix chain 'H' and resid 302 through 317 removed outlier: 3.604A pdb=" N ASN H 306 " --> pdb=" O ASP H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 337 Processing helix chain 'H' and resid 346 through 396 removed outlier: 3.681A pdb=" N TRP H 351 " --> pdb=" O PRO H 347 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU H 352 " --> pdb=" O GLN H 348 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA H 369 " --> pdb=" O ALA H 365 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER H 380 " --> pdb=" O ASP H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 403 through 407 removed outlier: 3.668A pdb=" N MET H 407 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 434 removed outlier: 3.638A pdb=" N MET H 421 " --> pdb=" O LYS H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 438 through 453 Processing helix chain 'H' and resid 457 through 481 removed outlier: 3.763A pdb=" N THR H 465 " --> pdb=" O THR H 461 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET H 466 " --> pdb=" O ALA H 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 487 through 500 Processing helix chain 'H' and resid 500 through 508 removed outlier: 3.563A pdb=" N ILE H 504 " --> pdb=" O ASP H 500 " (cutoff:3.500A) Processing helix chain 'H' and resid 508 through 525 Processing helix chain 'H' and resid 527 through 540 removed outlier: 4.280A pdb=" N ILE H 531 " --> pdb=" O ASP H 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS H 540 " --> pdb=" O ARG H 536 " (cutoff:3.500A) Processing helix chain 'H' and resid 542 through 559 removed outlier: 3.600A pdb=" N PHE H 547 " --> pdb=" O LYS H 543 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU H 548 " --> pdb=" O GLU H 544 " (cutoff:3.500A) Processing helix chain 'H' and resid 562 through 567 Processing helix chain 'H' and resid 569 through 587 removed outlier: 3.798A pdb=" N SER H 575 " --> pdb=" O SER H 571 " (cutoff:3.500A) Processing helix chain 'H' and resid 589 through 603 Processing helix chain 'H' and resid 624 through 626 No H-bonds generated for 'chain 'H' and resid 624 through 626' Processing helix chain 'H' and resid 631 through 633 No H-bonds generated for 'chain 'H' and resid 631 through 633' Processing helix chain 'H' and resid 634 through 653 removed outlier: 3.545A pdb=" N LYS H 647 " --> pdb=" O GLU H 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 685 through 705 Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.557A pdb=" N ASP G 5 " --> pdb=" O ASP G 2 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS G 6 " --> pdb=" O LYS G 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 15 through 24 Processing helix chain 'G' and resid 26 through 39 Processing helix chain 'G' and resid 57 through 64 Processing helix chain 'G' and resid 78 through 96 removed outlier: 3.737A pdb=" N ALA G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 105 No H-bonds generated for 'chain 'G' and resid 103 through 105' Processing helix chain 'G' and resid 106 through 111 removed outlier: 3.745A pdb=" N GLN G 110 " --> pdb=" O LEU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 126 Processing helix chain 'G' and resid 127 through 131 Processing helix chain 'G' and resid 132 through 141 Processing helix chain 'G' and resid 150 through 156 removed outlier: 3.696A pdb=" N GLU G 155 " --> pdb=" O ALA G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 173 Processing helix chain 'G' and resid 205 through 214 Processing helix chain 'G' and resid 217 through 226 Processing helix chain 'A' and resid 58 through 77 removed outlier: 3.547A pdb=" N LYS A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.770A pdb=" N ASN A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 127 removed outlier: 3.721A pdb=" N ASP A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 152 removed outlier: 3.783A pdb=" N ALA A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS A 148 " --> pdb=" O GLN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 170 through 203 removed outlier: 3.620A pdb=" N PHE A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 214 through 232 removed outlier: 3.975A pdb=" N ALA A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 252 Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 283 through 297 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.602A pdb=" N ASN A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 Processing helix chain 'A' and resid 346 through 396 removed outlier: 3.681A pdb=" N TRP A 351 " --> pdb=" O PRO A 347 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.668A pdb=" N MET A 407 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 434 removed outlier: 3.638A pdb=" N MET A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 453 Processing helix chain 'A' and resid 457 through 481 removed outlier: 3.763A pdb=" N THR A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 500 Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.562A pdb=" N ILE A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 525 Processing helix chain 'A' and resid 527 through 540 removed outlier: 4.280A pdb=" N ILE A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 559 removed outlier: 3.600A pdb=" N PHE A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 548 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 569 through 587 removed outlier: 3.798A pdb=" N SER A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 603 Processing helix chain 'A' and resid 624 through 626 No H-bonds generated for 'chain 'A' and resid 624 through 626' Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 634 through 653 removed outlier: 3.546A pdb=" N LYS A 647 " --> pdb=" O GLU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 705 Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.557A pdb=" N ASP B 5 " --> pdb=" O ASP B 2 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS B 6 " --> pdb=" O LYS B 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 6' Processing helix chain 'B' and resid 15 through 24 Processing helix chain 'B' and resid 26 through 39 Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 78 through 96 removed outlier: 3.738A pdb=" N ALA B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 106 through 111 removed outlier: 3.744A pdb=" N GLN B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 126 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 150 through 156 removed outlier: 3.697A pdb=" N GLU B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'C' and resid 58 through 77 removed outlier: 3.547A pdb=" N LYS C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.770A pdb=" N ASN C 88 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 127 removed outlier: 3.721A pdb=" N ASP C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 152 removed outlier: 3.784A pdb=" N ALA C 147 " --> pdb=" O LEU C 143 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS C 148 " --> pdb=" O GLN C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 170 through 203 removed outlier: 3.619A pdb=" N PHE C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 214 through 232 removed outlier: 3.975A pdb=" N ALA C 218 " --> pdb=" O ARG C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 252 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 283 through 297 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 302 through 317 removed outlier: 3.603A pdb=" N ASN C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 337 Processing helix chain 'C' and resid 346 through 396 removed outlier: 3.681A pdb=" N TRP C 351 " --> pdb=" O PRO C 347 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 369 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER C 380 " --> pdb=" O ASP C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.669A pdb=" N MET C 407 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 434 removed outlier: 3.639A pdb=" N MET C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 453 Processing helix chain 'C' and resid 457 through 481 removed outlier: 3.763A pdb=" N THR C 465 " --> pdb=" O THR C 461 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N MET C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 500 Processing helix chain 'C' and resid 500 through 508 removed outlier: 3.561A pdb=" N ILE C 504 " --> pdb=" O ASP C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 525 Processing helix chain 'C' and resid 527 through 540 removed outlier: 4.280A pdb=" N ILE C 531 " --> pdb=" O ASP C 527 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS C 540 " --> pdb=" O ARG C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 559 removed outlier: 3.600A pdb=" N PHE C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 548 " --> pdb=" O GLU C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 569 through 587 removed outlier: 3.798A pdb=" N SER C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 603 Processing helix chain 'C' and resid 624 through 626 No H-bonds generated for 'chain 'C' and resid 624 through 626' Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 634 through 653 removed outlier: 3.545A pdb=" N LYS C 647 " --> pdb=" O GLU C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 705 Processing helix chain 'D' and resid 2 through 6 removed outlier: 3.557A pdb=" N ASP D 5 " --> pdb=" O ASP D 2 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS D 6 " --> pdb=" O LYS D 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2 through 6' Processing helix chain 'D' and resid 15 through 24 Processing helix chain 'D' and resid 26 through 39 Processing helix chain 'D' and resid 57 through 64 Processing helix chain 'D' and resid 78 through 96 removed outlier: 3.738A pdb=" N ALA D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 106 through 111 removed outlier: 3.744A pdb=" N GLN D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 126 Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.697A pdb=" N GLU D 155 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 205 through 214 Processing helix chain 'D' and resid 217 through 226 Processing helix chain 'E' and resid 58 through 77 removed outlier: 3.546A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 90 removed outlier: 3.771A pdb=" N ASN E 88 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN E 89 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 127 removed outlier: 3.721A pdb=" N ASP E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL E 120 " --> pdb=" O VAL E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 152 removed outlier: 3.783A pdb=" N ALA E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS E 148 " --> pdb=" O GLN E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 169 Processing helix chain 'E' and resid 170 through 203 removed outlier: 3.619A pdb=" N PHE E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 214 through 232 removed outlier: 3.975A pdb=" N ALA E 218 " --> pdb=" O ARG E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 252 Processing helix chain 'E' and resid 256 through 265 Processing helix chain 'E' and resid 278 through 282 Processing helix chain 'E' and resid 283 through 297 Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 302 through 317 removed outlier: 3.603A pdb=" N ASN E 306 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 337 Processing helix chain 'E' and resid 346 through 396 removed outlier: 3.680A pdb=" N TRP E 351 " --> pdb=" O PRO E 347 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA E 369 " --> pdb=" O ALA E 365 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER E 380 " --> pdb=" O ASP E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 407 removed outlier: 3.668A pdb=" N MET E 407 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 434 removed outlier: 3.638A pdb=" N MET E 421 " --> pdb=" O LYS E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 453 Processing helix chain 'E' and resid 457 through 481 removed outlier: 3.763A pdb=" N THR E 465 " --> pdb=" O THR E 461 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N MET E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 500 Processing helix chain 'E' and resid 500 through 508 removed outlier: 3.562A pdb=" N ILE E 504 " --> pdb=" O ASP E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 525 Processing helix chain 'E' and resid 527 through 540 removed outlier: 4.280A pdb=" N ILE E 531 " --> pdb=" O ASP E 527 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS E 540 " --> pdb=" O ARG E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 559 removed outlier: 3.600A pdb=" N PHE E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU E 548 " --> pdb=" O GLU E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 567 Processing helix chain 'E' and resid 569 through 587 removed outlier: 3.798A pdb=" N SER E 575 " --> pdb=" O SER E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 603 Processing helix chain 'E' and resid 624 through 626 No H-bonds generated for 'chain 'E' and resid 624 through 626' Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 634 through 653 removed outlier: 3.545A pdb=" N LYS E 647 " --> pdb=" O GLU E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 685 through 705 Processing helix chain 'F' and resid 2 through 6 removed outlier: 3.558A pdb=" N ASP F 5 " --> pdb=" O ASP F 2 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS F 6 " --> pdb=" O LYS F 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2 through 6' Processing helix chain 'F' and resid 15 through 24 Processing helix chain 'F' and resid 26 through 39 Processing helix chain 'F' and resid 57 through 64 Processing helix chain 'F' and resid 78 through 96 removed outlier: 3.738A pdb=" N ALA F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 105 No H-bonds generated for 'chain 'F' and resid 103 through 105' Processing helix chain 'F' and resid 106 through 111 removed outlier: 3.744A pdb=" N GLN F 110 " --> pdb=" O LEU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 126 Processing helix chain 'F' and resid 127 through 131 Processing helix chain 'F' and resid 132 through 141 Processing helix chain 'F' and resid 150 through 156 removed outlier: 3.696A pdb=" N GLU F 155 " --> pdb=" O ALA F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 205 through 214 Processing helix chain 'F' and resid 217 through 226 Processing helix chain 'I' and resid 58 through 77 removed outlier: 3.547A pdb=" N LYS I 77 " --> pdb=" O GLU I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 removed outlier: 3.769A pdb=" N ASN I 88 " --> pdb=" O ARG I 84 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 127 removed outlier: 3.722A pdb=" N ASP I 119 " --> pdb=" O LEU I 115 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL I 120 " --> pdb=" O VAL I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 152 removed outlier: 3.783A pdb=" N ALA I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS I 148 " --> pdb=" O GLN I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 169 Processing helix chain 'I' and resid 170 through 203 removed outlier: 3.619A pdb=" N PHE I 185 " --> pdb=" O ALA I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 213 Processing helix chain 'I' and resid 214 through 232 removed outlier: 3.976A pdb=" N ALA I 218 " --> pdb=" O ARG I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 252 Processing helix chain 'I' and resid 256 through 265 Processing helix chain 'I' and resid 278 through 282 Processing helix chain 'I' and resid 283 through 297 Processing helix chain 'I' and resid 298 through 300 No H-bonds generated for 'chain 'I' and resid 298 through 300' Processing helix chain 'I' and resid 302 through 317 removed outlier: 3.602A pdb=" N ASN I 306 " --> pdb=" O ASP I 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 337 Processing helix chain 'I' and resid 346 through 396 removed outlier: 3.681A pdb=" N TRP I 351 " --> pdb=" O PRO I 347 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA I 369 " --> pdb=" O ALA I 365 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER I 380 " --> pdb=" O ASP I 376 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 407 removed outlier: 3.669A pdb=" N MET I 407 " --> pdb=" O PHE I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 417 through 434 removed outlier: 3.638A pdb=" N MET I 421 " --> pdb=" O LYS I 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 453 Processing helix chain 'I' and resid 457 through 481 removed outlier: 3.762A pdb=" N THR I 465 " --> pdb=" O THR I 461 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET I 466 " --> pdb=" O ALA I 462 " (cutoff:3.500A) Processing helix chain 'I' and resid 487 through 500 Processing helix chain 'I' and resid 500 through 508 removed outlier: 3.562A pdb=" N ILE I 504 " --> pdb=" O ASP I 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 508 through 525 Processing helix chain 'I' and resid 527 through 540 removed outlier: 4.279A pdb=" N ILE I 531 " --> pdb=" O ASP I 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS I 540 " --> pdb=" O ARG I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 542 through 559 removed outlier: 3.600A pdb=" N PHE I 547 " --> pdb=" O LYS I 543 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU I 548 " --> pdb=" O GLU I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 562 through 567 Processing helix chain 'I' and resid 569 through 587 removed outlier: 3.797A pdb=" N SER I 575 " --> pdb=" O SER I 571 " (cutoff:3.500A) Processing helix chain 'I' and resid 589 through 603 Processing helix chain 'I' and resid 624 through 626 No H-bonds generated for 'chain 'I' and resid 624 through 626' Processing helix chain 'I' and resid 631 through 633 No H-bonds generated for 'chain 'I' and resid 631 through 633' Processing helix chain 'I' and resid 634 through 653 removed outlier: 3.546A pdb=" N LYS I 647 " --> pdb=" O GLU I 643 " (cutoff:3.500A) Processing helix chain 'I' and resid 685 through 705 Processing helix chain 'J' and resid 2 through 6 removed outlier: 3.557A pdb=" N ASP J 5 " --> pdb=" O ASP J 2 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS J 6 " --> pdb=" O LYS J 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 2 through 6' Processing helix chain 'J' and resid 15 through 24 Processing helix chain 'J' and resid 26 through 39 Processing helix chain 'J' and resid 57 through 64 Processing helix chain 'J' and resid 78 through 96 removed outlier: 3.738A pdb=" N ALA J 82 " --> pdb=" O ASN J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 105 No H-bonds generated for 'chain 'J' and resid 103 through 105' Processing helix chain 'J' and resid 106 through 111 removed outlier: 3.744A pdb=" N GLN J 110 " --> pdb=" O LEU J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 126 Processing helix chain 'J' and resid 127 through 131 Processing helix chain 'J' and resid 132 through 141 Processing helix chain 'J' and resid 150 through 156 removed outlier: 3.696A pdb=" N GLU J 155 " --> pdb=" O ALA J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 173 Processing helix chain 'J' and resid 205 through 214 Processing helix chain 'J' and resid 217 through 226 Processing helix chain 'K' and resid 58 through 77 removed outlier: 3.546A pdb=" N LYS K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 90 removed outlier: 3.771A pdb=" N ASN K 88 " --> pdb=" O ARG K 84 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 127 removed outlier: 3.721A pdb=" N ASP K 119 " --> pdb=" O LEU K 115 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL K 120 " --> pdb=" O VAL K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 152 removed outlier: 3.782A pdb=" N ALA K 147 " --> pdb=" O LEU K 143 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS K 148 " --> pdb=" O GLN K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 169 Processing helix chain 'K' and resid 170 through 203 removed outlier: 3.619A pdb=" N PHE K 185 " --> pdb=" O ALA K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 213 Processing helix chain 'K' and resid 214 through 232 removed outlier: 3.975A pdb=" N ALA K 218 " --> pdb=" O ARG K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 252 Processing helix chain 'K' and resid 256 through 265 Processing helix chain 'K' and resid 278 through 282 Processing helix chain 'K' and resid 283 through 297 Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 302 through 317 removed outlier: 3.602A pdb=" N ASN K 306 " --> pdb=" O ASP K 302 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 337 Processing helix chain 'K' and resid 346 through 396 removed outlier: 3.681A pdb=" N TRP K 351 " --> pdb=" O PRO K 347 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU K 352 " --> pdb=" O GLN K 348 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA K 369 " --> pdb=" O ALA K 365 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER K 380 " --> pdb=" O ASP K 376 " (cutoff:3.500A) Processing helix chain 'K' and resid 403 through 407 removed outlier: 3.669A pdb=" N MET K 407 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 417 through 434 removed outlier: 3.638A pdb=" N MET K 421 " --> pdb=" O LYS K 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 438 through 453 Processing helix chain 'K' and resid 457 through 481 removed outlier: 3.762A pdb=" N THR K 465 " --> pdb=" O THR K 461 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET K 466 " --> pdb=" O ALA K 462 " (cutoff:3.500A) Processing helix chain 'K' and resid 487 through 500 Processing helix chain 'K' and resid 500 through 508 removed outlier: 3.561A pdb=" N ILE K 504 " --> pdb=" O ASP K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 508 through 525 Processing helix chain 'K' and resid 527 through 540 removed outlier: 4.279A pdb=" N ILE K 531 " --> pdb=" O ASP K 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS K 540 " --> pdb=" O ARG K 536 " (cutoff:3.500A) Processing helix chain 'K' and resid 542 through 559 removed outlier: 3.601A pdb=" N PHE K 547 " --> pdb=" O LYS K 543 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU K 548 " --> pdb=" O GLU K 544 " (cutoff:3.500A) Processing helix chain 'K' and resid 562 through 567 Processing helix chain 'K' and resid 569 through 587 removed outlier: 3.798A pdb=" N SER K 575 " --> pdb=" O SER K 571 " (cutoff:3.500A) Processing helix chain 'K' and resid 589 through 603 Processing helix chain 'K' and resid 624 through 626 No H-bonds generated for 'chain 'K' and resid 624 through 626' Processing helix chain 'K' and resid 631 through 633 No H-bonds generated for 'chain 'K' and resid 631 through 633' Processing helix chain 'K' and resid 634 through 653 removed outlier: 3.546A pdb=" N LYS K 647 " --> pdb=" O GLU K 643 " (cutoff:3.500A) Processing helix chain 'K' and resid 685 through 705 Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.557A pdb=" N ASP L 5 " --> pdb=" O ASP L 2 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS L 6 " --> pdb=" O LYS L 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2 through 6' Processing helix chain 'L' and resid 15 through 24 Processing helix chain 'L' and resid 26 through 39 Processing helix chain 'L' and resid 57 through 64 Processing helix chain 'L' and resid 78 through 96 removed outlier: 3.737A pdb=" N ALA L 82 " --> pdb=" O ASN L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 105 No H-bonds generated for 'chain 'L' and resid 103 through 105' Processing helix chain 'L' and resid 106 through 111 removed outlier: 3.744A pdb=" N GLN L 110 " --> pdb=" O LEU L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 126 Processing helix chain 'L' and resid 127 through 131 Processing helix chain 'L' and resid 132 through 141 Processing helix chain 'L' and resid 150 through 156 removed outlier: 3.696A pdb=" N GLU L 155 " --> pdb=" O ALA L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 173 Processing helix chain 'L' and resid 205 through 214 Processing helix chain 'L' and resid 217 through 226 Processing sheet with id=AA1, first strand: chain 'H' and resid 268 through 271 Processing sheet with id=AA2, first strand: chain 'H' and resid 605 through 609 removed outlier: 3.811A pdb=" N GLY H 619 " --> pdb=" O PHE H 608 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 662 through 666 Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 271 Processing sheet with id=AA5, first strand: chain 'A' and resid 605 through 609 removed outlier: 3.811A pdb=" N GLY A 619 " --> pdb=" O PHE A 608 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 662 through 666 Processing sheet with id=AA7, first strand: chain 'C' and resid 268 through 271 Processing sheet with id=AA8, first strand: chain 'C' and resid 605 through 609 removed outlier: 3.811A pdb=" N GLY C 619 " --> pdb=" O PHE C 608 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 662 through 666 Processing sheet with id=AB1, first strand: chain 'E' and resid 268 through 271 Processing sheet with id=AB2, first strand: chain 'E' and resid 605 through 609 removed outlier: 3.811A pdb=" N GLY E 619 " --> pdb=" O PHE E 608 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 662 through 666 Processing sheet with id=AB4, first strand: chain 'I' and resid 268 through 271 Processing sheet with id=AB5, first strand: chain 'I' and resid 605 through 609 removed outlier: 3.811A pdb=" N GLY I 619 " --> pdb=" O PHE I 608 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 662 through 666 Processing sheet with id=AB7, first strand: chain 'K' and resid 268 through 271 Processing sheet with id=AB8, first strand: chain 'K' and resid 605 through 609 removed outlier: 3.812A pdb=" N GLY K 619 " --> pdb=" O PHE K 608 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 662 through 666 2677 hydrogen bonds defined for protein. 7923 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: 14.70 Time building geometry restraints manager: 16.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14256 1.34 - 1.46: 4728 1.46 - 1.57: 22596 1.57 - 1.69: 0 1.69 - 1.81: 408 Bond restraints: 41988 Sorted by residual: bond pdb=" CA ARG G 76 " pdb=" CB ARG G 76 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.31e-02 5.83e+03 1.97e+00 bond pdb=" CA ARG J 76 " pdb=" CB ARG J 76 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.31e-02 5.83e+03 1.90e+00 bond pdb=" CA ARG F 76 " pdb=" CB ARG F 76 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.31e-02 5.83e+03 1.89e+00 bond pdb=" CA ARG B 76 " pdb=" CB ARG B 76 " ideal model delta sigma weight residual 1.524 1.541 -0.018 1.31e-02 5.83e+03 1.83e+00 bond pdb=" CA ARG D 76 " pdb=" CB ARG D 76 " ideal model delta sigma weight residual 1.524 1.541 -0.018 1.31e-02 5.83e+03 1.83e+00 ... (remaining 41983 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.00: 857 106.00 - 113.01: 22163 113.01 - 120.01: 14923 120.01 - 127.01: 18266 127.01 - 134.02: 365 Bond angle restraints: 56574 Sorted by residual: angle pdb=" CA ARG B 76 " pdb=" CB ARG B 76 " pdb=" CG ARG B 76 " ideal model delta sigma weight residual 114.10 118.81 -4.71 2.00e+00 2.50e-01 5.55e+00 angle pdb=" CA ARG L 76 " pdb=" CB ARG L 76 " pdb=" CG ARG L 76 " ideal model delta sigma weight residual 114.10 118.81 -4.71 2.00e+00 2.50e-01 5.54e+00 angle pdb=" CA ARG F 76 " pdb=" CB ARG F 76 " pdb=" CG ARG F 76 " ideal model delta sigma weight residual 114.10 118.79 -4.69 2.00e+00 2.50e-01 5.51e+00 angle pdb=" CA ARG J 76 " pdb=" CB ARG J 76 " pdb=" CG ARG J 76 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.45e+00 angle pdb=" CA ARG D 76 " pdb=" CB ARG D 76 " pdb=" CG ARG D 76 " ideal model delta sigma weight residual 114.10 118.76 -4.66 2.00e+00 2.50e-01 5.44e+00 ... (remaining 56569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 23372 17.51 - 35.03: 2122 35.03 - 52.54: 288 52.54 - 70.06: 102 70.06 - 87.57: 60 Dihedral angle restraints: 25944 sinusoidal: 10692 harmonic: 15252 Sorted by residual: dihedral pdb=" CA LEU J 106 " pdb=" C LEU J 106 " pdb=" N ALA J 107 " pdb=" CA ALA J 107 " ideal model delta harmonic sigma weight residual 180.00 154.87 25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LEU L 106 " pdb=" C LEU L 106 " pdb=" N ALA L 107 " pdb=" CA ALA L 107 " ideal model delta harmonic sigma weight residual 180.00 154.87 25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LEU D 106 " pdb=" C LEU D 106 " pdb=" N ALA D 107 " pdb=" CA ALA D 107 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 25941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 4213 0.037 - 0.074: 1425 0.074 - 0.111: 314 0.111 - 0.148: 114 0.148 - 0.186: 12 Chirality restraints: 6078 Sorted by residual: chirality pdb=" CA VAL J 8 " pdb=" N VAL J 8 " pdb=" C VAL J 8 " pdb=" CB VAL J 8 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA VAL F 8 " pdb=" N VAL F 8 " pdb=" C VAL F 8 " pdb=" CB VAL F 8 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA VAL L 8 " pdb=" N VAL L 8 " pdb=" C VAL L 8 " pdb=" CB VAL L 8 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 6075 not shown) Planarity restraints: 7560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 527 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO I 528 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO I 528 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 528 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 527 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO E 528 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 528 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 528 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 527 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO C 528 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 528 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 528 " -0.020 5.00e-02 4.00e+02 ... (remaining 7557 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3636 2.74 - 3.28: 41249 3.28 - 3.82: 70875 3.82 - 4.36: 84928 4.36 - 4.90: 146277 Nonbonded interactions: 346965 Sorted by model distance: nonbonded pdb=" O HOH I 811 " pdb=" O HOH I 835 " model vdw 2.201 2.440 nonbonded pdb=" OE2 GLU F 101 " pdb=" OG SER F 148 " model vdw 2.209 2.440 nonbonded pdb=" OE2 GLU J 101 " pdb=" OG SER J 148 " model vdw 2.209 2.440 nonbonded pdb=" OE2 GLU L 101 " pdb=" OG SER L 148 " model vdw 2.209 2.440 nonbonded pdb=" OE2 GLU G 101 " pdb=" OG SER G 148 " model vdw 2.210 2.440 ... (remaining 346960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 12.130 Check model and map are aligned: 0.660 Set scattering table: 0.430 Process input model: 100.730 Find NCS groups from input model: 2.810 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 : 0.004 0.038 41988 Z= 0.230 Angle : 0.528 5.750 56574 Z= 0.304 Chirality : 0.041 0.186 6078 Planarity : 0.004 0.036 7560 Dihedral : 14.166 87.572 16104 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.11), residues: 5244 helix: 1.52 (0.09), residues: 3678 sheet: 0.64 (0.38), residues: 150 loop : -1.27 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 366 HIS 0.007 0.001 HIS L 178 PHE 0.011 0.001 PHE A 391 TYR 0.013 0.001 TYR C 424 ARG 0.004 0.000 ARG E 486 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 874 time to evaluate : 4.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 69 GLU cc_start: 0.7428 (tt0) cc_final: 0.7175 (tt0) REVERT: H 266 ASP cc_start: 0.8066 (m-30) cc_final: 0.7824 (m-30) REVERT: H 328 MET cc_start: 0.8799 (mtp) cc_final: 0.8498 (mtp) REVERT: H 407 MET cc_start: 0.8979 (mmt) cc_final: 0.8777 (mmt) REVERT: H 690 LYS cc_start: 0.8049 (ttpp) cc_final: 0.7827 (mtpp) REVERT: H 694 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6790 (mt-10) REVERT: G 88 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7792 (tttm) REVERT: G 139 MET cc_start: 0.8742 (mtp) cc_final: 0.8294 (mtm) REVERT: G 156 THR cc_start: 0.8668 (t) cc_final: 0.8318 (p) REVERT: G 219 ASP cc_start: 0.7746 (m-30) cc_final: 0.7382 (m-30) REVERT: A 102 GLU cc_start: 0.7824 (tt0) cc_final: 0.7205 (tt0) REVERT: A 119 ASP cc_start: 0.8286 (t0) cc_final: 0.8074 (t0) REVERT: A 162 ASP cc_start: 0.8301 (m-30) cc_final: 0.7814 (m-30) REVERT: A 207 GLN cc_start: 0.8641 (tt0) cc_final: 0.8316 (tt0) REVERT: A 239 GLN cc_start: 0.8693 (tt0) cc_final: 0.8487 (tt0) REVERT: A 328 MET cc_start: 0.8787 (mtp) cc_final: 0.8361 (mtp) REVERT: A 358 GLN cc_start: 0.8498 (mt0) cc_final: 0.8252 (mt0) REVERT: A 456 ASP cc_start: 0.7586 (m-30) cc_final: 0.7338 (m-30) REVERT: A 518 MET cc_start: 0.8622 (mtp) cc_final: 0.8385 (mtm) REVERT: A 522 ASP cc_start: 0.7960 (m-30) cc_final: 0.7398 (m-30) REVERT: A 543 LYS cc_start: 0.8432 (ttpp) cc_final: 0.8176 (ttpp) REVERT: A 572 LEU cc_start: 0.8932 (mp) cc_final: 0.8688 (mt) REVERT: A 594 MET cc_start: 0.8680 (tpt) cc_final: 0.8395 (tpp) REVERT: A 683 TYR cc_start: 0.8809 (m-80) cc_final: 0.8605 (m-80) REVERT: A 690 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7721 (ttmm) REVERT: C 102 GLU cc_start: 0.7882 (tt0) cc_final: 0.7395 (tt0) REVERT: C 162 ASP cc_start: 0.7798 (m-30) cc_final: 0.7590 (m-30) REVERT: C 219 ASP cc_start: 0.7827 (m-30) cc_final: 0.7533 (m-30) REVERT: C 226 ASP cc_start: 0.7549 (m-30) cc_final: 0.7135 (m-30) REVERT: C 227 ASN cc_start: 0.8108 (t0) cc_final: 0.7530 (m-40) REVERT: C 323 ARG cc_start: 0.8162 (mpp80) cc_final: 0.7894 (mtt90) REVERT: C 421 MET cc_start: 0.8637 (mmm) cc_final: 0.8398 (mmt) REVERT: C 466 MET cc_start: 0.9030 (ttm) cc_final: 0.8797 (ttp) REVERT: C 510 ASP cc_start: 0.7045 (m-30) cc_final: 0.6813 (m-30) REVERT: C 518 MET cc_start: 0.8598 (mtp) cc_final: 0.8264 (mtp) REVERT: C 522 ASP cc_start: 0.7808 (m-30) cc_final: 0.7521 (m-30) REVERT: C 690 LYS cc_start: 0.8276 (ttpp) cc_final: 0.8015 (ttpp) REVERT: D 37 GLU cc_start: 0.6203 (mm-30) cc_final: 0.5986 (mm-30) REVERT: D 130 SER cc_start: 0.8885 (m) cc_final: 0.8630 (m) REVERT: D 156 THR cc_start: 0.8663 (t) cc_final: 0.8441 (p) REVERT: E 70 ARG cc_start: 0.8748 (mtt180) cc_final: 0.8520 (mtt180) REVERT: E 102 GLU cc_start: 0.7864 (tt0) cc_final: 0.7613 (tt0) REVERT: E 121 MET cc_start: 0.9055 (tpp) cc_final: 0.8623 (tpt) REVERT: E 135 MET cc_start: 0.9104 (tmm) cc_final: 0.8629 (tmt) REVERT: E 161 VAL cc_start: 0.8606 (m) cc_final: 0.8299 (p) REVERT: E 227 ASN cc_start: 0.7816 (t0) cc_final: 0.7404 (m110) REVERT: E 363 MET cc_start: 0.8501 (tpt) cc_final: 0.8178 (tpt) REVERT: E 433 ASP cc_start: 0.8133 (m-30) cc_final: 0.7931 (m-30) REVERT: E 445 MET cc_start: 0.8189 (mtp) cc_final: 0.7980 (mtm) REVERT: E 546 ARG cc_start: 0.8452 (mtt180) cc_final: 0.7875 (mtt180) REVERT: E 550 ASP cc_start: 0.8401 (m-30) cc_final: 0.8007 (m-30) REVERT: E 572 LEU cc_start: 0.8899 (mp) cc_final: 0.8511 (mt) REVERT: E 594 MET cc_start: 0.8577 (tpt) cc_final: 0.8152 (tpt) REVERT: E 673 MET cc_start: 0.8970 (ttt) cc_final: 0.8449 (ttt) REVERT: E 690 LYS cc_start: 0.8226 (ttpp) cc_final: 0.8022 (ttpp) REVERT: I 69 GLU cc_start: 0.7417 (tt0) cc_final: 0.7134 (tt0) REVERT: I 101 MET cc_start: 0.8532 (mmp) cc_final: 0.8230 (mmp) REVERT: I 219 ASP cc_start: 0.7693 (m-30) cc_final: 0.7492 (m-30) REVERT: I 227 ASN cc_start: 0.7989 (t0) cc_final: 0.7593 (m-40) REVERT: I 338 LYS cc_start: 0.8521 (mttp) cc_final: 0.8254 (mtmt) REVERT: I 372 LYS cc_start: 0.8249 (tttm) cc_final: 0.8033 (ttpt) REVERT: I 396 ASN cc_start: 0.7977 (m-40) cc_final: 0.7741 (m-40) REVERT: I 435 MET cc_start: 0.8662 (mtt) cc_final: 0.8442 (mtt) REVERT: I 466 MET cc_start: 0.9034 (ttm) cc_final: 0.8752 (ttp) REVERT: I 518 MET cc_start: 0.8672 (mtp) cc_final: 0.8361 (mtp) REVERT: I 546 ARG cc_start: 0.8477 (mtt180) cc_final: 0.8247 (mtt180) REVERT: I 607 THR cc_start: 0.9290 (t) cc_final: 0.8982 (m) REVERT: I 690 LYS cc_start: 0.8317 (ttpp) cc_final: 0.8115 (ttmm) REVERT: J 36 THR cc_start: 0.7964 (m) cc_final: 0.7606 (p) REVERT: J 88 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8115 (tmmt) REVERT: J 156 THR cc_start: 0.8760 (t) cc_final: 0.8492 (p) REVERT: J 219 ASP cc_start: 0.7736 (m-30) cc_final: 0.7425 (m-30) REVERT: K 119 ASP cc_start: 0.7998 (t0) cc_final: 0.7660 (t70) REVERT: K 121 MET cc_start: 0.9034 (tpp) cc_final: 0.8792 (tpt) REVERT: K 219 ASP cc_start: 0.7725 (m-30) cc_final: 0.7347 (m-30) REVERT: K 227 ASN cc_start: 0.7942 (t0) cc_final: 0.7441 (m-40) REVERT: K 239 GLN cc_start: 0.8553 (tt0) cc_final: 0.8304 (tt0) REVERT: K 323 ARG cc_start: 0.8156 (mpp80) cc_final: 0.7928 (mtt90) REVERT: K 372 LYS cc_start: 0.8394 (tttm) cc_final: 0.8176 (tttp) REVERT: K 421 MET cc_start: 0.8536 (mmm) cc_final: 0.8123 (mmm) REVERT: K 445 MET cc_start: 0.8161 (mtp) cc_final: 0.7870 (mtp) REVERT: K 543 LYS cc_start: 0.8357 (ttpp) cc_final: 0.7934 (ttpp) REVERT: K 550 ASP cc_start: 0.8322 (m-30) cc_final: 0.8103 (m-30) REVERT: K 572 LEU cc_start: 0.8813 (mp) cc_final: 0.8606 (mt) REVERT: K 625 MET cc_start: 0.8357 (mtp) cc_final: 0.8106 (mtp) REVERT: K 690 LYS cc_start: 0.8359 (ttpp) cc_final: 0.8129 (tttp) REVERT: L 30 LEU cc_start: 0.8084 (tp) cc_final: 0.7759 (tt) REVERT: L 54 MET cc_start: 0.6727 (mmt) cc_final: 0.6513 (mpt) outliers start: 0 outliers final: 2 residues processed: 874 average time/residue: 1.6831 time to fit residues: 1758.8167 Evaluate side-chains 698 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 696 time to evaluate : 4.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain I residue 668 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 440 optimal weight: 0.9980 chunk 395 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 409 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 304 optimal weight: 1.9990 chunk 474 optimal weight: 0.4980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 188 GLN H 451 GLN H 695 ASN G 178 HIS A 95 GLN A 164 GLN A 410 ASN A 629 ASN A 695 ASN B 23 ASN B 153 GLN B 184 GLN C 164 GLN C 191 GLN C 695 ASN D 141 ASN E 95 GLN E 191 GLN E 298 GLN E 629 ASN F 178 HIS F 184 GLN I 95 GLN I 203 ASN I 629 ASN J 180 GLN J 184 GLN K 95 GLN K 629 ASN K 695 ASN L 178 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 41988 Z= 0.179 Angle : 0.472 9.376 56574 Z= 0.250 Chirality : 0.039 0.152 6078 Planarity : 0.004 0.037 7560 Dihedral : 4.492 159.793 5717 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.11 % Allowed : 7.67 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.12), residues: 5244 helix: 1.94 (0.09), residues: 3726 sheet: 1.26 (0.49), residues: 90 loop : -0.87 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 366 HIS 0.003 0.001 HIS D 178 PHE 0.013 0.001 PHE H 391 TYR 0.015 0.001 TYR E 424 ARG 0.003 0.000 ARG K 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 736 time to evaluate : 4.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 69 GLU cc_start: 0.7381 (tt0) cc_final: 0.7137 (tt0) REVERT: H 152 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7420 (pt0) REVERT: H 161 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8402 (m) REVERT: H 211 MET cc_start: 0.8233 (mtp) cc_final: 0.7985 (mtp) REVERT: H 266 ASP cc_start: 0.8001 (m-30) cc_final: 0.7780 (m-30) REVERT: H 286 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: H 328 MET cc_start: 0.8862 (mtp) cc_final: 0.8540 (mtp) REVERT: H 520 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7761 (tpp) REVERT: H 543 LYS cc_start: 0.8371 (ttpp) cc_final: 0.7934 (tttm) REVERT: H 597 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8959 (ttp) REVERT: H 690 LYS cc_start: 0.8113 (ttpp) cc_final: 0.7820 (ttmm) REVERT: H 694 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6765 (mt-10) REVERT: G 54 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.7136 (mpt) REVERT: G 88 LYS cc_start: 0.8063 (ttmt) cc_final: 0.7857 (ttpt) REVERT: G 139 MET cc_start: 0.8580 (mtp) cc_final: 0.8327 (mtm) REVERT: G 141 ASN cc_start: 0.8561 (m-40) cc_final: 0.8260 (m110) REVERT: G 219 ASP cc_start: 0.7820 (m-30) cc_final: 0.7486 (m-30) REVERT: A 102 GLU cc_start: 0.7801 (tt0) cc_final: 0.7141 (tt0) REVERT: A 119 ASP cc_start: 0.8227 (t0) cc_final: 0.8017 (t0) REVERT: A 162 ASP cc_start: 0.8285 (m-30) cc_final: 0.7678 (m-30) REVERT: A 207 GLN cc_start: 0.8663 (tt0) cc_final: 0.8355 (tt0) REVERT: A 239 GLN cc_start: 0.8690 (tt0) cc_final: 0.8436 (tt0) REVERT: A 307 GLU cc_start: 0.8386 (tt0) cc_final: 0.8091 (tt0) REVERT: A 328 MET cc_start: 0.8794 (mtp) cc_final: 0.8278 (mtp) REVERT: A 358 GLN cc_start: 0.8471 (mt0) cc_final: 0.8267 (mt0) REVERT: A 543 LYS cc_start: 0.8310 (ttpp) cc_final: 0.8082 (ttpp) REVERT: A 546 ARG cc_start: 0.8465 (mtt180) cc_final: 0.8062 (mtt90) REVERT: A 548 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7853 (mm-30) REVERT: A 572 LEU cc_start: 0.8858 (mp) cc_final: 0.8624 (mt) REVERT: A 594 MET cc_start: 0.8591 (tpt) cc_final: 0.8373 (tpp) REVERT: A 597 MET cc_start: 0.9130 (ttp) cc_final: 0.8885 (tmm) REVERT: A 690 LYS cc_start: 0.8131 (ttpp) cc_final: 0.7727 (ttmm) REVERT: B 193 ASP cc_start: 0.7595 (t70) cc_final: 0.7391 (t0) REVERT: C 102 GLU cc_start: 0.7846 (tt0) cc_final: 0.7433 (tt0) REVERT: C 162 ASP cc_start: 0.7875 (m-30) cc_final: 0.7640 (m-30) REVERT: C 219 ASP cc_start: 0.7733 (m-30) cc_final: 0.7454 (m-30) REVERT: C 226 ASP cc_start: 0.7543 (m-30) cc_final: 0.7170 (m-30) REVERT: C 227 ASN cc_start: 0.8139 (t0) cc_final: 0.7534 (m-40) REVERT: C 239 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: C 421 MET cc_start: 0.8538 (mmm) cc_final: 0.8252 (mmt) REVERT: C 466 MET cc_start: 0.9041 (ttm) cc_final: 0.8717 (ttp) REVERT: C 510 ASP cc_start: 0.7220 (m-30) cc_final: 0.6976 (m-30) REVERT: C 518 MET cc_start: 0.8468 (mtp) cc_final: 0.8179 (mtp) REVERT: C 554 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7196 (mt-10) REVERT: C 690 LYS cc_start: 0.8251 (ttpp) cc_final: 0.8007 (tttp) REVERT: D 13 ASP cc_start: 0.5923 (p0) cc_final: 0.5244 (m-30) REVERT: D 37 GLU cc_start: 0.6612 (mm-30) cc_final: 0.6058 (mm-30) REVERT: D 188 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: E 70 ARG cc_start: 0.8697 (mtt180) cc_final: 0.8497 (mtt180) REVERT: E 102 GLU cc_start: 0.7947 (tt0) cc_final: 0.7700 (tt0) REVERT: E 121 MET cc_start: 0.9061 (tpp) cc_final: 0.8614 (tpt) REVERT: E 161 VAL cc_start: 0.8536 (m) cc_final: 0.8219 (p) REVERT: E 211 MET cc_start: 0.8079 (mtp) cc_final: 0.7723 (mtp) REVERT: E 227 ASN cc_start: 0.7815 (t0) cc_final: 0.7397 (m110) REVERT: E 286 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7342 (mp10) REVERT: E 363 MET cc_start: 0.8379 (tpt) cc_final: 0.8133 (tpt) REVERT: E 445 MET cc_start: 0.8237 (mtp) cc_final: 0.8000 (mtt) REVERT: E 546 ARG cc_start: 0.8386 (mtt180) cc_final: 0.8094 (mtm180) REVERT: E 572 LEU cc_start: 0.8904 (mp) cc_final: 0.8561 (mt) REVERT: E 592 MET cc_start: 0.9013 (ttt) cc_final: 0.8669 (ttt) REVERT: E 594 MET cc_start: 0.8494 (tpt) cc_final: 0.8176 (tpt) REVERT: E 673 MET cc_start: 0.8925 (ttt) cc_final: 0.8497 (ttp) REVERT: E 690 LYS cc_start: 0.8261 (ttpp) cc_final: 0.7909 (ttmm) REVERT: F 28 ASP cc_start: 0.7215 (m-30) cc_final: 0.6948 (OUTLIER) REVERT: F 130 SER cc_start: 0.8735 (m) cc_final: 0.8526 (m) REVERT: I 69 GLU cc_start: 0.7444 (tt0) cc_final: 0.7061 (tt0) REVERT: I 219 ASP cc_start: 0.7669 (m-30) cc_final: 0.7416 (m-30) REVERT: I 223 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8055 (mttp) REVERT: I 227 ASN cc_start: 0.7989 (t0) cc_final: 0.7509 (m-40) REVERT: I 286 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7466 (mp10) REVERT: I 338 LYS cc_start: 0.8547 (mttp) cc_final: 0.8279 (mtmt) REVERT: I 372 LYS cc_start: 0.8237 (tttm) cc_final: 0.8022 (ttpt) REVERT: I 374 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8260 (mt) REVERT: I 378 MET cc_start: 0.8379 (ttm) cc_final: 0.7970 (ttp) REVERT: I 466 MET cc_start: 0.9046 (ttm) cc_final: 0.8735 (ttm) REVERT: I 518 MET cc_start: 0.8656 (mtp) cc_final: 0.8395 (mtp) REVERT: I 546 ARG cc_start: 0.8490 (mtt180) cc_final: 0.8263 (mtt180) REVERT: I 607 THR cc_start: 0.9248 (t) cc_final: 0.8836 (m) REVERT: I 636 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: J 36 THR cc_start: 0.7886 (m) cc_final: 0.7520 (p) REVERT: J 102 LEU cc_start: 0.8219 (tp) cc_final: 0.7995 (mt) REVERT: J 156 THR cc_start: 0.8634 (t) cc_final: 0.8379 (m) REVERT: J 219 ASP cc_start: 0.7751 (m-30) cc_final: 0.7473 (m-30) REVERT: K 119 ASP cc_start: 0.7966 (t0) cc_final: 0.7686 (t70) REVERT: K 121 MET cc_start: 0.9018 (tpp) cc_final: 0.8774 (tpt) REVERT: K 188 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7954 (pt0) REVERT: K 211 MET cc_start: 0.8227 (mtp) cc_final: 0.7997 (mtm) REVERT: K 219 ASP cc_start: 0.7592 (m-30) cc_final: 0.7261 (m-30) REVERT: K 227 ASN cc_start: 0.7813 (t0) cc_final: 0.7353 (m-40) REVERT: K 239 GLN cc_start: 0.8561 (tt0) cc_final: 0.8276 (tt0) REVERT: K 372 LYS cc_start: 0.8471 (tttm) cc_final: 0.8258 (tttp) REVERT: K 445 MET cc_start: 0.8225 (mtp) cc_final: 0.7982 (mtp) REVERT: K 543 LYS cc_start: 0.8276 (ttpp) cc_final: 0.7877 (ttpp) REVERT: K 625 MET cc_start: 0.8349 (mtp) cc_final: 0.8098 (mtp) REVERT: K 690 LYS cc_start: 0.8327 (ttpp) cc_final: 0.8081 (tttp) REVERT: L 1 MET cc_start: 0.4885 (mtm) cc_final: 0.4143 (ppp) REVERT: L 30 LEU cc_start: 0.7982 (tp) cc_final: 0.7706 (tp) REVERT: L 54 MET cc_start: 0.6924 (mmt) cc_final: 0.6414 (mpt) REVERT: L 188 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7004 (mp0) outliers start: 92 outliers final: 27 residues processed: 770 average time/residue: 1.6743 time to fit residues: 1547.2841 Evaluate side-chains 735 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 693 time to evaluate : 5.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 286 GLN Chi-restraints excluded: chain H residue 368 LYS Chi-restraints excluded: chain H residue 520 MET Chi-restraints excluded: chain H residue 539 VAL Chi-restraints excluded: chain H residue 597 MET Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 223 LYS Chi-restraints excluded: chain I residue 239 GLN Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 510 ASP Chi-restraints excluded: chain I residue 636 GLU Chi-restraints excluded: chain K residue 188 GLN Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 285 GLU Chi-restraints excluded: chain K residue 298 GLN Chi-restraints excluded: chain K residue 694 GLU Chi-restraints excluded: chain L residue 188 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 263 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 394 optimal weight: 3.9990 chunk 322 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 474 optimal weight: 0.9980 chunk 513 optimal weight: 4.9990 chunk 422 optimal weight: 10.0000 chunk 470 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 380 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 451 GLN H 695 ASN G 109 ASN A 164 GLN A 188 GLN A 308 GLN A 695 ASN B 178 HIS B 184 GLN C 164 GLN C 191 GLN C 203 ASN C 629 ASN D 178 HIS E 191 GLN E 203 ASN F 153 GLN I 191 GLN ** J 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 629 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 41988 Z= 0.220 Angle : 0.482 7.554 56574 Z= 0.255 Chirality : 0.040 0.165 6078 Planarity : 0.004 0.039 7560 Dihedral : 4.501 157.233 5715 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.50 % Allowed : 9.53 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.12), residues: 5244 helix: 2.08 (0.09), residues: 3720 sheet: 1.29 (0.48), residues: 90 loop : -0.87 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 399 HIS 0.005 0.001 HIS D 178 PHE 0.012 0.001 PHE A 404 TYR 0.015 0.001 TYR E 424 ARG 0.003 0.000 ARG E 497 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 712 time to evaluate : 4.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 69 GLU cc_start: 0.7414 (tt0) cc_final: 0.7164 (tt0) REVERT: H 152 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7438 (pt0) REVERT: H 161 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8403 (m) REVERT: H 211 MET cc_start: 0.8299 (mtp) cc_final: 0.8013 (mtp) REVERT: H 266 ASP cc_start: 0.8028 (m-30) cc_final: 0.7809 (m-30) REVERT: H 286 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7661 (mp10) REVERT: H 328 MET cc_start: 0.8839 (mtp) cc_final: 0.8532 (mtp) REVERT: H 520 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7841 (tpp) REVERT: H 684 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7260 (p0) REVERT: H 690 LYS cc_start: 0.8278 (ttpp) cc_final: 0.7932 (ttmm) REVERT: H 694 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6807 (mt-10) REVERT: G 88 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7781 (ttpt) REVERT: G 219 ASP cc_start: 0.7822 (m-30) cc_final: 0.7521 (m-30) REVERT: A 102 GLU cc_start: 0.7826 (tt0) cc_final: 0.7447 (tt0) REVERT: A 119 ASP cc_start: 0.8269 (t0) cc_final: 0.8061 (t0) REVERT: A 207 GLN cc_start: 0.8634 (tt0) cc_final: 0.8326 (tt0) REVERT: A 239 GLN cc_start: 0.8720 (tt0) cc_final: 0.8447 (tt0) REVERT: A 298 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: A 307 GLU cc_start: 0.8409 (tt0) cc_final: 0.8095 (tt0) REVERT: A 543 LYS cc_start: 0.8375 (ttpp) cc_final: 0.8126 (ttpp) REVERT: A 546 ARG cc_start: 0.8456 (mtt180) cc_final: 0.8211 (mtt90) REVERT: A 548 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7933 (mm-30) REVERT: A 554 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: A 572 LEU cc_start: 0.8831 (mp) cc_final: 0.8577 (mt) REVERT: A 597 MET cc_start: 0.9168 (ttp) cc_final: 0.8919 (tmm) REVERT: A 636 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: A 690 LYS cc_start: 0.8147 (ttpp) cc_final: 0.7712 (ttmm) REVERT: B 193 ASP cc_start: 0.7610 (t70) cc_final: 0.7383 (t0) REVERT: C 68 ASP cc_start: 0.8079 (t0) cc_final: 0.7780 (t0) REVERT: C 102 GLU cc_start: 0.7866 (tt0) cc_final: 0.7493 (tt0) REVERT: C 162 ASP cc_start: 0.7875 (m-30) cc_final: 0.7645 (m-30) REVERT: C 219 ASP cc_start: 0.7724 (m-30) cc_final: 0.7391 (m-30) REVERT: C 223 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7979 (mtpt) REVERT: C 226 ASP cc_start: 0.7429 (m-30) cc_final: 0.7042 (m-30) REVERT: C 227 ASN cc_start: 0.8211 (t0) cc_final: 0.7571 (m-40) REVERT: C 239 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: C 262 MET cc_start: 0.8505 (ttp) cc_final: 0.8281 (ttp) REVERT: C 421 MET cc_start: 0.8618 (mmm) cc_final: 0.8258 (mmt) REVERT: C 510 ASP cc_start: 0.7355 (m-30) cc_final: 0.7148 (m-30) REVERT: C 518 MET cc_start: 0.8433 (mtp) cc_final: 0.8201 (mtp) REVERT: C 554 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7196 (mt-10) REVERT: C 690 LYS cc_start: 0.8252 (ttpp) cc_final: 0.7983 (tttp) REVERT: D 13 ASP cc_start: 0.5745 (p0) cc_final: 0.5475 (m-30) REVERT: D 37 GLU cc_start: 0.6606 (mm-30) cc_final: 0.5903 (mm-30) REVERT: D 156 THR cc_start: 0.8626 (t) cc_final: 0.8293 (m) REVERT: D 188 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: E 70 ARG cc_start: 0.8671 (mtt180) cc_final: 0.8455 (mtt180) REVERT: E 121 MET cc_start: 0.9065 (tpp) cc_final: 0.8617 (tpt) REVERT: E 211 MET cc_start: 0.8183 (mtp) cc_final: 0.7836 (mtp) REVERT: E 227 ASN cc_start: 0.7948 (t0) cc_final: 0.7462 (m110) REVERT: E 286 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7390 (mp10) REVERT: E 445 MET cc_start: 0.8131 (mtp) cc_final: 0.7835 (mtt) REVERT: E 546 ARG cc_start: 0.8390 (mtt180) cc_final: 0.8164 (mtm180) REVERT: E 572 LEU cc_start: 0.8955 (mp) cc_final: 0.8586 (mt) REVERT: E 592 MET cc_start: 0.9019 (ttt) cc_final: 0.8709 (ttt) REVERT: E 594 MET cc_start: 0.8499 (tpt) cc_final: 0.8208 (tpt) REVERT: E 673 MET cc_start: 0.8899 (ttt) cc_final: 0.8444 (ttp) REVERT: F 77 LEU cc_start: 0.5759 (OUTLIER) cc_final: 0.5348 (mm) REVERT: I 69 GLU cc_start: 0.7499 (tt0) cc_final: 0.7097 (tt0) REVERT: I 219 ASP cc_start: 0.7677 (m-30) cc_final: 0.7405 (m-30) REVERT: I 227 ASN cc_start: 0.7947 (t0) cc_final: 0.7423 (m-40) REVERT: I 285 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7196 (pp20) REVERT: I 286 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7155 (mp10) REVERT: I 338 LYS cc_start: 0.8602 (mttp) cc_final: 0.8342 (mtmt) REVERT: I 372 LYS cc_start: 0.8262 (tttm) cc_final: 0.8004 (tttp) REVERT: I 374 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8245 (mt) REVERT: I 378 MET cc_start: 0.8357 (ttm) cc_final: 0.7977 (ttp) REVERT: I 518 MET cc_start: 0.8663 (mtp) cc_final: 0.8369 (mtp) REVERT: I 546 ARG cc_start: 0.8520 (mtt180) cc_final: 0.8280 (mtt180) REVERT: I 607 THR cc_start: 0.9261 (t) cc_final: 0.8920 (m) REVERT: I 636 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: J 1 MET cc_start: 0.3946 (OUTLIER) cc_final: 0.2720 (tmm) REVERT: J 36 THR cc_start: 0.7909 (m) cc_final: 0.7500 (p) REVERT: J 88 LYS cc_start: 0.8424 (ttpp) cc_final: 0.8197 (tttt) REVERT: J 156 THR cc_start: 0.8713 (t) cc_final: 0.8261 (p) REVERT: J 219 ASP cc_start: 0.7768 (m-30) cc_final: 0.7486 (m-30) REVERT: K 85 GLU cc_start: 0.7526 (pt0) cc_final: 0.7249 (pt0) REVERT: K 119 ASP cc_start: 0.7956 (t70) cc_final: 0.7670 (t70) REVERT: K 211 MET cc_start: 0.8212 (mtp) cc_final: 0.7981 (mtm) REVERT: K 219 ASP cc_start: 0.7648 (m-30) cc_final: 0.7322 (m-30) REVERT: K 227 ASN cc_start: 0.7791 (t0) cc_final: 0.7388 (m-40) REVERT: K 239 GLN cc_start: 0.8606 (tt0) cc_final: 0.8325 (tt0) REVERT: K 372 LYS cc_start: 0.8510 (tttm) cc_final: 0.8270 (tttp) REVERT: K 445 MET cc_start: 0.8236 (mtp) cc_final: 0.7998 (mtp) REVERT: K 543 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7929 (ttpp) REVERT: K 554 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7013 (mt-10) REVERT: K 625 MET cc_start: 0.8393 (mtp) cc_final: 0.8131 (mtp) REVERT: K 690 LYS cc_start: 0.8324 (ttpp) cc_final: 0.8046 (tttp) REVERT: L 1 MET cc_start: 0.4988 (mtm) cc_final: 0.4319 (ppp) REVERT: L 13 ASP cc_start: 0.6230 (p0) cc_final: 0.5976 (m-30) REVERT: L 30 LEU cc_start: 0.7974 (tp) cc_final: 0.7685 (tp) REVERT: L 54 MET cc_start: 0.7117 (mmt) cc_final: 0.6542 (mpt) REVERT: L 188 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7064 (mp0) outliers start: 109 outliers final: 49 residues processed: 759 average time/residue: 1.6701 time to fit residues: 1521.8342 Evaluate side-chains 753 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 683 time to evaluate : 4.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 286 GLN Chi-restraints excluded: chain H residue 368 LYS Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 520 MET Chi-restraints excluded: chain H residue 523 LYS Chi-restraints excluded: chain H residue 539 VAL Chi-restraints excluded: chain H residue 684 ASP Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 164 GLN Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 285 GLU Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 523 LYS Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 636 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 298 GLN Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain K residue 554 GLU Chi-restraints excluded: chain K residue 694 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 188 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 469 optimal weight: 0.8980 chunk 357 optimal weight: 5.9990 chunk 246 optimal weight: 30.0000 chunk 52 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 chunk 476 optimal weight: 0.7980 chunk 504 optimal weight: 0.0040 chunk 248 optimal weight: 9.9990 chunk 451 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 451 GLN H 695 ASN G 109 ASN A 95 GLN A 695 ASN C 88 ASN C 164 GLN C 191 GLN C 246 GLN C 308 GLN D 141 ASN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 191 GLN I 191 GLN I 308 GLN ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 GLN K 629 ASN K 695 ASN L 184 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 41988 Z= 0.156 Angle : 0.442 8.056 56574 Z= 0.233 Chirality : 0.038 0.178 6078 Planarity : 0.003 0.038 7560 Dihedral : 4.272 155.167 5715 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.30 % Allowed : 10.95 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.12), residues: 5244 helix: 2.29 (0.08), residues: 3720 sheet: 1.36 (0.48), residues: 90 loop : -0.78 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 366 HIS 0.002 0.001 HIS F 178 PHE 0.008 0.001 PHE A 404 TYR 0.012 0.001 TYR C 508 ARG 0.002 0.000 ARG E 497 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 718 time to evaluate : 4.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 69 GLU cc_start: 0.7350 (tt0) cc_final: 0.6996 (tt0) REVERT: H 152 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7400 (pt0) REVERT: H 161 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8310 (m) REVERT: H 211 MET cc_start: 0.8195 (mtp) cc_final: 0.7897 (mtp) REVERT: H 266 ASP cc_start: 0.8064 (m-30) cc_final: 0.7764 (m-30) REVERT: H 286 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7381 (mp10) REVERT: H 328 MET cc_start: 0.8828 (mtp) cc_final: 0.8531 (mtp) REVERT: H 520 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7897 (tpp) REVERT: H 644 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: H 690 LYS cc_start: 0.8229 (ttpp) cc_final: 0.7875 (ttmm) REVERT: H 694 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6655 (mt-10) REVERT: G 88 LYS cc_start: 0.8052 (ttmt) cc_final: 0.7810 (ttpt) REVERT: G 219 ASP cc_start: 0.7698 (m-30) cc_final: 0.7388 (m-30) REVERT: A 102 GLU cc_start: 0.7663 (tt0) cc_final: 0.7321 (tt0) REVERT: A 119 ASP cc_start: 0.8234 (t0) cc_final: 0.8016 (t0) REVERT: A 207 GLN cc_start: 0.8625 (tt0) cc_final: 0.8318 (tt0) REVERT: A 239 GLN cc_start: 0.8689 (tt0) cc_final: 0.8408 (tt0) REVERT: A 307 GLU cc_start: 0.8382 (tt0) cc_final: 0.8084 (tt0) REVERT: A 451 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7313 (tp40) REVERT: A 490 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8535 (mtp) REVERT: A 543 LYS cc_start: 0.8319 (ttpp) cc_final: 0.8034 (ttpp) REVERT: A 546 ARG cc_start: 0.8427 (mtt180) cc_final: 0.8169 (mtt90) REVERT: A 554 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: A 572 LEU cc_start: 0.8802 (mp) cc_final: 0.8559 (mt) REVERT: A 597 MET cc_start: 0.9150 (ttp) cc_final: 0.8905 (tmm) REVERT: A 636 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: A 690 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7706 (ttmm) REVERT: B 1 MET cc_start: 0.5757 (ppp) cc_final: 0.4651 (mpp) REVERT: C 68 ASP cc_start: 0.7974 (t0) cc_final: 0.7752 (t70) REVERT: C 102 GLU cc_start: 0.7787 (tt0) cc_final: 0.7450 (tt0) REVERT: C 162 ASP cc_start: 0.7823 (m-30) cc_final: 0.7580 (m-30) REVERT: C 164 GLN cc_start: 0.8145 (mt0) cc_final: 0.7927 (mm110) REVERT: C 219 ASP cc_start: 0.7689 (m-30) cc_final: 0.7351 (m-30) REVERT: C 223 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7920 (mtpt) REVERT: C 226 ASP cc_start: 0.7507 (m-30) cc_final: 0.7131 (m-30) REVERT: C 227 ASN cc_start: 0.8208 (t0) cc_final: 0.7563 (m-40) REVERT: C 239 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: C 392 GLN cc_start: 0.8054 (tp-100) cc_final: 0.7852 (tp40) REVERT: C 421 MET cc_start: 0.8704 (mmm) cc_final: 0.8234 (mmt) REVERT: C 451 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7353 (tp40) REVERT: C 510 ASP cc_start: 0.7332 (m-30) cc_final: 0.7091 (m-30) REVERT: C 518 MET cc_start: 0.8393 (mtp) cc_final: 0.8159 (mtp) REVERT: C 550 ASP cc_start: 0.7990 (m-30) cc_final: 0.7587 (m-30) REVERT: C 554 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7218 (mt-10) REVERT: C 690 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7950 (tttp) REVERT: D 37 GLU cc_start: 0.6637 (mm-30) cc_final: 0.5988 (mm-30) REVERT: D 53 MET cc_start: 0.4162 (tpp) cc_final: 0.2849 (mtp) REVERT: E 70 ARG cc_start: 0.8605 (mtt180) cc_final: 0.8398 (mtt180) REVERT: E 121 MET cc_start: 0.9082 (tpp) cc_final: 0.8631 (tpp) REVERT: E 211 MET cc_start: 0.8098 (mtp) cc_final: 0.7782 (mtp) REVERT: E 227 ASN cc_start: 0.7949 (t0) cc_final: 0.7449 (m110) REVERT: E 286 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7314 (mp10) REVERT: E 445 MET cc_start: 0.8143 (mtp) cc_final: 0.7837 (mtt) REVERT: E 546 ARG cc_start: 0.8359 (mtt180) cc_final: 0.8142 (mtm180) REVERT: E 592 MET cc_start: 0.8984 (ttt) cc_final: 0.8690 (ttt) REVERT: E 594 MET cc_start: 0.8504 (tpt) cc_final: 0.8260 (tpt) REVERT: E 673 MET cc_start: 0.8889 (ttt) cc_final: 0.8337 (ttt) REVERT: F 77 LEU cc_start: 0.5634 (OUTLIER) cc_final: 0.5249 (mm) REVERT: F 180 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7645 (mm110) REVERT: F 198 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6626 (tp30) REVERT: I 188 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7959 (tm-30) REVERT: I 219 ASP cc_start: 0.7638 (m-30) cc_final: 0.7363 (m-30) REVERT: I 227 ASN cc_start: 0.7936 (t0) cc_final: 0.7369 (m-40) REVERT: I 230 VAL cc_start: 0.8801 (t) cc_final: 0.8553 (p) REVERT: I 286 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7280 (mp10) REVERT: I 338 LYS cc_start: 0.8538 (mttp) cc_final: 0.8271 (mtmt) REVERT: I 372 LYS cc_start: 0.8225 (tttm) cc_final: 0.7995 (tttp) REVERT: I 374 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8268 (mt) REVERT: I 378 MET cc_start: 0.8309 (ttm) cc_final: 0.7997 (ttp) REVERT: I 518 MET cc_start: 0.8647 (mtp) cc_final: 0.8341 (mtp) REVERT: I 546 ARG cc_start: 0.8470 (mtt180) cc_final: 0.8189 (mtt180) REVERT: I 607 THR cc_start: 0.9259 (t) cc_final: 0.8935 (m) REVERT: J 1 MET cc_start: 0.4445 (OUTLIER) cc_final: 0.3264 (tmm) REVERT: J 36 THR cc_start: 0.7870 (m) cc_final: 0.7501 (p) REVERT: J 88 LYS cc_start: 0.8432 (ttpp) cc_final: 0.7880 (tmmt) REVERT: J 219 ASP cc_start: 0.7764 (m-30) cc_final: 0.7487 (m-30) REVERT: K 85 GLU cc_start: 0.7526 (pt0) cc_final: 0.7251 (pt0) REVERT: K 119 ASP cc_start: 0.7964 (t70) cc_final: 0.7669 (t70) REVERT: K 211 MET cc_start: 0.8173 (mtp) cc_final: 0.7959 (mtm) REVERT: K 219 ASP cc_start: 0.7629 (m-30) cc_final: 0.7287 (m-30) REVERT: K 227 ASN cc_start: 0.7783 (t0) cc_final: 0.7420 (m-40) REVERT: K 239 GLN cc_start: 0.8547 (tt0) cc_final: 0.8278 (mt0) REVERT: K 286 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7883 (mm-40) REVERT: K 372 LYS cc_start: 0.8484 (tttm) cc_final: 0.8253 (tttp) REVERT: K 445 MET cc_start: 0.8245 (mtp) cc_final: 0.7999 (mtp) REVERT: K 543 LYS cc_start: 0.8229 (ttpp) cc_final: 0.7833 (ttpp) REVERT: K 554 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7005 (mt-10) REVERT: K 690 LYS cc_start: 0.8312 (ttpp) cc_final: 0.8044 (tttp) REVERT: L 1 MET cc_start: 0.5051 (mtm) cc_final: 0.4403 (pp-130) REVERT: L 30 LEU cc_start: 0.7976 (tp) cc_final: 0.7697 (tp) REVERT: L 54 MET cc_start: 0.7157 (mmt) cc_final: 0.6652 (mpt) REVERT: L 141 ASN cc_start: 0.8688 (m-40) cc_final: 0.8464 (m-40) REVERT: L 188 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7016 (mp0) outliers start: 100 outliers final: 35 residues processed: 759 average time/residue: 1.6720 time to fit residues: 1529.1745 Evaluate side-chains 754 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 698 time to evaluate : 4.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 286 GLN Chi-restraints excluded: chain H residue 520 MET Chi-restraints excluded: chain H residue 523 LYS Chi-restraints excluded: chain H residue 644 GLU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 188 GLN Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 510 ASP Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 285 GLU Chi-restraints excluded: chain K residue 298 GLN Chi-restraints excluded: chain K residue 374 LEU Chi-restraints excluded: chain K residue 523 LYS Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain K residue 554 GLU Chi-restraints excluded: chain K residue 694 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 188 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 420 optimal weight: 0.9990 chunk 286 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 375 optimal weight: 2.9990 chunk 208 optimal weight: 0.0770 chunk 430 optimal weight: 0.0470 chunk 348 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 257 optimal weight: 10.0000 chunk 452 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 451 GLN H 695 ASN G 141 ASN A 308 GLN A 695 ASN C 88 ASN C 191 GLN C 246 GLN C 308 GLN D 141 ASN E 95 GLN E 191 GLN E 298 GLN F 184 GLN I 191 GLN I 308 GLN I 410 ASN ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 199 GLN K 246 GLN L 184 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41988 Z= 0.186 Angle : 0.456 8.276 56574 Z= 0.239 Chirality : 0.038 0.186 6078 Planarity : 0.004 0.038 7560 Dihedral : 4.284 152.344 5715 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.48 % Allowed : 11.59 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.12), residues: 5244 helix: 2.32 (0.08), residues: 3720 sheet: 1.42 (0.49), residues: 90 loop : -0.78 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 366 HIS 0.003 0.001 HIS L 178 PHE 0.011 0.001 PHE A 404 TYR 0.013 0.001 TYR E 424 ARG 0.005 0.000 ARG E 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 704 time to evaluate : 5.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 69 GLU cc_start: 0.7371 (tt0) cc_final: 0.7009 (tt0) REVERT: H 152 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7364 (pt0) REVERT: H 201 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7328 (tm-30) REVERT: H 211 MET cc_start: 0.8222 (mtp) cc_final: 0.7932 (mtp) REVERT: H 266 ASP cc_start: 0.8036 (m-30) cc_final: 0.7747 (m-30) REVERT: H 286 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7467 (mp10) REVERT: H 328 MET cc_start: 0.8822 (mtp) cc_final: 0.8520 (mtp) REVERT: H 520 MET cc_start: 0.8094 (ttp) cc_final: 0.7840 (tpp) REVERT: H 636 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: H 684 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7233 (p0) REVERT: H 690 LYS cc_start: 0.8284 (ttpp) cc_final: 0.7921 (ttmm) REVERT: H 694 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6655 (mt-10) REVERT: G 54 MET cc_start: 0.6866 (mpt) cc_final: 0.6322 (mpm) REVERT: G 88 LYS cc_start: 0.8029 (ttmt) cc_final: 0.7777 (ttpt) REVERT: G 219 ASP cc_start: 0.7847 (m-30) cc_final: 0.7564 (m-30) REVERT: A 102 GLU cc_start: 0.7711 (tt0) cc_final: 0.7374 (tt0) REVERT: A 119 ASP cc_start: 0.8267 (t0) cc_final: 0.8052 (t0) REVERT: A 207 GLN cc_start: 0.8625 (tt0) cc_final: 0.8311 (tt0) REVERT: A 298 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7626 (mp10) REVERT: A 307 GLU cc_start: 0.8405 (tt0) cc_final: 0.8095 (tt0) REVERT: A 451 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7284 (tp40) REVERT: A 490 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8544 (mtp) REVERT: A 543 LYS cc_start: 0.8285 (ttpp) cc_final: 0.8049 (ttpp) REVERT: A 546 ARG cc_start: 0.8428 (mtt180) cc_final: 0.8092 (mtt90) REVERT: A 554 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: A 572 LEU cc_start: 0.8896 (mp) cc_final: 0.8658 (mt) REVERT: A 597 MET cc_start: 0.9163 (ttp) cc_final: 0.8921 (tmm) REVERT: A 690 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7758 (ttmm) REVERT: C 68 ASP cc_start: 0.8017 (t0) cc_final: 0.7720 (t0) REVERT: C 102 GLU cc_start: 0.7853 (tt0) cc_final: 0.7518 (tt0) REVERT: C 162 ASP cc_start: 0.7878 (m-30) cc_final: 0.7602 (m-30) REVERT: C 164 GLN cc_start: 0.8218 (mt0) cc_final: 0.7998 (mm110) REVERT: C 219 ASP cc_start: 0.7710 (m-30) cc_final: 0.7365 (m-30) REVERT: C 223 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7935 (mtpt) REVERT: C 226 ASP cc_start: 0.7413 (m-30) cc_final: 0.7024 (m-30) REVERT: C 227 ASN cc_start: 0.8185 (t0) cc_final: 0.7566 (m-40) REVERT: C 239 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: C 421 MET cc_start: 0.8721 (mmm) cc_final: 0.8269 (mmt) REVERT: C 451 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7358 (tp40) REVERT: C 510 ASP cc_start: 0.7336 (m-30) cc_final: 0.7116 (m-30) REVERT: C 518 MET cc_start: 0.8388 (mtp) cc_final: 0.8134 (mtp) REVERT: C 550 ASP cc_start: 0.8002 (m-30) cc_final: 0.7592 (m-30) REVERT: C 554 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7156 (mt-10) REVERT: C 690 LYS cc_start: 0.8227 (ttpp) cc_final: 0.7961 (tttp) REVERT: D 37 GLU cc_start: 0.6647 (mm-30) cc_final: 0.5975 (mm-30) REVERT: D 53 MET cc_start: 0.4185 (tpp) cc_final: 0.2874 (mtp) REVERT: D 54 MET cc_start: 0.7325 (mmt) cc_final: 0.6762 (mmp) REVERT: D 88 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7695 (ttmt) REVERT: D 156 THR cc_start: 0.8569 (t) cc_final: 0.8251 (m) REVERT: D 180 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8322 (mm-40) REVERT: E 121 MET cc_start: 0.9071 (tpp) cc_final: 0.8614 (tpt) REVERT: E 211 MET cc_start: 0.8139 (mtp) cc_final: 0.7801 (mtp) REVERT: E 227 ASN cc_start: 0.7926 (t0) cc_final: 0.7428 (m110) REVERT: E 286 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: E 445 MET cc_start: 0.8132 (mtp) cc_final: 0.7840 (mtt) REVERT: E 592 MET cc_start: 0.9003 (ttt) cc_final: 0.8701 (ttt) REVERT: E 594 MET cc_start: 0.8538 (tpt) cc_final: 0.8279 (tpt) REVERT: E 673 MET cc_start: 0.8888 (ttt) cc_final: 0.8462 (ttp) REVERT: F 77 LEU cc_start: 0.5609 (OUTLIER) cc_final: 0.5234 (mm) REVERT: F 156 THR cc_start: 0.8680 (t) cc_final: 0.8443 (m) REVERT: F 180 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7695 (mm110) REVERT: F 198 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6601 (tp30) REVERT: I 188 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7941 (tm-30) REVERT: I 219 ASP cc_start: 0.7651 (m-30) cc_final: 0.7372 (m-30) REVERT: I 227 ASN cc_start: 0.7973 (t0) cc_final: 0.7430 (m-40) REVERT: I 286 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7236 (mp10) REVERT: I 338 LYS cc_start: 0.8596 (mttp) cc_final: 0.8319 (mtmt) REVERT: I 368 LYS cc_start: 0.8479 (tttm) cc_final: 0.8263 (tttp) REVERT: I 372 LYS cc_start: 0.8227 (tttm) cc_final: 0.7995 (tttp) REVERT: I 374 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8261 (mt) REVERT: I 378 MET cc_start: 0.8314 (ttm) cc_final: 0.8030 (ttp) REVERT: I 510 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7159 (m-30) REVERT: I 518 MET cc_start: 0.8668 (mtp) cc_final: 0.8359 (mtp) REVERT: I 546 ARG cc_start: 0.8500 (mtt180) cc_final: 0.8127 (mtt180) REVERT: I 607 THR cc_start: 0.9273 (t) cc_final: 0.8929 (m) REVERT: I 636 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: J 1 MET cc_start: 0.4511 (pp-130) cc_final: 0.3011 (tmm) REVERT: J 36 THR cc_start: 0.7879 (m) cc_final: 0.7489 (p) REVERT: J 88 LYS cc_start: 0.8431 (ttpp) cc_final: 0.7892 (tmmt) REVERT: J 156 THR cc_start: 0.8694 (t) cc_final: 0.8252 (p) REVERT: J 219 ASP cc_start: 0.7634 (m-30) cc_final: 0.7399 (m-30) REVERT: K 85 GLU cc_start: 0.7551 (pt0) cc_final: 0.7279 (pt0) REVERT: K 119 ASP cc_start: 0.7995 (t70) cc_final: 0.7700 (t70) REVERT: K 145 GLU cc_start: 0.7283 (pt0) cc_final: 0.6969 (mt-10) REVERT: K 211 MET cc_start: 0.8143 (mtp) cc_final: 0.7928 (mtm) REVERT: K 219 ASP cc_start: 0.7642 (m-30) cc_final: 0.7296 (m-30) REVERT: K 227 ASN cc_start: 0.7796 (t0) cc_final: 0.7419 (m-40) REVERT: K 239 GLN cc_start: 0.8633 (tt0) cc_final: 0.8349 (mt0) REVERT: K 372 LYS cc_start: 0.8497 (tttm) cc_final: 0.8264 (tttp) REVERT: K 445 MET cc_start: 0.8235 (mtp) cc_final: 0.7995 (mtp) REVERT: K 543 LYS cc_start: 0.8235 (ttpp) cc_final: 0.7845 (ttpp) REVERT: K 690 LYS cc_start: 0.8351 (ttpp) cc_final: 0.8104 (tttp) REVERT: L 1 MET cc_start: 0.5176 (mtm) cc_final: 0.4492 (pp-130) REVERT: L 30 LEU cc_start: 0.7919 (tp) cc_final: 0.7638 (tp) REVERT: L 54 MET cc_start: 0.7197 (mmt) cc_final: 0.6715 (mpt) REVERT: L 188 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6955 (mp0) outliers start: 108 outliers final: 46 residues processed: 753 average time/residue: 1.6704 time to fit residues: 1510.4543 Evaluate side-chains 757 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 690 time to evaluate : 4.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 286 GLN Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 539 VAL Chi-restraints excluded: chain H residue 636 GLU Chi-restraints excluded: chain H residue 684 ASP Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 188 GLN Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 510 ASP Chi-restraints excluded: chain I residue 523 LYS Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 636 GLU Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 298 GLN Chi-restraints excluded: chain K residue 368 LYS Chi-restraints excluded: chain K residue 374 LEU Chi-restraints excluded: chain K residue 523 LYS Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain K residue 694 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 188 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 169 optimal weight: 0.2980 chunk 454 optimal weight: 0.0980 chunk 99 optimal weight: 6.9990 chunk 296 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 505 optimal weight: 0.0270 chunk 419 optimal weight: 9.9990 chunk 233 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 265 optimal weight: 6.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 308 GLN H 451 GLN H 695 ASN G 141 ASN G 184 GLN A 95 GLN A 188 GLN A 239 GLN A 308 GLN A 695 ASN C 88 ASN C 191 GLN C 246 GLN C 308 GLN D 141 ASN D 153 GLN E 95 GLN E 191 GLN E 308 GLN F 141 ASN I 191 GLN I 246 GLN I 308 GLN I 392 GLN I 410 ASN ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 GLN K 695 ASN L 184 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 41988 Z= 0.124 Angle : 0.417 7.922 56574 Z= 0.218 Chirality : 0.037 0.203 6078 Planarity : 0.003 0.036 7560 Dihedral : 4.055 156.342 5715 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.81 % Allowed : 13.18 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.12), residues: 5244 helix: 2.50 (0.08), residues: 3726 sheet: 1.50 (0.49), residues: 90 loop : -0.64 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 366 HIS 0.002 0.000 HIS B 178 PHE 0.005 0.001 PHE F 16 TYR 0.011 0.001 TYR L 123 ARG 0.006 0.000 ARG K 541 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 724 time to evaluate : 4.204 Fit side-chains revert: symmetry clash REVERT: H 69 GLU cc_start: 0.7229 (tt0) cc_final: 0.6889 (tt0) REVERT: H 201 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7241 (tm-30) REVERT: H 211 MET cc_start: 0.8179 (mtp) cc_final: 0.7919 (mtp) REVERT: H 266 ASP cc_start: 0.7956 (m-30) cc_final: 0.7642 (m-30) REVERT: H 328 MET cc_start: 0.8815 (mtp) cc_final: 0.8502 (mtp) REVERT: H 520 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7840 (tpp) REVERT: H 636 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: H 644 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: H 690 LYS cc_start: 0.8252 (ttpp) cc_final: 0.7894 (ttmm) REVERT: H 694 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6636 (mt-10) REVERT: G 36 THR cc_start: 0.7772 (m) cc_final: 0.7407 (p) REVERT: G 54 MET cc_start: 0.6972 (mpt) cc_final: 0.6439 (mpm) REVERT: G 88 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7836 (ttpt) REVERT: G 130 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.8189 (m) REVERT: G 141 ASN cc_start: 0.8409 (m-40) cc_final: 0.8202 (m-40) REVERT: G 209 ASP cc_start: 0.8028 (t0) cc_final: 0.7376 (t0) REVERT: G 219 ASP cc_start: 0.7748 (m-30) cc_final: 0.7517 (m-30) REVERT: A 102 GLU cc_start: 0.7603 (tt0) cc_final: 0.7288 (tt0) REVERT: A 119 ASP cc_start: 0.8210 (t0) cc_final: 0.7988 (t0) REVERT: A 164 GLN cc_start: 0.8079 (mt0) cc_final: 0.7794 (mm110) REVERT: A 207 GLN cc_start: 0.8608 (tt0) cc_final: 0.8309 (tt0) REVERT: A 307 GLU cc_start: 0.8368 (tt0) cc_final: 0.8084 (tt0) REVERT: A 451 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7276 (tp40) REVERT: A 466 MET cc_start: 0.8999 (ttm) cc_final: 0.8771 (ttp) REVERT: A 490 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8497 (mtp) REVERT: A 543 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7933 (ttpp) REVERT: A 546 ARG cc_start: 0.8388 (mtt180) cc_final: 0.7866 (mtt90) REVERT: A 550 ASP cc_start: 0.7943 (m-30) cc_final: 0.7725 (m-30) REVERT: A 554 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: A 597 MET cc_start: 0.9128 (ttp) cc_final: 0.8829 (tmm) REVERT: A 690 LYS cc_start: 0.8151 (ttpp) cc_final: 0.7678 (ttmm) REVERT: B 1 MET cc_start: 0.5541 (ppp) cc_final: 0.4641 (mpp) REVERT: B 216 GLU cc_start: 0.7949 (pt0) cc_final: 0.7739 (pt0) REVERT: C 102 GLU cc_start: 0.7796 (tt0) cc_final: 0.7491 (tt0) REVERT: C 121 MET cc_start: 0.8932 (tpp) cc_final: 0.8440 (tpt) REVERT: C 162 ASP cc_start: 0.7845 (m-30) cc_final: 0.7583 (m-30) REVERT: C 219 ASP cc_start: 0.7659 (m-30) cc_final: 0.7334 (m-30) REVERT: C 226 ASP cc_start: 0.7473 (m-30) cc_final: 0.7097 (m-30) REVERT: C 227 ASN cc_start: 0.8151 (t0) cc_final: 0.7548 (m-40) REVERT: C 421 MET cc_start: 0.8713 (mmm) cc_final: 0.8190 (mmt) REVERT: C 510 ASP cc_start: 0.7334 (m-30) cc_final: 0.7126 (m-30) REVERT: C 550 ASP cc_start: 0.8004 (m-30) cc_final: 0.7613 (m-30) REVERT: C 554 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7143 (mt-10) REVERT: C 690 LYS cc_start: 0.8227 (ttpp) cc_final: 0.7928 (tttp) REVERT: D 53 MET cc_start: 0.4276 (tpp) cc_final: 0.3002 (mtp) REVERT: D 54 MET cc_start: 0.7341 (mmt) cc_final: 0.6849 (mmp) REVERT: E 121 MET cc_start: 0.9056 (tpp) cc_final: 0.8622 (tpt) REVERT: E 211 MET cc_start: 0.8009 (mtp) cc_final: 0.7714 (mtp) REVERT: E 227 ASN cc_start: 0.7945 (t0) cc_final: 0.7467 (m110) REVERT: E 286 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: E 445 MET cc_start: 0.8139 (mtp) cc_final: 0.7815 (mtt) REVERT: E 673 MET cc_start: 0.8851 (ttt) cc_final: 0.8314 (ttp) REVERT: F 198 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6579 (tp30) REVERT: I 219 ASP cc_start: 0.7644 (m-30) cc_final: 0.7332 (m-30) REVERT: I 227 ASN cc_start: 0.7928 (t0) cc_final: 0.7418 (m-40) REVERT: I 286 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7087 (mp10) REVERT: I 338 LYS cc_start: 0.8485 (mttp) cc_final: 0.8233 (mtmt) REVERT: I 368 LYS cc_start: 0.8435 (tttm) cc_final: 0.8205 (tttm) REVERT: I 372 LYS cc_start: 0.8192 (tttm) cc_final: 0.7980 (tttp) REVERT: I 374 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8246 (OUTLIER) REVERT: I 378 MET cc_start: 0.8219 (ttm) cc_final: 0.7908 (ttp) REVERT: I 518 MET cc_start: 0.8604 (mtp) cc_final: 0.8320 (mtp) REVERT: I 546 ARG cc_start: 0.8432 (mtt180) cc_final: 0.8151 (mtt180) REVERT: I 607 THR cc_start: 0.9229 (t) cc_final: 0.8882 (m) REVERT: I 636 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: J 1 MET cc_start: 0.4343 (OUTLIER) cc_final: 0.3018 (tmm) REVERT: J 36 THR cc_start: 0.7906 (m) cc_final: 0.7503 (p) REVERT: J 88 LYS cc_start: 0.8433 (ttpp) cc_final: 0.7880 (tmmt) REVERT: J 127 ASP cc_start: 0.7106 (t70) cc_final: 0.6799 (t0) REVERT: J 180 GLN cc_start: 0.7705 (mm110) cc_final: 0.7395 (mm110) REVERT: J 219 ASP cc_start: 0.7600 (m-30) cc_final: 0.7360 (m-30) REVERT: K 85 GLU cc_start: 0.7526 (pt0) cc_final: 0.7257 (pt0) REVERT: K 119 ASP cc_start: 0.7956 (t70) cc_final: 0.7658 (t70) REVERT: K 145 GLU cc_start: 0.7154 (pt0) cc_final: 0.6872 (mt-10) REVERT: K 219 ASP cc_start: 0.7650 (m-30) cc_final: 0.7309 (m-30) REVERT: K 227 ASN cc_start: 0.7773 (t0) cc_final: 0.7427 (m-40) REVERT: K 239 GLN cc_start: 0.8555 (tt0) cc_final: 0.8311 (mt0) REVERT: K 372 LYS cc_start: 0.8470 (tttm) cc_final: 0.8238 (tttp) REVERT: K 445 MET cc_start: 0.8241 (mtp) cc_final: 0.7991 (mtp) REVERT: K 543 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7834 (ttpp) REVERT: K 690 LYS cc_start: 0.8375 (ttpp) cc_final: 0.8138 (tttp) REVERT: L 1 MET cc_start: 0.5105 (mtm) cc_final: 0.4525 (pp-130) REVERT: L 30 LEU cc_start: 0.7918 (tp) cc_final: 0.7638 (tp) REVERT: L 54 MET cc_start: 0.7203 (mmt) cc_final: 0.6733 (mpt) REVERT: L 180 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7677 (mm110) REVERT: L 188 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6854 (mp0) outliers start: 79 outliers final: 24 residues processed: 760 average time/residue: 1.6188 time to fit residues: 1483.1873 Evaluate side-chains 732 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 695 time to evaluate : 4.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 520 MET Chi-restraints excluded: chain H residue 636 GLU Chi-restraints excluded: chain H residue 644 GLU Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 510 ASP Chi-restraints excluded: chain I residue 636 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 374 LEU Chi-restraints excluded: chain K residue 523 LYS Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 188 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 486 optimal weight: 3.9990 chunk 56 optimal weight: 0.1980 chunk 287 optimal weight: 0.6980 chunk 368 optimal weight: 5.9990 chunk 285 optimal weight: 4.9990 chunk 425 optimal weight: 7.9990 chunk 282 optimal weight: 2.9990 chunk 503 optimal weight: 7.9990 chunk 314 optimal weight: 7.9990 chunk 306 optimal weight: 0.9980 chunk 232 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 392 GLN H 410 ASN H 451 GLN H 695 ASN G 199 GLN A 308 GLN A 695 ASN C 88 ASN C 191 GLN C 246 GLN C 308 GLN C 358 GLN C 392 GLN D 137 ASN D 153 GLN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 191 GLN E 308 GLN E 364 ASN E 629 ASN F 141 ASN I 308 GLN I 410 ASN I 624 ASN ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 GLN K 695 ASN L 178 HIS L 184 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41988 Z= 0.243 Angle : 0.494 9.298 56574 Z= 0.259 Chirality : 0.040 0.212 6078 Planarity : 0.004 0.041 7560 Dihedral : 3.815 20.966 5712 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.07 % Allowed : 13.38 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.12), residues: 5244 helix: 2.33 (0.08), residues: 3732 sheet: 1.43 (0.50), residues: 90 loop : -0.74 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 366 HIS 0.003 0.001 HIS J 178 PHE 0.013 0.001 PHE A 404 TYR 0.018 0.002 TYR L 123 ARG 0.005 0.000 ARG K 541 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 709 time to evaluate : 4.734 Fit side-chains revert: symmetry clash REVERT: H 201 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7238 (tm-30) REVERT: H 266 ASP cc_start: 0.8076 (m-30) cc_final: 0.7787 (m-30) REVERT: H 286 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: H 328 MET cc_start: 0.8822 (mtp) cc_final: 0.8540 (mtp) REVERT: H 636 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: H 644 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: H 684 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7263 (p0) REVERT: H 690 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7933 (ttmm) REVERT: H 694 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6612 (mt-10) REVERT: G 54 MET cc_start: 0.7094 (mpt) cc_final: 0.6707 (mpm) REVERT: G 88 LYS cc_start: 0.8044 (ttmt) cc_final: 0.7810 (ttpt) REVERT: A 102 GLU cc_start: 0.7752 (tt0) cc_final: 0.7449 (tt0) REVERT: A 207 GLN cc_start: 0.8629 (tt0) cc_final: 0.8313 (tt0) REVERT: A 298 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7670 (mp10) REVERT: A 307 GLU cc_start: 0.8428 (tt0) cc_final: 0.8113 (tt0) REVERT: A 451 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7322 (tp40) REVERT: A 490 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8565 (mtp) REVERT: A 543 LYS cc_start: 0.8325 (ttpp) cc_final: 0.8079 (ttpp) REVERT: A 546 ARG cc_start: 0.8453 (mtt180) cc_final: 0.8164 (mtt90) REVERT: A 554 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: A 572 LEU cc_start: 0.8933 (mp) cc_final: 0.8693 (mt) REVERT: A 597 MET cc_start: 0.9176 (ttp) cc_final: 0.8957 (tmm) REVERT: A 636 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: A 690 LYS cc_start: 0.8215 (ttpp) cc_final: 0.7754 (ttmm) REVERT: C 68 ASP cc_start: 0.8094 (t0) cc_final: 0.7865 (t0) REVERT: C 102 GLU cc_start: 0.7860 (tt0) cc_final: 0.7533 (tt0) REVERT: C 152 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: C 162 ASP cc_start: 0.7888 (m-30) cc_final: 0.7628 (m-30) REVERT: C 219 ASP cc_start: 0.7753 (m-30) cc_final: 0.7420 (m-30) REVERT: C 226 ASP cc_start: 0.7416 (m-30) cc_final: 0.7015 (m-30) REVERT: C 227 ASN cc_start: 0.8210 (t0) cc_final: 0.7583 (m-40) REVERT: C 421 MET cc_start: 0.8629 (mmm) cc_final: 0.8251 (mmt) REVERT: C 510 ASP cc_start: 0.7275 (m-30) cc_final: 0.7066 (m-30) REVERT: C 550 ASP cc_start: 0.8034 (m-30) cc_final: 0.7618 (m-30) REVERT: C 554 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: C 663 MET cc_start: 0.8408 (mtp) cc_final: 0.7841 (mtt) REVERT: C 690 LYS cc_start: 0.8234 (ttpp) cc_final: 0.7965 (tttp) REVERT: D 53 MET cc_start: 0.4500 (tpp) cc_final: 0.3246 (mtp) REVERT: D 54 MET cc_start: 0.7296 (mmt) cc_final: 0.6748 (mmp) REVERT: D 88 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7753 (ttmt) REVERT: D 156 THR cc_start: 0.8540 (t) cc_final: 0.8224 (m) REVERT: E 121 MET cc_start: 0.9081 (tpp) cc_final: 0.8616 (tpt) REVERT: E 211 MET cc_start: 0.8163 (mtp) cc_final: 0.7823 (mtp) REVERT: E 227 ASN cc_start: 0.7848 (t0) cc_final: 0.7361 (m110) REVERT: E 286 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7372 (mp10) REVERT: E 445 MET cc_start: 0.8148 (mtp) cc_final: 0.7872 (mtt) REVERT: E 572 LEU cc_start: 0.8962 (mp) cc_final: 0.8595 (mt) REVERT: E 592 MET cc_start: 0.9011 (ttt) cc_final: 0.8629 (ttt) REVERT: E 673 MET cc_start: 0.8885 (ttt) cc_final: 0.8437 (ttp) REVERT: F 156 THR cc_start: 0.8674 (t) cc_final: 0.8434 (m) REVERT: I 219 ASP cc_start: 0.7694 (m-30) cc_final: 0.7405 (m-30) REVERT: I 227 ASN cc_start: 0.7984 (t0) cc_final: 0.7424 (m-40) REVERT: I 286 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7361 (mp10) REVERT: I 338 LYS cc_start: 0.8593 (mttp) cc_final: 0.8343 (mtmt) REVERT: I 372 LYS cc_start: 0.8267 (tttm) cc_final: 0.8006 (tttp) REVERT: I 374 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8288 (mt) REVERT: I 378 MET cc_start: 0.8324 (ttm) cc_final: 0.7994 (ttp) REVERT: I 510 ASP cc_start: 0.7438 (m-30) cc_final: 0.7155 (m-30) REVERT: I 518 MET cc_start: 0.8687 (mtp) cc_final: 0.8368 (mtp) REVERT: I 546 ARG cc_start: 0.8497 (mtt180) cc_final: 0.8220 (mtt180) REVERT: I 607 THR cc_start: 0.9280 (t) cc_final: 0.8926 (m) REVERT: I 636 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: J 1 MET cc_start: 0.4743 (OUTLIER) cc_final: 0.2976 (tmm) REVERT: J 88 LYS cc_start: 0.8443 (ttpp) cc_final: 0.7885 (tmmt) REVERT: J 156 THR cc_start: 0.8691 (t) cc_final: 0.8274 (p) REVERT: J 219 ASP cc_start: 0.7546 (m-30) cc_final: 0.7302 (m-30) REVERT: K 85 GLU cc_start: 0.7529 (pt0) cc_final: 0.7266 (pt0) REVERT: K 119 ASP cc_start: 0.8015 (t70) cc_final: 0.7717 (t70) REVERT: K 145 GLU cc_start: 0.7283 (pt0) cc_final: 0.7019 (mt-10) REVERT: K 219 ASP cc_start: 0.7625 (m-30) cc_final: 0.7306 (m-30) REVERT: K 227 ASN cc_start: 0.7811 (t0) cc_final: 0.7416 (m-40) REVERT: K 239 GLN cc_start: 0.8678 (tt0) cc_final: 0.8403 (mt0) REVERT: K 372 LYS cc_start: 0.8480 (tttm) cc_final: 0.8245 (tttp) REVERT: K 445 MET cc_start: 0.8234 (mtp) cc_final: 0.7585 (mtt) REVERT: K 543 LYS cc_start: 0.8342 (ttpp) cc_final: 0.7972 (ttpp) REVERT: K 690 LYS cc_start: 0.8321 (ttpp) cc_final: 0.8100 (tttp) REVERT: L 1 MET cc_start: 0.5225 (mtm) cc_final: 0.4440 (pp-130) REVERT: L 11 ASP cc_start: 0.4932 (p0) cc_final: 0.4173 (p0) REVERT: L 30 LEU cc_start: 0.7960 (tp) cc_final: 0.7679 (tp) REVERT: L 54 MET cc_start: 0.7231 (mmt) cc_final: 0.6692 (mpt) outliers start: 90 outliers final: 41 residues processed: 746 average time/residue: 1.6777 time to fit residues: 1509.6245 Evaluate side-chains 747 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 689 time to evaluate : 5.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 286 GLN Chi-restraints excluded: chain H residue 609 THR Chi-restraints excluded: chain H residue 636 GLU Chi-restraints excluded: chain H residue 644 GLU Chi-restraints excluded: chain H residue 684 ASP Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 523 LYS Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 609 THR Chi-restraints excluded: chain I residue 636 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 298 GLN Chi-restraints excluded: chain K residue 368 LYS Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain K residue 609 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 127 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 311 optimal weight: 0.6980 chunk 200 optimal weight: 6.9990 chunk 300 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 319 optimal weight: 2.9990 chunk 342 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 395 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 308 GLN H 451 GLN H 695 ASN G 141 ASN A 95 GLN A 695 ASN C 88 ASN C 191 GLN C 246 GLN E 95 GLN E 191 GLN E 629 ASN F 141 ASN I 624 ASN ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 GLN K 695 ASN L 184 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41988 Z= 0.257 Angle : 0.504 10.522 56574 Z= 0.263 Chirality : 0.040 0.227 6078 Planarity : 0.004 0.043 7560 Dihedral : 3.904 22.125 5712 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.13 % Allowed : 13.75 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.12), residues: 5244 helix: 2.24 (0.08), residues: 3726 sheet: 1.53 (0.50), residues: 90 loop : -0.83 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 366 HIS 0.003 0.001 HIS A 140 PHE 0.013 0.001 PHE A 404 TYR 0.016 0.002 TYR E 424 ARG 0.006 0.000 ARG K 541 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 688 time to evaluate : 4.671 Fit side-chains revert: symmetry clash REVERT: H 201 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7357 (tm-30) REVERT: H 266 ASP cc_start: 0.8041 (m-30) cc_final: 0.7758 (m-30) REVERT: H 286 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: H 328 MET cc_start: 0.8823 (mtp) cc_final: 0.8545 (mtp) REVERT: H 636 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: H 644 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: H 684 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7321 (p0) REVERT: H 690 LYS cc_start: 0.8353 (ttpp) cc_final: 0.7956 (ttmm) REVERT: H 694 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6650 (mt-10) REVERT: G 54 MET cc_start: 0.7171 (mpt) cc_final: 0.6812 (mpm) REVERT: G 88 LYS cc_start: 0.8081 (ttmt) cc_final: 0.7831 (ttpt) REVERT: A 102 GLU cc_start: 0.7852 (tt0) cc_final: 0.7533 (tt0) REVERT: A 207 GLN cc_start: 0.8637 (tt0) cc_final: 0.8322 (tt0) REVERT: A 298 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7675 (mp10) REVERT: A 307 GLU cc_start: 0.8408 (tt0) cc_final: 0.8132 (tt0) REVERT: A 451 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7312 (tp40) REVERT: A 490 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8578 (mtp) REVERT: A 543 LYS cc_start: 0.8379 (ttpp) cc_final: 0.8136 (ttpp) REVERT: A 546 ARG cc_start: 0.8453 (mtt180) cc_final: 0.7986 (mtt90) REVERT: A 550 ASP cc_start: 0.7954 (m-30) cc_final: 0.7681 (m-30) REVERT: A 554 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: A 572 LEU cc_start: 0.8953 (mp) cc_final: 0.8707 (mt) REVERT: A 597 MET cc_start: 0.9176 (ttp) cc_final: 0.8954 (tmm) REVERT: A 636 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: A 690 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7755 (ttmm) REVERT: B 106 LEU cc_start: 0.5155 (mm) cc_final: 0.4884 (mp) REVERT: C 68 ASP cc_start: 0.8112 (t0) cc_final: 0.7877 (t0) REVERT: C 102 GLU cc_start: 0.7892 (tt0) cc_final: 0.7545 (tt0) REVERT: C 152 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: C 162 ASP cc_start: 0.7892 (m-30) cc_final: 0.7629 (m-30) REVERT: C 219 ASP cc_start: 0.7754 (m-30) cc_final: 0.7431 (m-30) REVERT: C 226 ASP cc_start: 0.7475 (m-30) cc_final: 0.7091 (m-30) REVERT: C 227 ASN cc_start: 0.8211 (t0) cc_final: 0.7546 (m-40) REVERT: C 421 MET cc_start: 0.8640 (mmm) cc_final: 0.8250 (mmt) REVERT: C 510 ASP cc_start: 0.7290 (m-30) cc_final: 0.7081 (m-30) REVERT: C 550 ASP cc_start: 0.8035 (m-30) cc_final: 0.7614 (m-30) REVERT: C 554 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7130 (mt-10) REVERT: C 663 MET cc_start: 0.8518 (mtp) cc_final: 0.8188 (mtt) REVERT: C 690 LYS cc_start: 0.8242 (ttpp) cc_final: 0.7975 (tttp) REVERT: D 53 MET cc_start: 0.4273 (tpp) cc_final: 0.3030 (mtp) REVERT: D 88 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7729 (ttmt) REVERT: E 121 MET cc_start: 0.9072 (tpp) cc_final: 0.8752 (tpp) REVERT: E 152 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7455 (mm-30) REVERT: E 211 MET cc_start: 0.8185 (mtp) cc_final: 0.7830 (mtp) REVERT: E 227 ASN cc_start: 0.7809 (t0) cc_final: 0.7341 (m110) REVERT: E 286 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7379 (mp10) REVERT: E 445 MET cc_start: 0.8160 (mtp) cc_final: 0.7910 (mtt) REVERT: E 451 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7255 (tp40) REVERT: E 592 MET cc_start: 0.9010 (ttt) cc_final: 0.8667 (ttt) REVERT: E 673 MET cc_start: 0.8891 (ttt) cc_final: 0.8448 (ttp) REVERT: F 198 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6605 (tp30) REVERT: I 219 ASP cc_start: 0.7685 (m-30) cc_final: 0.7481 (m-30) REVERT: I 227 ASN cc_start: 0.7914 (t0) cc_final: 0.7372 (m-40) REVERT: I 286 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7365 (mp10) REVERT: I 338 LYS cc_start: 0.8574 (mttp) cc_final: 0.8324 (mtmt) REVERT: I 372 LYS cc_start: 0.8271 (tttm) cc_final: 0.8001 (tttp) REVERT: I 374 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8347 (mt) REVERT: I 378 MET cc_start: 0.8321 (ttm) cc_final: 0.8004 (ttp) REVERT: I 510 ASP cc_start: 0.7412 (m-30) cc_final: 0.7127 (m-30) REVERT: I 518 MET cc_start: 0.8671 (mtp) cc_final: 0.8384 (mtp) REVERT: I 546 ARG cc_start: 0.8497 (mtt180) cc_final: 0.8216 (mtt180) REVERT: I 607 THR cc_start: 0.9303 (t) cc_final: 0.8935 (m) REVERT: I 636 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: J 1 MET cc_start: 0.4704 (OUTLIER) cc_final: 0.4076 (ppp) REVERT: J 88 LYS cc_start: 0.8399 (ttpp) cc_final: 0.8176 (tttt) REVERT: J 127 ASP cc_start: 0.7351 (t70) cc_final: 0.6746 (t0) REVERT: J 156 THR cc_start: 0.8669 (t) cc_final: 0.8282 (p) REVERT: J 219 ASP cc_start: 0.7558 (m-30) cc_final: 0.7313 (m-30) REVERT: K 85 GLU cc_start: 0.7517 (pt0) cc_final: 0.7169 (pt0) REVERT: K 119 ASP cc_start: 0.7967 (t70) cc_final: 0.7702 (t70) REVERT: K 145 GLU cc_start: 0.7298 (pt0) cc_final: 0.7019 (mt-10) REVERT: K 211 MET cc_start: 0.8103 (mtm) cc_final: 0.7858 (mtm) REVERT: K 219 ASP cc_start: 0.7572 (m-30) cc_final: 0.7241 (m-30) REVERT: K 227 ASN cc_start: 0.7864 (t0) cc_final: 0.7442 (m-40) REVERT: K 239 GLN cc_start: 0.8669 (tt0) cc_final: 0.8399 (mt0) REVERT: K 372 LYS cc_start: 0.8487 (tttm) cc_final: 0.8252 (tttp) REVERT: K 445 MET cc_start: 0.8235 (mtp) cc_final: 0.7649 (mtt) REVERT: K 543 LYS cc_start: 0.8262 (ttpp) cc_final: 0.7888 (ttpp) REVERT: K 554 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6978 (mt-10) REVERT: K 690 LYS cc_start: 0.8305 (ttpp) cc_final: 0.8085 (tttp) REVERT: L 1 MET cc_start: 0.5133 (mtm) cc_final: 0.4315 (pp-130) REVERT: L 54 MET cc_start: 0.7296 (mmt) cc_final: 0.6783 (mpt) outliers start: 93 outliers final: 53 residues processed: 729 average time/residue: 1.6748 time to fit residues: 1470.6215 Evaluate side-chains 747 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 675 time to evaluate : 5.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 286 GLN Chi-restraints excluded: chain H residue 523 LYS Chi-restraints excluded: chain H residue 609 THR Chi-restraints excluded: chain H residue 636 GLU Chi-restraints excluded: chain H residue 644 GLU Chi-restraints excluded: chain H residue 684 ASP Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 191 GLN Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 368 LYS Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 523 LYS Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 609 THR Chi-restraints excluded: chain I residue 636 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 285 GLU Chi-restraints excluded: chain K residue 298 GLN Chi-restraints excluded: chain K residue 368 LYS Chi-restraints excluded: chain K residue 523 LYS Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain K residue 554 GLU Chi-restraints excluded: chain K residue 609 THR Chi-restraints excluded: chain K residue 694 GLU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 127 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 457 optimal weight: 0.0270 chunk 482 optimal weight: 0.0980 chunk 439 optimal weight: 0.8980 chunk 468 optimal weight: 1.9990 chunk 481 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 368 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 423 optimal weight: 0.9990 chunk 443 optimal weight: 3.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 308 GLN H 451 GLN H 695 ASN G 141 ASN A 95 GLN A 188 GLN A 308 GLN A 695 ASN B 55 GLN C 88 ASN C 191 GLN C 246 GLN C 308 GLN D 141 ASN D 153 GLN E 95 GLN E 191 GLN E 246 GLN E 308 GLN F 141 ASN F 180 GLN I 308 GLN I 624 ASN ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 214 HIS K 246 GLN K 695 ASN L 184 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 41988 Z= 0.135 Angle : 0.439 11.465 56574 Z= 0.228 Chirality : 0.037 0.226 6078 Planarity : 0.003 0.037 7560 Dihedral : 3.519 17.708 5712 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.54 % Allowed : 14.62 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.12), residues: 5244 helix: 2.48 (0.08), residues: 3732 sheet: 1.66 (0.50), residues: 90 loop : -0.64 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 366 HIS 0.004 0.001 HIS A 140 PHE 0.008 0.001 PHE B 97 TYR 0.020 0.001 TYR F 138 ARG 0.005 0.000 ARG K 541 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 706 time to evaluate : 4.688 Fit side-chains revert: symmetry clash REVERT: H 266 ASP cc_start: 0.7980 (m-30) cc_final: 0.7667 (m-30) REVERT: H 328 MET cc_start: 0.8816 (mtp) cc_final: 0.8532 (mtp) REVERT: H 636 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7807 (mt-10) REVERT: H 644 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: H 690 LYS cc_start: 0.8254 (ttpp) cc_final: 0.7822 (ttmm) REVERT: H 694 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6576 (mt-10) REVERT: G 54 MET cc_start: 0.7154 (mpt) cc_final: 0.6771 (mpm) REVERT: G 88 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7871 (ttpt) REVERT: G 141 ASN cc_start: 0.8352 (m-40) cc_final: 0.8151 (m-40) REVERT: A 102 GLU cc_start: 0.7690 (tt0) cc_final: 0.7373 (tt0) REVERT: A 164 GLN cc_start: 0.8198 (mt0) cc_final: 0.7809 (mm110) REVERT: A 207 GLN cc_start: 0.8637 (tt0) cc_final: 0.8347 (tt0) REVERT: A 298 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7578 (mp10) REVERT: A 307 GLU cc_start: 0.8370 (tt0) cc_final: 0.8078 (tt0) REVERT: A 451 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7248 (tp40) REVERT: A 466 MET cc_start: 0.8998 (ttm) cc_final: 0.8769 (ttp) REVERT: A 490 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8531 (mtp) REVERT: A 543 LYS cc_start: 0.8277 (ttpp) cc_final: 0.8042 (ttpp) REVERT: A 546 ARG cc_start: 0.8420 (mtt180) cc_final: 0.7915 (mtt90) REVERT: A 550 ASP cc_start: 0.7926 (m-30) cc_final: 0.7670 (m-30) REVERT: A 554 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: A 597 MET cc_start: 0.9124 (ttp) cc_final: 0.8824 (tmm) REVERT: A 636 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: A 690 LYS cc_start: 0.8215 (ttpp) cc_final: 0.7728 (ttmm) REVERT: B 170 GLU cc_start: 0.7534 (pt0) cc_final: 0.7281 (pt0) REVERT: B 216 GLU cc_start: 0.7963 (pt0) cc_final: 0.7746 (pt0) REVERT: C 121 MET cc_start: 0.8935 (tpp) cc_final: 0.8447 (tpt) REVERT: C 152 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: C 219 ASP cc_start: 0.7632 (m-30) cc_final: 0.7299 (m-30) REVERT: C 226 ASP cc_start: 0.7371 (m-30) cc_final: 0.6979 (m-30) REVERT: C 227 ASN cc_start: 0.8184 (t0) cc_final: 0.7588 (m-40) REVERT: C 421 MET cc_start: 0.8750 (mmm) cc_final: 0.8215 (mmt) REVERT: C 451 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7354 (tp40) REVERT: C 510 ASP cc_start: 0.7299 (m-30) cc_final: 0.7091 (m-30) REVERT: C 520 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7696 (ttt) REVERT: C 550 ASP cc_start: 0.8020 (m-30) cc_final: 0.7614 (m-30) REVERT: C 554 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7114 (mt-10) REVERT: C 663 MET cc_start: 0.8396 (mtp) cc_final: 0.7866 (mtt) REVERT: C 690 LYS cc_start: 0.8225 (ttpp) cc_final: 0.7958 (tttp) REVERT: D 53 MET cc_start: 0.4149 (tpp) cc_final: 0.3114 (mtp) REVERT: D 54 MET cc_start: 0.7235 (mmt) cc_final: 0.6959 (mmp) REVERT: D 156 THR cc_start: 0.8470 (t) cc_final: 0.8189 (m) REVERT: E 121 MET cc_start: 0.9065 (tpp) cc_final: 0.8623 (tpp) REVERT: E 152 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7414 (mm-30) REVERT: E 211 MET cc_start: 0.8080 (mtp) cc_final: 0.7773 (mtp) REVERT: E 227 ASN cc_start: 0.7845 (t0) cc_final: 0.7379 (m110) REVERT: E 286 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7287 (mp10) REVERT: E 335 GLU cc_start: 0.7096 (tt0) cc_final: 0.6882 (mt-10) REVERT: E 445 MET cc_start: 0.8138 (mtp) cc_final: 0.7823 (mtt) REVERT: E 592 MET cc_start: 0.8944 (ttt) cc_final: 0.8663 (ttt) REVERT: E 616 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6825 (t0) REVERT: E 673 MET cc_start: 0.8855 (ttt) cc_final: 0.8315 (ttt) REVERT: F 53 MET cc_start: 0.3532 (tpp) cc_final: 0.3081 (tpp) REVERT: F 156 THR cc_start: 0.8671 (t) cc_final: 0.8440 (m) REVERT: F 180 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7791 (mm110) REVERT: F 198 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6542 (tp30) REVERT: I 227 ASN cc_start: 0.7908 (t0) cc_final: 0.7338 (m-40) REVERT: I 230 VAL cc_start: 0.8788 (t) cc_final: 0.8561 (p) REVERT: I 286 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7331 (mp10) REVERT: I 338 LYS cc_start: 0.8511 (mttp) cc_final: 0.8228 (mtmt) REVERT: I 372 LYS cc_start: 0.8233 (tttm) cc_final: 0.8008 (ttpt) REVERT: I 378 MET cc_start: 0.8216 (ttm) cc_final: 0.7885 (ttp) REVERT: I 518 MET cc_start: 0.8604 (mtp) cc_final: 0.8315 (mtp) REVERT: I 546 ARG cc_start: 0.8390 (mtt180) cc_final: 0.8153 (mtt180) REVERT: I 607 THR cc_start: 0.9227 (t) cc_final: 0.8872 (m) REVERT: I 636 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: J 1 MET cc_start: 0.4919 (OUTLIER) cc_final: 0.4464 (OUTLIER) REVERT: J 36 THR cc_start: 0.8132 (m) cc_final: 0.7672 (p) REVERT: J 88 LYS cc_start: 0.8409 (ttpp) cc_final: 0.7847 (tmmt) REVERT: J 127 ASP cc_start: 0.7224 (t70) cc_final: 0.6837 (t70) REVERT: J 156 THR cc_start: 0.8619 (t) cc_final: 0.8197 (p) REVERT: J 219 ASP cc_start: 0.7649 (m-30) cc_final: 0.7388 (m-30) REVERT: K 85 GLU cc_start: 0.7513 (pt0) cc_final: 0.7249 (pt0) REVERT: K 102 GLU cc_start: 0.7968 (tt0) cc_final: 0.7750 (tt0) REVERT: K 119 ASP cc_start: 0.7968 (t70) cc_final: 0.7694 (t70) REVERT: K 145 GLU cc_start: 0.7157 (pt0) cc_final: 0.6849 (mt-10) REVERT: K 152 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7452 (mp0) REVERT: K 210 ASP cc_start: 0.8173 (m-30) cc_final: 0.7847 (m-30) REVERT: K 211 MET cc_start: 0.8013 (mtm) cc_final: 0.7757 (mtm) REVERT: K 219 ASP cc_start: 0.7684 (m-30) cc_final: 0.7341 (m-30) REVERT: K 227 ASN cc_start: 0.7793 (t0) cc_final: 0.7437 (m-40) REVERT: K 239 GLN cc_start: 0.8572 (tt0) cc_final: 0.8346 (mt0) REVERT: K 372 LYS cc_start: 0.8469 (tttm) cc_final: 0.8249 (tttp) REVERT: K 445 MET cc_start: 0.8244 (mtp) cc_final: 0.7991 (mtp) REVERT: K 543 LYS cc_start: 0.8300 (ttpp) cc_final: 0.7932 (ttpp) REVERT: K 690 LYS cc_start: 0.8378 (ttpp) cc_final: 0.8139 (tttp) REVERT: L 1 MET cc_start: 0.5094 (mtm) cc_final: 0.4462 (pp-130) REVERT: L 54 MET cc_start: 0.7293 (mmt) cc_final: 0.6800 (mpt) REVERT: L 180 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7651 (mm110) outliers start: 67 outliers final: 31 residues processed: 735 average time/residue: 1.7125 time to fit residues: 1524.7684 Evaluate side-chains 727 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 681 time to evaluate : 4.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 445 MET Chi-restraints excluded: chain H residue 609 THR Chi-restraints excluded: chain H residue 636 GLU Chi-restraints excluded: chain H residue 644 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 616 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 636 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 298 GLN Chi-restraints excluded: chain K residue 368 LYS Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain K residue 694 GLU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 127 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 467 optimal weight: 1.9990 chunk 307 optimal weight: 0.9980 chunk 495 optimal weight: 0.7980 chunk 302 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 chunk 344 optimal weight: 1.9990 chunk 520 optimal weight: 0.6980 chunk 478 optimal weight: 0.2980 chunk 414 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 319 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 410 ASN H 451 GLN H 524 GLN H 695 ASN A 95 GLN A 191 GLN A 695 ASN B 55 GLN C 89 ASN C 191 GLN C 246 GLN E 95 GLN E 191 GLN E 364 ASN E 629 ASN F 141 ASN I 410 ASN ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 GLN K 695 ASN L 184 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 41988 Z= 0.148 Angle : 0.448 12.018 56574 Z= 0.232 Chirality : 0.037 0.240 6078 Planarity : 0.003 0.037 7560 Dihedral : 3.540 17.777 5712 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.22 % Allowed : 15.22 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.12), residues: 5244 helix: 2.49 (0.08), residues: 3738 sheet: 1.68 (0.50), residues: 90 loop : -0.58 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 366 HIS 0.002 0.001 HIS A 140 PHE 0.008 0.001 PHE A 404 TYR 0.024 0.001 TYR F 138 ARG 0.005 0.000 ARG K 541 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 683 time to evaluate : 4.730 Fit side-chains revert: symmetry clash REVERT: H 266 ASP cc_start: 0.7987 (m-30) cc_final: 0.7682 (m-30) REVERT: H 328 MET cc_start: 0.8815 (mtp) cc_final: 0.8524 (mtp) REVERT: H 636 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: H 644 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: H 690 LYS cc_start: 0.8268 (ttpp) cc_final: 0.7819 (ttmm) REVERT: H 694 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6580 (mt-10) REVERT: G 36 THR cc_start: 0.7736 (m) cc_final: 0.7343 (p) REVERT: G 54 MET cc_start: 0.7147 (mpt) cc_final: 0.6749 (mpm) REVERT: G 88 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7875 (ttpt) REVERT: G 141 ASN cc_start: 0.8368 (m-40) cc_final: 0.8110 (m-40) REVERT: A 102 GLU cc_start: 0.7690 (tt0) cc_final: 0.7360 (tt0) REVERT: A 164 GLN cc_start: 0.8210 (mt0) cc_final: 0.7820 (mm110) REVERT: A 207 GLN cc_start: 0.8643 (tt0) cc_final: 0.8349 (tt0) REVERT: A 298 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7598 (mp10) REVERT: A 307 GLU cc_start: 0.8386 (tt0) cc_final: 0.8069 (tt0) REVERT: A 451 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7272 (tp40) REVERT: A 490 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8536 (mtp) REVERT: A 543 LYS cc_start: 0.8278 (ttpp) cc_final: 0.8032 (ttpp) REVERT: A 546 ARG cc_start: 0.8422 (mtt180) cc_final: 0.7954 (mtt90) REVERT: A 550 ASP cc_start: 0.7938 (m-30) cc_final: 0.7685 (m-30) REVERT: A 554 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: A 597 MET cc_start: 0.9140 (ttp) cc_final: 0.8864 (tmm) REVERT: A 690 LYS cc_start: 0.8218 (ttpp) cc_final: 0.7726 (ttmm) REVERT: B 216 GLU cc_start: 0.7969 (pt0) cc_final: 0.7747 (pt0) REVERT: C 152 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: C 219 ASP cc_start: 0.7642 (m-30) cc_final: 0.7311 (m-30) REVERT: C 226 ASP cc_start: 0.7359 (m-30) cc_final: 0.6984 (m-30) REVERT: C 227 ASN cc_start: 0.8200 (t0) cc_final: 0.7591 (m-40) REVERT: C 421 MET cc_start: 0.8732 (mmm) cc_final: 0.8247 (mmt) REVERT: C 451 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7383 (tp40) REVERT: C 510 ASP cc_start: 0.7324 (m-30) cc_final: 0.7116 (m-30) REVERT: C 550 ASP cc_start: 0.8018 (m-30) cc_final: 0.7617 (m-30) REVERT: C 554 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7077 (mt-10) REVERT: C 663 MET cc_start: 0.8471 (mtp) cc_final: 0.8083 (mtt) REVERT: C 690 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7941 (tttp) REVERT: D 53 MET cc_start: 0.4165 (tpp) cc_final: 0.3136 (mtp) REVERT: D 156 THR cc_start: 0.8470 (t) cc_final: 0.8180 (m) REVERT: E 121 MET cc_start: 0.9077 (tpp) cc_final: 0.8624 (tpp) REVERT: E 152 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7435 (mm-30) REVERT: E 211 MET cc_start: 0.8087 (mtp) cc_final: 0.7760 (mtp) REVERT: E 227 ASN cc_start: 0.7841 (t0) cc_final: 0.7358 (m110) REVERT: E 286 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: E 335 GLU cc_start: 0.7145 (tt0) cc_final: 0.6928 (mt-10) REVERT: E 445 MET cc_start: 0.8156 (mtp) cc_final: 0.7857 (mtt) REVERT: E 592 MET cc_start: 0.8969 (ttt) cc_final: 0.8654 (ttt) REVERT: E 673 MET cc_start: 0.8866 (ttt) cc_final: 0.8290 (ttt) REVERT: F 53 MET cc_start: 0.3528 (tpp) cc_final: 0.3120 (tpp) REVERT: F 156 THR cc_start: 0.8638 (t) cc_final: 0.8418 (m) REVERT: F 198 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6572 (tp30) REVERT: I 148 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7915 (mtmp) REVERT: I 227 ASN cc_start: 0.7994 (t0) cc_final: 0.7443 (m-40) REVERT: I 230 VAL cc_start: 0.8782 (t) cc_final: 0.8566 (p) REVERT: I 286 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7196 (mp10) REVERT: I 338 LYS cc_start: 0.8527 (mttp) cc_final: 0.8246 (mtmt) REVERT: I 372 LYS cc_start: 0.8227 (tttm) cc_final: 0.7986 (tttp) REVERT: I 378 MET cc_start: 0.8219 (ttm) cc_final: 0.7893 (ttp) REVERT: I 518 MET cc_start: 0.8622 (mtp) cc_final: 0.8317 (mtp) REVERT: I 546 ARG cc_start: 0.8384 (mtt180) cc_final: 0.8152 (mtt180) REVERT: I 607 THR cc_start: 0.9247 (t) cc_final: 0.8881 (m) REVERT: I 636 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: J 1 MET cc_start: 0.4677 (OUTLIER) cc_final: 0.4354 (OUTLIER) REVERT: J 36 THR cc_start: 0.8096 (m) cc_final: 0.7573 (p) REVERT: J 127 ASP cc_start: 0.7104 (t70) cc_final: 0.6802 (t70) REVERT: J 156 THR cc_start: 0.8622 (t) cc_final: 0.8207 (p) REVERT: J 219 ASP cc_start: 0.7580 (m-30) cc_final: 0.7317 (m-30) REVERT: K 85 GLU cc_start: 0.7499 (pt0) cc_final: 0.7253 (pt0) REVERT: K 119 ASP cc_start: 0.8018 (t70) cc_final: 0.7743 (t70) REVERT: K 145 GLU cc_start: 0.7174 (pt0) cc_final: 0.6873 (mt-10) REVERT: K 152 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7450 (mp0) REVERT: K 210 ASP cc_start: 0.8180 (m-30) cc_final: 0.7843 (m-30) REVERT: K 211 MET cc_start: 0.7986 (mtm) cc_final: 0.7727 (mtm) REVERT: K 219 ASP cc_start: 0.7699 (m-30) cc_final: 0.7349 (m-30) REVERT: K 227 ASN cc_start: 0.7821 (t0) cc_final: 0.7450 (m-40) REVERT: K 239 GLN cc_start: 0.8603 (tt0) cc_final: 0.8373 (mt0) REVERT: K 242 GLN cc_start: 0.8171 (mt0) cc_final: 0.7887 (mt0) REVERT: K 372 LYS cc_start: 0.8486 (tttm) cc_final: 0.8254 (tttp) REVERT: K 445 MET cc_start: 0.8249 (mtp) cc_final: 0.7992 (mtp) REVERT: K 543 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7853 (ttpp) REVERT: K 690 LYS cc_start: 0.8379 (ttpp) cc_final: 0.8146 (tttp) REVERT: L 1 MET cc_start: 0.5149 (mtm) cc_final: 0.4462 (pp-130) REVERT: L 54 MET cc_start: 0.7290 (mmt) cc_final: 0.6803 (mpt) REVERT: L 180 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7678 (mm110) outliers start: 53 outliers final: 34 residues processed: 708 average time/residue: 1.6702 time to fit residues: 1418.7449 Evaluate side-chains 718 residues out of total 4404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 672 time to evaluate : 4.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 445 MET Chi-restraints excluded: chain H residue 609 THR Chi-restraints excluded: chain H residue 636 GLU Chi-restraints excluded: chain H residue 644 GLU Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 523 LYS Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 636 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 298 GLN Chi-restraints excluded: chain K residue 368 LYS Chi-restraints excluded: chain K residue 523 LYS Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain K residue 694 GLU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 127 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 253 optimal weight: 0.4980 chunk 328 optimal weight: 20.0000 chunk 441 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 381 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 115 optimal weight: 0.4980 chunk 414 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 425 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 451 GLN H 524 GLN H 695 ASN A 95 GLN A 191 GLN A 695 ASN C 191 GLN C 246 GLN E 95 GLN E 191 GLN E 364 ASN E 629 ASN F 141 ASN F 180 GLN ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 GLN K 695 ASN L 184 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.157088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113194 restraints weight = 44029.973| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.58 r_work: 0.3120 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 41988 Z= 0.143 Angle : 0.448 12.115 56574 Z= 0.232 Chirality : 0.037 0.239 6078 Planarity : 0.003 0.037 7560 Dihedral : 3.504 17.622 5712 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.42 % Allowed : 15.11 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.12), residues: 5244 helix: 2.51 (0.08), residues: 3738 sheet: 1.67 (0.50), residues: 90 loop : -0.54 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 366 HIS 0.003 0.001 HIS A 140 PHE 0.007 0.001 PHE A 404 TYR 0.023 0.001 TYR L 138 ARG 0.005 0.000 ARG K 541 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20594.16 seconds wall clock time: 361 minutes 39.21 seconds (21699.21 seconds total)