Starting phenix.real_space_refine on Fri Apr 5 13:34:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5w_17455/04_2024/8p5w_17455_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5w_17455/04_2024/8p5w_17455.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5w_17455/04_2024/8p5w_17455_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5w_17455/04_2024/8p5w_17455_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5w_17455/04_2024/8p5w_17455_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5w_17455/04_2024/8p5w_17455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5w_17455/04_2024/8p5w_17455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5w_17455/04_2024/8p5w_17455_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5w_17455/04_2024/8p5w_17455_updated.pdb" } resolution = 2.26 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= 0.012 sd= 1.183 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 6 5.21 5 S 228 5.16 5 C 33018 2.51 5 N 9228 2.21 5 O 10140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 408": "OD1" <-> "OD2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A ASP 418": "OD1" <-> "OD2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A ASP 460": "OD1" <-> "OD2" Residue "A ASP 462": "OD1" <-> "OD2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 587": "OE1" <-> "OE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A ARG 781": "NH1" <-> "NH2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A GLU 901": "OE1" <-> "OE2" Residue "A ASP 902": "OD1" <-> "OD2" Residue "A GLU 923": "OE1" <-> "OE2" Residue "A GLU 956": "OE1" <-> "OE2" Residue "A GLU 971": "OE1" <-> "OE2" Residue "A PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1023": "OE1" <-> "OE2" Residue "A PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1056": "OD1" <-> "OD2" Residue "A GLU 1084": "OE1" <-> "OE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1156": "OE1" <-> "OE2" Residue "A PHE 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1164": "OE1" <-> "OE2" Residue "A GLU 1176": "OE1" <-> "OE2" Residue "A ARG 1190": "NH1" <-> "NH2" Residue "A PHE 1219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1220": "OE1" <-> "OE2" Residue "B TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 185": "OD1" <-> "OD2" Residue "B ASP 248": "OD1" <-> "OD2" Residue "B ASP 249": "OD1" <-> "OD2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 315": "OD1" <-> "OD2" Residue "B TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 408": "OD1" <-> "OD2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B ASP 418": "OD1" <-> "OD2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B GLU 454": "OE1" <-> "OE2" Residue "B ASP 460": "OD1" <-> "OD2" Residue "B ASP 462": "OD1" <-> "OD2" Residue "B ASP 469": "OD1" <-> "OD2" Residue "B GLU 482": "OE1" <-> "OE2" Residue "B GLU 513": "OE1" <-> "OE2" Residue "B GLU 536": "OE1" <-> "OE2" Residue "B TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 587": "OE1" <-> "OE2" Residue "B GLU 611": "OE1" <-> "OE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 767": "NH1" <-> "NH2" Residue "B ARG 781": "NH1" <-> "NH2" Residue "B GLU 816": "OE1" <-> "OE2" Residue "B GLU 901": "OE1" <-> "OE2" Residue "B ASP 902": "OD1" <-> "OD2" Residue "B GLU 923": "OE1" <-> "OE2" Residue "B TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 956": "OE1" <-> "OE2" Residue "B GLU 971": "OE1" <-> "OE2" Residue "B PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1023": "OE1" <-> "OE2" Residue "B PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1056": "OD1" <-> "OD2" Residue "B GLU 1084": "OE1" <-> "OE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1156": "OE1" <-> "OE2" Residue "B PHE 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1164": "OE1" <-> "OE2" Residue "B GLU 1176": "OE1" <-> "OE2" Residue "B ARG 1190": "NH1" <-> "NH2" Residue "B PHE 1219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1220": "OE1" <-> "OE2" Residue "C TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C ASP 208": "OD1" <-> "OD2" Residue "C ASP 248": "OD1" <-> "OD2" Residue "C ASP 249": "OD1" <-> "OD2" Residue "C TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 315": "OD1" <-> "OD2" Residue "C TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 408": "OD1" <-> "OD2" Residue "C GLU 410": "OE1" <-> "OE2" Residue "C ASP 418": "OD1" <-> "OD2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C GLU 454": "OE1" <-> "OE2" Residue "C ASP 460": "OD1" <-> "OD2" Residue "C ASP 462": "OD1" <-> "OD2" Residue "C ASP 469": "OD1" <-> "OD2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C GLU 513": "OE1" <-> "OE2" Residue "C GLU 536": "OE1" <-> "OE2" Residue "C TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 587": "OE1" <-> "OE2" Residue "C GLU 611": "OE1" <-> "OE2" Residue "C GLU 618": "OE1" <-> "OE2" Residue "C TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 767": "NH1" <-> "NH2" Residue "C ARG 781": "NH1" <-> "NH2" Residue "C GLU 816": "OE1" <-> "OE2" Residue "C GLU 901": "OE1" <-> "OE2" Residue "C ASP 902": "OD1" <-> "OD2" Residue "C GLU 923": "OE1" <-> "OE2" Residue "C TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 956": "OE1" <-> "OE2" Residue "C GLU 971": "OE1" <-> "OE2" Residue "C PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1023": "OE1" <-> "OE2" Residue "C PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1056": "OD1" <-> "OD2" Residue "C GLU 1084": "OE1" <-> "OE2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "C PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1156": "OE1" <-> "OE2" Residue "C PHE 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1164": "OE1" <-> "OE2" Residue "C GLU 1176": "OE1" <-> "OE2" Residue "C ARG 1190": "NH1" <-> "NH2" Residue "C PHE 1219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1220": "OE1" <-> "OE2" Residue "D TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 185": "OD1" <-> "OD2" Residue "D ASP 208": "OD1" <-> "OD2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "D ASP 249": "OD1" <-> "OD2" Residue "D TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 315": "OD1" <-> "OD2" Residue "D TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 408": "OD1" <-> "OD2" Residue "D GLU 410": "OE1" <-> "OE2" Residue "D ASP 418": "OD1" <-> "OD2" Residue "D ASP 420": "OD1" <-> "OD2" Residue "D ARG 442": "NH1" <-> "NH2" Residue "D GLU 454": "OE1" <-> "OE2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D ASP 462": "OD1" <-> "OD2" Residue "D ASP 469": "OD1" <-> "OD2" Residue "D GLU 482": "OE1" <-> "OE2" Residue "D GLU 513": "OE1" <-> "OE2" Residue "D GLU 536": "OE1" <-> "OE2" Residue "D TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 587": "OE1" <-> "OE2" Residue "D GLU 611": "OE1" <-> "OE2" Residue "D GLU 618": "OE1" <-> "OE2" Residue "D TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 767": "NH1" <-> "NH2" Residue "D ARG 781": "NH1" <-> "NH2" Residue "D GLU 816": "OE1" <-> "OE2" Residue "D GLU 901": "OE1" <-> "OE2" Residue "D ASP 902": "OD1" <-> "OD2" Residue "D GLU 923": "OE1" <-> "OE2" Residue "D TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 956": "OE1" <-> "OE2" Residue "D GLU 971": "OE1" <-> "OE2" Residue "D PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1023": "OE1" <-> "OE2" Residue "D PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1056": "OD1" <-> "OD2" Residue "D GLU 1084": "OE1" <-> "OE2" Residue "D ASP 1127": "OD1" <-> "OD2" Residue "D PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1156": "OE1" <-> "OE2" Residue "D PHE 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1164": "OE1" <-> "OE2" Residue "D GLU 1176": "OE1" <-> "OE2" Residue "D ARG 1190": "NH1" <-> "NH2" Residue "D PHE 1219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1220": "OE1" <-> "OE2" Residue "E TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 185": "OD1" <-> "OD2" Residue "E ASP 208": "OD1" <-> "OD2" Residue "E ASP 248": "OD1" <-> "OD2" Residue "E ASP 249": "OD1" <-> "OD2" Residue "E TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 315": "OD1" <-> "OD2" Residue "E TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 408": "OD1" <-> "OD2" Residue "E GLU 410": "OE1" <-> "OE2" Residue "E ASP 418": "OD1" <-> "OD2" Residue "E ASP 420": "OD1" <-> "OD2" Residue "E ARG 442": "NH1" <-> "NH2" Residue "E GLU 454": "OE1" <-> "OE2" Residue "E ASP 460": "OD1" <-> "OD2" Residue "E ASP 462": "OD1" <-> "OD2" Residue "E ASP 469": "OD1" <-> "OD2" Residue "E GLU 482": "OE1" <-> "OE2" Residue "E GLU 513": "OE1" <-> "OE2" Residue "E GLU 536": "OE1" <-> "OE2" Residue "E TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 587": "OE1" <-> "OE2" Residue "E GLU 611": "OE1" <-> "OE2" Residue "E GLU 618": "OE1" <-> "OE2" Residue "E TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 767": "NH1" <-> "NH2" Residue "E ARG 781": "NH1" <-> "NH2" Residue "E GLU 816": "OE1" <-> "OE2" Residue "E GLU 901": "OE1" <-> "OE2" Residue "E ASP 902": "OD1" <-> "OD2" Residue "E GLU 923": "OE1" <-> "OE2" Residue "E TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 956": "OE1" <-> "OE2" Residue "E GLU 971": "OE1" <-> "OE2" Residue "E PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1023": "OE1" <-> "OE2" Residue "E PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1056": "OD1" <-> "OD2" Residue "E GLU 1084": "OE1" <-> "OE2" Residue "E ASP 1127": "OD1" <-> "OD2" Residue "E PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1156": "OE1" <-> "OE2" Residue "E PHE 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1164": "OE1" <-> "OE2" Residue "E GLU 1176": "OE1" <-> "OE2" Residue "E ARG 1190": "NH1" <-> "NH2" Residue "E PHE 1219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1220": "OE1" <-> "OE2" Residue "F TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 185": "OD1" <-> "OD2" Residue "F ASP 208": "OD1" <-> "OD2" Residue "F ASP 248": "OD1" <-> "OD2" Residue "F ASP 249": "OD1" <-> "OD2" Residue "F TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 315": "OD1" <-> "OD2" Residue "F TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 408": "OD1" <-> "OD2" Residue "F GLU 410": "OE1" <-> "OE2" Residue "F ASP 418": "OD1" <-> "OD2" Residue "F ASP 420": "OD1" <-> "OD2" Residue "F ARG 442": "NH1" <-> "NH2" Residue "F GLU 454": "OE1" <-> "OE2" Residue "F ASP 460": "OD1" <-> "OD2" Residue "F ASP 462": "OD1" <-> "OD2" Residue "F ASP 469": "OD1" <-> "OD2" Residue "F GLU 482": "OE1" <-> "OE2" Residue "F GLU 513": "OE1" <-> "OE2" Residue "F GLU 536": "OE1" <-> "OE2" Residue "F TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 587": "OE1" <-> "OE2" Residue "F GLU 611": "OE1" <-> "OE2" Residue "F GLU 618": "OE1" <-> "OE2" Residue "F TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 767": "NH1" <-> "NH2" Residue "F ARG 781": "NH1" <-> "NH2" Residue "F GLU 816": "OE1" <-> "OE2" Residue "F GLU 901": "OE1" <-> "OE2" Residue "F ASP 902": "OD1" <-> "OD2" Residue "F GLU 923": "OE1" <-> "OE2" Residue "F TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 956": "OE1" <-> "OE2" Residue "F GLU 971": "OE1" <-> "OE2" Residue "F PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1023": "OE1" <-> "OE2" Residue "F PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1056": "OD1" <-> "OD2" Residue "F GLU 1084": "OE1" <-> "OE2" Residue "F ASP 1127": "OD1" <-> "OD2" Residue "F PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1156": "OE1" <-> "OE2" Residue "F PHE 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1164": "OE1" <-> "OE2" Residue "F GLU 1176": "OE1" <-> "OE2" Residue "F ARG 1190": "NH1" <-> "NH2" Residue "F PHE 1219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1220": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 52656 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1064} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' MG': 1, 'ACO': 1, 'QSP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' MG': 1, 'ACO': 1, 'QSP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' MG': 1, 'ACO': 1, 'QSP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' MG': 1, 'ACO': 1, 'QSP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' MG': 1, 'ACO': 1, 'QSP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' MG': 1, 'ACO': 1, 'QSP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 20.13, per 1000 atoms: 0.38 Number of scatterers: 52656 At special positions: 0 Unit cell: (227.9, 209.84, 171.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 228 16.00 P 36 15.00 Mg 6 11.99 O 10140 8.00 N 9228 7.00 C 33018 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: 14.44 Conformation dependent library (CDL) restraints added in 6.9 seconds 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12252 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 294 helices and 36 sheets defined 43.4% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.60 Creating SS restraints... Processing helix chain 'A' and resid 110 through 123 removed outlier: 3.896A pdb=" N LEU A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.534A pdb=" N GLN A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 173 Processing helix chain 'A' and resid 175 through 178 Processing helix chain 'A' and resid 226 through 242 Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 321 through 336 removed outlier: 3.982A pdb=" N THR A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 368 through 386 removed outlier: 6.551A pdb=" N HIS A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 436 through 447 Processing helix chain 'A' and resid 461 through 473 Processing helix chain 'A' and resid 480 through 503 Processing helix chain 'A' and resid 516 through 532 Proline residue: A 520 - end of helix removed outlier: 3.583A pdb=" N ASP A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 526 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 552 Processing helix chain 'A' and resid 558 through 566 Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 614 through 628 Processing helix chain 'A' and resid 645 through 650 Processing helix chain 'A' and resid 653 through 660 removed outlier: 4.165A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 697 through 702 Processing helix chain 'A' and resid 714 through 731 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 760 through 764 removed outlier: 3.503A pdb=" N ILE A 764 " --> pdb=" O MET A 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 760 through 764' Processing helix chain 'A' and resid 770 through 781 Processing helix chain 'A' and resid 786 through 809 removed outlier: 3.921A pdb=" N VAL A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 removed outlier: 4.474A pdb=" N PHE A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 873 Proline residue: A 862 - end of helix removed outlier: 4.222A pdb=" N VAL A 871 " --> pdb=" O ARG A 867 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N THR A 872 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 892 Processing helix chain 'A' and resid 926 through 933 Processing helix chain 'A' and resid 950 through 962 Processing helix chain 'A' and resid 975 through 987 removed outlier: 3.560A pdb=" N ALA A 978 " --> pdb=" O GLY A 975 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN A 979 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 982 " --> pdb=" O ASN A 979 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR A 983 " --> pdb=" O GLY A 980 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 987 " --> pdb=" O ILE A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 996 Processing helix chain 'A' and resid 1022 through 1028 Processing helix chain 'A' and resid 1042 through 1054 Processing helix chain 'A' and resid 1069 through 1071 No H-bonds generated for 'chain 'A' and resid 1069 through 1071' Processing helix chain 'A' and resid 1073 through 1075 No H-bonds generated for 'chain 'A' and resid 1073 through 1075' Processing helix chain 'A' and resid 1079 through 1083 Processing helix chain 'A' and resid 1100 through 1102 No H-bonds generated for 'chain 'A' and resid 1100 through 1102' Processing helix chain 'A' and resid 1112 through 1124 removed outlier: 4.217A pdb=" N ALA A1118 " --> pdb=" O TYR A1115 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A1124 " --> pdb=" O LYS A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1151 Processing helix chain 'A' and resid 1171 through 1181 removed outlier: 3.676A pdb=" N GLU A1176 " --> pdb=" O PRO A1172 " (cutoff:3.500A) Proline residue: A1179 - end of helix Processing helix chain 'A' and resid 1204 through 1218 Processing helix chain 'B' and resid 110 through 123 removed outlier: 3.900A pdb=" N LEU B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLU B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 151 removed outlier: 3.534A pdb=" N GLN B 148 " --> pdb=" O MET B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 173 Processing helix chain 'B' and resid 175 through 178 Processing helix chain 'B' and resid 226 through 242 Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 289 through 291 No H-bonds generated for 'chain 'B' and resid 289 through 291' Processing helix chain 'B' and resid 296 through 302 Processing helix chain 'B' and resid 321 through 336 removed outlier: 3.983A pdb=" N THR B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 368 through 386 removed outlier: 6.550A pdb=" N HIS B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE B 386 " --> pdb=" O ARG B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 428 through 430 No H-bonds generated for 'chain 'B' and resid 428 through 430' Processing helix chain 'B' and resid 436 through 447 Processing helix chain 'B' and resid 461 through 473 Processing helix chain 'B' and resid 480 through 503 Processing helix chain 'B' and resid 516 through 532 Proline residue: B 520 - end of helix removed outlier: 3.582A pdb=" N ASP B 523 " --> pdb=" O PRO B 520 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 526 " --> pdb=" O ASP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 552 Processing helix chain 'B' and resid 558 through 566 Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 614 through 628 Processing helix chain 'B' and resid 645 through 650 Processing helix chain 'B' and resid 653 through 660 removed outlier: 4.164A pdb=" N LEU B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 688 No H-bonds generated for 'chain 'B' and resid 686 through 688' Processing helix chain 'B' and resid 697 through 702 Processing helix chain 'B' and resid 714 through 731 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 760 through 764 removed outlier: 3.502A pdb=" N ILE B 764 " --> pdb=" O MET B 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 760 through 764' Processing helix chain 'B' and resid 770 through 781 Processing helix chain 'B' and resid 786 through 809 removed outlier: 3.920A pdb=" N VAL B 793 " --> pdb=" O ALA B 789 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 847 removed outlier: 4.476A pdb=" N PHE B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 873 Proline residue: B 862 - end of helix removed outlier: 4.223A pdb=" N VAL B 871 " --> pdb=" O ARG B 867 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N THR B 872 " --> pdb=" O VAL B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 892 Processing helix chain 'B' and resid 926 through 933 Processing helix chain 'B' and resid 950 through 962 Processing helix chain 'B' and resid 975 through 987 removed outlier: 3.561A pdb=" N ALA B 978 " --> pdb=" O GLY B 975 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 979 " --> pdb=" O ASP B 976 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 982 " --> pdb=" O ASN B 979 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR B 983 " --> pdb=" O GLY B 980 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 987 " --> pdb=" O ILE B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 996 Processing helix chain 'B' and resid 1022 through 1028 Processing helix chain 'B' and resid 1042 through 1054 Processing helix chain 'B' and resid 1069 through 1071 No H-bonds generated for 'chain 'B' and resid 1069 through 1071' Processing helix chain 'B' and resid 1073 through 1075 No H-bonds generated for 'chain 'B' and resid 1073 through 1075' Processing helix chain 'B' and resid 1079 through 1083 Processing helix chain 'B' and resid 1100 through 1102 No H-bonds generated for 'chain 'B' and resid 1100 through 1102' Processing helix chain 'B' and resid 1112 through 1124 removed outlier: 4.216A pdb=" N ALA B1118 " --> pdb=" O TYR B1115 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP B1124 " --> pdb=" O LYS B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1151 Processing helix chain 'B' and resid 1171 through 1181 removed outlier: 3.676A pdb=" N GLU B1176 " --> pdb=" O PRO B1172 " (cutoff:3.500A) Proline residue: B1179 - end of helix Processing helix chain 'B' and resid 1204 through 1218 Processing helix chain 'C' and resid 110 through 123 removed outlier: 3.897A pdb=" N LEU C 122 " --> pdb=" O MET C 118 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLU C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.535A pdb=" N GLN C 148 " --> pdb=" O MET C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 173 Processing helix chain 'C' and resid 175 through 178 Processing helix chain 'C' and resid 226 through 242 Processing helix chain 'C' and resid 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'C' and resid 321 through 336 removed outlier: 3.982A pdb=" N THR C 336 " --> pdb=" O SER C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 368 through 386 removed outlier: 6.552A pdb=" N HIS C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE C 386 " --> pdb=" O ARG C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 428 through 430 No H-bonds generated for 'chain 'C' and resid 428 through 430' Processing helix chain 'C' and resid 436 through 447 Processing helix chain 'C' and resid 461 through 473 Processing helix chain 'C' and resid 480 through 503 Processing helix chain 'C' and resid 516 through 532 Proline residue: C 520 - end of helix removed outlier: 3.582A pdb=" N ASP C 523 " --> pdb=" O PRO C 520 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 526 " --> pdb=" O ASP C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 552 Processing helix chain 'C' and resid 558 through 566 Processing helix chain 'C' and resid 581 through 583 No H-bonds generated for 'chain 'C' and resid 581 through 583' Processing helix chain 'C' and resid 614 through 628 Processing helix chain 'C' and resid 645 through 650 Processing helix chain 'C' and resid 653 through 660 removed outlier: 4.164A pdb=" N LEU C 660 " --> pdb=" O GLU C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 688 No H-bonds generated for 'chain 'C' and resid 686 through 688' Processing helix chain 'C' and resid 697 through 702 Processing helix chain 'C' and resid 714 through 731 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 760 through 764 removed outlier: 3.502A pdb=" N ILE C 764 " --> pdb=" O MET C 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 760 through 764' Processing helix chain 'C' and resid 770 through 781 Processing helix chain 'C' and resid 786 through 809 removed outlier: 3.921A pdb=" N VAL C 793 " --> pdb=" O ALA C 789 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 847 removed outlier: 4.478A pdb=" N PHE C 847 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 873 Proline residue: C 862 - end of helix removed outlier: 4.223A pdb=" N VAL C 871 " --> pdb=" O ARG C 867 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N THR C 872 " --> pdb=" O VAL C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 892 Processing helix chain 'C' and resid 926 through 933 Processing helix chain 'C' and resid 950 through 962 Processing helix chain 'C' and resid 975 through 987 removed outlier: 3.561A pdb=" N ALA C 978 " --> pdb=" O GLY C 975 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN C 979 " --> pdb=" O ASP C 976 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 982 " --> pdb=" O ASN C 979 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N THR C 983 " --> pdb=" O GLY C 980 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU C 987 " --> pdb=" O ILE C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 996 Processing helix chain 'C' and resid 1022 through 1028 Processing helix chain 'C' and resid 1042 through 1054 Processing helix chain 'C' and resid 1069 through 1071 No H-bonds generated for 'chain 'C' and resid 1069 through 1071' Processing helix chain 'C' and resid 1073 through 1075 No H-bonds generated for 'chain 'C' and resid 1073 through 1075' Processing helix chain 'C' and resid 1079 through 1083 Processing helix chain 'C' and resid 1100 through 1102 No H-bonds generated for 'chain 'C' and resid 1100 through 1102' Processing helix chain 'C' and resid 1112 through 1124 removed outlier: 4.216A pdb=" N ALA C1118 " --> pdb=" O TYR C1115 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP C1124 " --> pdb=" O LYS C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1151 Processing helix chain 'C' and resid 1171 through 1181 removed outlier: 3.674A pdb=" N GLU C1176 " --> pdb=" O PRO C1172 " (cutoff:3.500A) Proline residue: C1179 - end of helix Processing helix chain 'C' and resid 1204 through 1218 Processing helix chain 'D' and resid 110 through 123 removed outlier: 3.897A pdb=" N LEU D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 151 removed outlier: 3.535A pdb=" N GLN D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 173 Processing helix chain 'D' and resid 175 through 178 Processing helix chain 'D' and resid 226 through 242 Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 296 through 302 Processing helix chain 'D' and resid 321 through 336 removed outlier: 3.978A pdb=" N THR D 336 " --> pdb=" O SER D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 348 Processing helix chain 'D' and resid 368 through 386 removed outlier: 6.550A pdb=" N HIS D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE D 386 " --> pdb=" O ARG D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 428 through 430 No H-bonds generated for 'chain 'D' and resid 428 through 430' Processing helix chain 'D' and resid 436 through 447 Processing helix chain 'D' and resid 461 through 473 Processing helix chain 'D' and resid 480 through 503 Processing helix chain 'D' and resid 516 through 532 Proline residue: D 520 - end of helix removed outlier: 3.583A pdb=" N ASP D 523 " --> pdb=" O PRO D 520 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 526 " --> pdb=" O ASP D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 552 Processing helix chain 'D' and resid 558 through 566 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 614 through 628 Processing helix chain 'D' and resid 645 through 650 Processing helix chain 'D' and resid 653 through 660 removed outlier: 4.165A pdb=" N LEU D 660 " --> pdb=" O GLU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 688 No H-bonds generated for 'chain 'D' and resid 686 through 688' Processing helix chain 'D' and resid 697 through 702 Processing helix chain 'D' and resid 714 through 731 Processing helix chain 'D' and resid 753 through 755 No H-bonds generated for 'chain 'D' and resid 753 through 755' Processing helix chain 'D' and resid 760 through 764 removed outlier: 3.503A pdb=" N ILE D 764 " --> pdb=" O MET D 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 760 through 764' Processing helix chain 'D' and resid 770 through 781 Processing helix chain 'D' and resid 786 through 809 removed outlier: 3.921A pdb=" N VAL D 793 " --> pdb=" O ALA D 789 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 837 through 847 removed outlier: 4.474A pdb=" N PHE D 847 " --> pdb=" O LEU D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 858 through 873 Proline residue: D 862 - end of helix removed outlier: 4.222A pdb=" N VAL D 871 " --> pdb=" O ARG D 867 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N THR D 872 " --> pdb=" O VAL D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 892 Processing helix chain 'D' and resid 926 through 933 Processing helix chain 'D' and resid 950 through 962 Processing helix chain 'D' and resid 975 through 987 removed outlier: 3.560A pdb=" N ALA D 978 " --> pdb=" O GLY D 975 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN D 979 " --> pdb=" O ASP D 976 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN D 982 " --> pdb=" O ASN D 979 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR D 983 " --> pdb=" O GLY D 980 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU D 987 " --> pdb=" O ILE D 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 996 Processing helix chain 'D' and resid 1022 through 1028 Processing helix chain 'D' and resid 1042 through 1054 Processing helix chain 'D' and resid 1069 through 1071 No H-bonds generated for 'chain 'D' and resid 1069 through 1071' Processing helix chain 'D' and resid 1073 through 1075 No H-bonds generated for 'chain 'D' and resid 1073 through 1075' Processing helix chain 'D' and resid 1079 through 1083 Processing helix chain 'D' and resid 1100 through 1102 No H-bonds generated for 'chain 'D' and resid 1100 through 1102' Processing helix chain 'D' and resid 1112 through 1124 removed outlier: 4.217A pdb=" N ALA D1118 " --> pdb=" O TYR D1115 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP D1124 " --> pdb=" O LYS D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1142 through 1151 Processing helix chain 'D' and resid 1171 through 1181 removed outlier: 3.675A pdb=" N GLU D1176 " --> pdb=" O PRO D1172 " (cutoff:3.500A) Proline residue: D1179 - end of helix Processing helix chain 'D' and resid 1204 through 1218 Processing helix chain 'E' and resid 110 through 123 removed outlier: 3.896A pdb=" N LEU E 122 " --> pdb=" O MET E 118 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLU E 123 " --> pdb=" O ASP E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 151 removed outlier: 3.535A pdb=" N GLN E 148 " --> pdb=" O MET E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 173 Processing helix chain 'E' and resid 175 through 178 Processing helix chain 'E' and resid 226 through 242 Processing helix chain 'E' and resid 248 through 250 No H-bonds generated for 'chain 'E' and resid 248 through 250' Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'E' and resid 289 through 291 No H-bonds generated for 'chain 'E' and resid 289 through 291' Processing helix chain 'E' and resid 296 through 302 Processing helix chain 'E' and resid 321 through 336 removed outlier: 3.978A pdb=" N THR E 336 " --> pdb=" O SER E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 348 Processing helix chain 'E' and resid 368 through 386 removed outlier: 6.554A pdb=" N HIS E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU E 385 " --> pdb=" O SER E 381 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE E 386 " --> pdb=" O ARG E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 416 through 418 No H-bonds generated for 'chain 'E' and resid 416 through 418' Processing helix chain 'E' and resid 428 through 430 No H-bonds generated for 'chain 'E' and resid 428 through 430' Processing helix chain 'E' and resid 436 through 447 Processing helix chain 'E' and resid 461 through 473 Processing helix chain 'E' and resid 480 through 503 Processing helix chain 'E' and resid 516 through 532 Proline residue: E 520 - end of helix removed outlier: 3.583A pdb=" N ASP E 523 " --> pdb=" O PRO E 520 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE E 526 " --> pdb=" O ASP E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 552 Processing helix chain 'E' and resid 558 through 566 Processing helix chain 'E' and resid 581 through 583 No H-bonds generated for 'chain 'E' and resid 581 through 583' Processing helix chain 'E' and resid 614 through 628 Processing helix chain 'E' and resid 645 through 650 Processing helix chain 'E' and resid 653 through 660 removed outlier: 4.167A pdb=" N LEU E 660 " --> pdb=" O GLU E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 686 through 688 No H-bonds generated for 'chain 'E' and resid 686 through 688' Processing helix chain 'E' and resid 697 through 702 Processing helix chain 'E' and resid 714 through 731 Processing helix chain 'E' and resid 753 through 755 No H-bonds generated for 'chain 'E' and resid 753 through 755' Processing helix chain 'E' and resid 760 through 764 removed outlier: 3.503A pdb=" N ILE E 764 " --> pdb=" O MET E 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 760 through 764' Processing helix chain 'E' and resid 770 through 781 Processing helix chain 'E' and resid 786 through 809 removed outlier: 3.920A pdb=" N VAL E 793 " --> pdb=" O ALA E 789 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE E 796 " --> pdb=" O VAL E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 837 through 847 removed outlier: 4.473A pdb=" N PHE E 847 " --> pdb=" O LEU E 843 " (cutoff:3.500A) Processing helix chain 'E' and resid 858 through 873 Proline residue: E 862 - end of helix removed outlier: 4.224A pdb=" N VAL E 871 " --> pdb=" O ARG E 867 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N THR E 872 " --> pdb=" O VAL E 868 " (cutoff:3.500A) Processing helix chain 'E' and resid 878 through 892 Processing helix chain 'E' and resid 926 through 933 Processing helix chain 'E' and resid 950 through 962 Processing helix chain 'E' and resid 975 through 987 removed outlier: 3.559A pdb=" N ALA E 978 " --> pdb=" O GLY E 975 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN E 979 " --> pdb=" O ASP E 976 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN E 982 " --> pdb=" O ASN E 979 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR E 983 " --> pdb=" O GLY E 980 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU E 987 " --> pdb=" O ILE E 984 " (cutoff:3.500A) Processing helix chain 'E' and resid 992 through 996 Processing helix chain 'E' and resid 1022 through 1028 Processing helix chain 'E' and resid 1042 through 1054 Processing helix chain 'E' and resid 1069 through 1071 No H-bonds generated for 'chain 'E' and resid 1069 through 1071' Processing helix chain 'E' and resid 1073 through 1075 No H-bonds generated for 'chain 'E' and resid 1073 through 1075' Processing helix chain 'E' and resid 1079 through 1083 Processing helix chain 'E' and resid 1100 through 1102 No H-bonds generated for 'chain 'E' and resid 1100 through 1102' Processing helix chain 'E' and resid 1112 through 1124 removed outlier: 4.216A pdb=" N ALA E1118 " --> pdb=" O TYR E1115 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP E1124 " --> pdb=" O LYS E1121 " (cutoff:3.500A) Processing helix chain 'E' and resid 1142 through 1151 Processing helix chain 'E' and resid 1171 through 1181 removed outlier: 3.674A pdb=" N GLU E1176 " --> pdb=" O PRO E1172 " (cutoff:3.500A) Proline residue: E1179 - end of helix Processing helix chain 'E' and resid 1204 through 1218 Processing helix chain 'F' and resid 110 through 123 removed outlier: 3.896A pdb=" N LEU F 122 " --> pdb=" O MET F 118 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 151 removed outlier: 3.534A pdb=" N GLN F 148 " --> pdb=" O MET F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 173 Processing helix chain 'F' and resid 175 through 178 Processing helix chain 'F' and resid 226 through 242 Processing helix chain 'F' and resid 248 through 250 No H-bonds generated for 'chain 'F' and resid 248 through 250' Processing helix chain 'F' and resid 260 through 262 No H-bonds generated for 'chain 'F' and resid 260 through 262' Processing helix chain 'F' and resid 289 through 291 No H-bonds generated for 'chain 'F' and resid 289 through 291' Processing helix chain 'F' and resid 296 through 302 Processing helix chain 'F' and resid 321 through 336 removed outlier: 3.979A pdb=" N THR F 336 " --> pdb=" O SER F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 348 Processing helix chain 'F' and resid 368 through 386 removed outlier: 6.549A pdb=" N HIS F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU F 385 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE F 386 " --> pdb=" O ARG F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 407 No H-bonds generated for 'chain 'F' and resid 405 through 407' Processing helix chain 'F' and resid 416 through 418 No H-bonds generated for 'chain 'F' and resid 416 through 418' Processing helix chain 'F' and resid 428 through 430 No H-bonds generated for 'chain 'F' and resid 428 through 430' Processing helix chain 'F' and resid 436 through 447 Processing helix chain 'F' and resid 461 through 473 Processing helix chain 'F' and resid 480 through 503 Processing helix chain 'F' and resid 516 through 532 Proline residue: F 520 - end of helix removed outlier: 3.583A pdb=" N ASP F 523 " --> pdb=" O PRO F 520 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 526 " --> pdb=" O ASP F 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 552 Processing helix chain 'F' and resid 558 through 566 Processing helix chain 'F' and resid 581 through 583 No H-bonds generated for 'chain 'F' and resid 581 through 583' Processing helix chain 'F' and resid 614 through 628 Processing helix chain 'F' and resid 645 through 650 Processing helix chain 'F' and resid 653 through 660 removed outlier: 4.162A pdb=" N LEU F 660 " --> pdb=" O GLU F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 688 No H-bonds generated for 'chain 'F' and resid 686 through 688' Processing helix chain 'F' and resid 697 through 702 Processing helix chain 'F' and resid 714 through 731 Processing helix chain 'F' and resid 753 through 755 No H-bonds generated for 'chain 'F' and resid 753 through 755' Processing helix chain 'F' and resid 760 through 764 removed outlier: 3.501A pdb=" N ILE F 764 " --> pdb=" O MET F 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 760 through 764' Processing helix chain 'F' and resid 770 through 781 Processing helix chain 'F' and resid 786 through 809 removed outlier: 3.919A pdb=" N VAL F 793 " --> pdb=" O ALA F 789 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE F 796 " --> pdb=" O VAL F 792 " (cutoff:3.500A) Processing helix chain 'F' and resid 837 through 847 removed outlier: 4.476A pdb=" N PHE F 847 " --> pdb=" O LEU F 843 " (cutoff:3.500A) Processing helix chain 'F' and resid 858 through 873 Proline residue: F 862 - end of helix removed outlier: 4.222A pdb=" N VAL F 871 " --> pdb=" O ARG F 867 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N THR F 872 " --> pdb=" O VAL F 868 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 892 Processing helix chain 'F' and resid 926 through 933 Processing helix chain 'F' and resid 950 through 962 Processing helix chain 'F' and resid 975 through 987 removed outlier: 3.563A pdb=" N ALA F 978 " --> pdb=" O GLY F 975 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN F 979 " --> pdb=" O ASP F 976 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN F 982 " --> pdb=" O ASN F 979 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR F 983 " --> pdb=" O GLY F 980 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU F 987 " --> pdb=" O ILE F 984 " (cutoff:3.500A) Processing helix chain 'F' and resid 992 through 996 Processing helix chain 'F' and resid 1022 through 1028 Processing helix chain 'F' and resid 1042 through 1054 Processing helix chain 'F' and resid 1069 through 1071 No H-bonds generated for 'chain 'F' and resid 1069 through 1071' Processing helix chain 'F' and resid 1073 through 1075 No H-bonds generated for 'chain 'F' and resid 1073 through 1075' Processing helix chain 'F' and resid 1079 through 1083 Processing helix chain 'F' and resid 1100 through 1102 No H-bonds generated for 'chain 'F' and resid 1100 through 1102' Processing helix chain 'F' and resid 1112 through 1124 removed outlier: 4.216A pdb=" N ALA F1118 " --> pdb=" O TYR F1115 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP F1124 " --> pdb=" O LYS F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1142 through 1151 Processing helix chain 'F' and resid 1171 through 1181 removed outlier: 3.676A pdb=" N GLU F1176 " --> pdb=" O PRO F1172 " (cutoff:3.500A) Proline residue: F1179 - end of helix Processing helix chain 'F' and resid 1204 through 1218 Processing sheet with id= A, first strand: chain 'A' and resid 126 through 134 removed outlier: 6.575A pdb=" N SER A 256 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL A 282 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR A 258 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 201 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 202 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 214 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 204 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 180 through 184 Processing sheet with id= C, first strand: chain 'A' and resid 422 through 424 Processing sheet with id= D, first strand: chain 'A' and resid 451 through 454 removed outlier: 6.870A pdb=" N PHE A 736 " --> pdb=" O PHE A 707 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL A 709 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP A 738 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N ILE A 672 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE A 674 " --> pdb=" O PRO A 639 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 641 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A 676 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N HIS A 643 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU A 536 " --> pdb=" O VAL A 638 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU A 640 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 538 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU A 642 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY A 540 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N GLY A 644 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N VAL A 537 " --> pdb=" O GLU A 598 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS A 600 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE A 539 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER A 602 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 939 through 944 removed outlier: 3.513A pdb=" N GLY A 900 " --> pdb=" O TYR A 943 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 967 " --> pdb=" O ARG A 897 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ALA A 899 " --> pdb=" O ILE A 967 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA A 969 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE A1003 " --> pdb=" O TRP A 970 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ALA A 972 " --> pdb=" O ILE A1003 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU A1005 " --> pdb=" O ALA A 972 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU A1061 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU A1006 " --> pdb=" O LEU A1061 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A1063 " --> pdb=" O LEU A1006 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A1035 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE A1064 " --> pdb=" O THR A1035 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ALA A1037 " --> pdb=" O PHE A1064 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1129 through 1133 removed outlier: 6.800A pdb=" N LYS A1105 " --> pdb=" O ALA A1130 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL A1132 " --> pdb=" O LYS A1105 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N MET A1107 " --> pdb=" O VAL A1132 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU A1157 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU A1108 " --> pdb=" O GLU A1157 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A1159 " --> pdb=" O LEU A1108 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 126 through 134 removed outlier: 6.571A pdb=" N SER B 256 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL B 282 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR B 258 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 201 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 202 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 214 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 204 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 180 through 184 Processing sheet with id= I, first strand: chain 'B' and resid 422 through 424 Processing sheet with id= J, first strand: chain 'B' and resid 451 through 454 removed outlier: 6.868A pdb=" N PHE B 736 " --> pdb=" O PHE B 707 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL B 709 " --> pdb=" O PHE B 736 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASP B 738 " --> pdb=" O VAL B 709 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N ILE B 672 " --> pdb=" O VAL B 637 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE B 674 " --> pdb=" O PRO B 639 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 641 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL B 676 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N HIS B 643 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU B 536 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU B 640 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL B 538 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU B 642 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY B 540 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N GLY B 644 " --> pdb=" O GLY B 540 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL B 537 " --> pdb=" O GLU B 598 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS B 600 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE B 539 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER B 602 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 939 through 944 removed outlier: 3.513A pdb=" N GLY B 900 " --> pdb=" O TYR B 943 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 967 " --> pdb=" O ARG B 897 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ALA B 899 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA B 969 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B1003 " --> pdb=" O TRP B 970 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ALA B 972 " --> pdb=" O ILE B1003 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU B1005 " --> pdb=" O ALA B 972 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU B1061 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU B1006 " --> pdb=" O LEU B1061 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B1063 " --> pdb=" O LEU B1006 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR B1035 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE B1064 " --> pdb=" O THR B1035 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA B1037 " --> pdb=" O PHE B1064 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 1129 through 1133 removed outlier: 6.800A pdb=" N LYS B1105 " --> pdb=" O ALA B1130 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL B1132 " --> pdb=" O LYS B1105 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N MET B1107 " --> pdb=" O VAL B1132 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU B1157 " --> pdb=" O VAL B1106 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU B1108 " --> pdb=" O GLU B1157 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B1159 " --> pdb=" O LEU B1108 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 126 through 134 removed outlier: 6.575A pdb=" N SER C 256 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL C 282 " --> pdb=" O SER C 256 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR C 258 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 201 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 202 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL C 214 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 204 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 180 through 184 Processing sheet with id= O, first strand: chain 'C' and resid 422 through 424 Processing sheet with id= P, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.868A pdb=" N PHE C 736 " --> pdb=" O PHE C 707 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL C 709 " --> pdb=" O PHE C 736 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP C 738 " --> pdb=" O VAL C 709 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ILE C 672 " --> pdb=" O VAL C 637 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE C 674 " --> pdb=" O PRO C 639 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU C 641 " --> pdb=" O ILE C 674 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL C 676 " --> pdb=" O LEU C 641 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N HIS C 643 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU C 536 " --> pdb=" O VAL C 638 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU C 640 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL C 538 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU C 642 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY C 540 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N GLY C 644 " --> pdb=" O GLY C 540 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N VAL C 537 " --> pdb=" O GLU C 598 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS C 600 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE C 539 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER C 602 " --> pdb=" O ILE C 539 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 939 through 944 removed outlier: 3.514A pdb=" N GLY C 900 " --> pdb=" O TYR C 943 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE C 967 " --> pdb=" O ARG C 897 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ALA C 899 " --> pdb=" O ILE C 967 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA C 969 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C1003 " --> pdb=" O TRP C 970 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ALA C 972 " --> pdb=" O ILE C1003 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU C1005 " --> pdb=" O ALA C 972 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU C1061 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU C1006 " --> pdb=" O LEU C1061 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE C1063 " --> pdb=" O LEU C1006 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR C1035 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE C1064 " --> pdb=" O THR C1035 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA C1037 " --> pdb=" O PHE C1064 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 1129 through 1133 removed outlier: 6.801A pdb=" N LYS C1105 " --> pdb=" O ALA C1130 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL C1132 " --> pdb=" O LYS C1105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET C1107 " --> pdb=" O VAL C1132 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU C1157 " --> pdb=" O VAL C1106 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU C1108 " --> pdb=" O GLU C1157 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU C1159 " --> pdb=" O LEU C1108 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 126 through 134 removed outlier: 6.575A pdb=" N SER D 256 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL D 282 " --> pdb=" O SER D 256 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR D 258 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 201 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE D 202 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 214 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 204 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 180 through 184 Processing sheet with id= U, first strand: chain 'D' and resid 422 through 424 Processing sheet with id= V, first strand: chain 'D' and resid 451 through 454 removed outlier: 6.867A pdb=" N PHE D 736 " --> pdb=" O PHE D 707 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL D 709 " --> pdb=" O PHE D 736 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASP D 738 " --> pdb=" O VAL D 709 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ILE D 672 " --> pdb=" O VAL D 637 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE D 674 " --> pdb=" O PRO D 639 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU D 641 " --> pdb=" O ILE D 674 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL D 676 " --> pdb=" O LEU D 641 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N HIS D 643 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU D 536 " --> pdb=" O VAL D 638 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU D 640 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL D 538 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU D 642 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY D 540 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N GLY D 644 " --> pdb=" O GLY D 540 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N VAL D 537 " --> pdb=" O GLU D 598 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS D 600 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE D 539 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER D 602 " --> pdb=" O ILE D 539 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 939 through 944 removed outlier: 3.514A pdb=" N GLY D 900 " --> pdb=" O TYR D 943 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE D 967 " --> pdb=" O ARG D 897 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ALA D 899 " --> pdb=" O ILE D 967 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA D 969 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE D1003 " --> pdb=" O TRP D 970 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ALA D 972 " --> pdb=" O ILE D1003 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU D1005 " --> pdb=" O ALA D 972 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU D1061 " --> pdb=" O LEU D1004 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU D1006 " --> pdb=" O LEU D1061 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE D1063 " --> pdb=" O LEU D1006 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR D1035 " --> pdb=" O VAL D1062 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N PHE D1064 " --> pdb=" O THR D1035 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA D1037 " --> pdb=" O PHE D1064 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 1129 through 1133 removed outlier: 6.802A pdb=" N LYS D1105 " --> pdb=" O ALA D1130 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL D1132 " --> pdb=" O LYS D1105 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N MET D1107 " --> pdb=" O VAL D1132 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU D1157 " --> pdb=" O VAL D1106 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU D1108 " --> pdb=" O GLU D1157 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU D1159 " --> pdb=" O LEU D1108 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 126 through 134 removed outlier: 6.570A pdb=" N SER E 256 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL E 282 " --> pdb=" O SER E 256 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR E 258 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 201 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE E 202 " --> pdb=" O VAL E 214 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL E 214 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU E 204 " --> pdb=" O ALA E 212 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 180 through 184 Processing sheet with id= AA, first strand: chain 'E' and resid 422 through 424 Processing sheet with id= AB, first strand: chain 'E' and resid 451 through 454 removed outlier: 6.871A pdb=" N PHE E 736 " --> pdb=" O PHE E 707 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N VAL E 709 " --> pdb=" O PHE E 736 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP E 738 " --> pdb=" O VAL E 709 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ILE E 672 " --> pdb=" O VAL E 637 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE E 674 " --> pdb=" O PRO E 639 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU E 641 " --> pdb=" O ILE E 674 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL E 676 " --> pdb=" O LEU E 641 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N HIS E 643 " --> pdb=" O VAL E 676 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU E 536 " --> pdb=" O VAL E 638 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU E 640 " --> pdb=" O GLU E 536 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL E 538 " --> pdb=" O LEU E 640 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU E 642 " --> pdb=" O VAL E 538 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLY E 540 " --> pdb=" O LEU E 642 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY E 644 " --> pdb=" O GLY E 540 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N VAL E 537 " --> pdb=" O GLU E 598 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS E 600 " --> pdb=" O VAL E 537 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE E 539 " --> pdb=" O LYS E 600 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER E 602 " --> pdb=" O ILE E 539 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 939 through 944 removed outlier: 3.514A pdb=" N GLY E 900 " --> pdb=" O TYR E 943 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE E 967 " --> pdb=" O ARG E 897 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ALA E 899 " --> pdb=" O ILE E 967 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA E 969 " --> pdb=" O ALA E 899 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE E1003 " --> pdb=" O TRP E 970 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA E 972 " --> pdb=" O ILE E1003 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU E1005 " --> pdb=" O ALA E 972 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU E1061 " --> pdb=" O LEU E1004 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU E1006 " --> pdb=" O LEU E1061 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE E1063 " --> pdb=" O LEU E1006 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR E1035 " --> pdb=" O VAL E1062 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N PHE E1064 " --> pdb=" O THR E1035 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ALA E1037 " --> pdb=" O PHE E1064 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 1129 through 1133 removed outlier: 6.801A pdb=" N LYS E1105 " --> pdb=" O ALA E1130 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL E1132 " --> pdb=" O LYS E1105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET E1107 " --> pdb=" O VAL E1132 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU E1157 " --> pdb=" O VAL E1106 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU E1108 " --> pdb=" O GLU E1157 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU E1159 " --> pdb=" O LEU E1108 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 126 through 134 removed outlier: 6.574A pdb=" N SER F 256 " --> pdb=" O ILE F 280 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL F 282 " --> pdb=" O SER F 256 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR F 258 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA F 201 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE F 202 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL F 214 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU F 204 " --> pdb=" O ALA F 212 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 180 through 184 Processing sheet with id= AG, first strand: chain 'F' and resid 422 through 424 Processing sheet with id= AH, first strand: chain 'F' and resid 451 through 454 removed outlier: 6.868A pdb=" N PHE F 736 " --> pdb=" O PHE F 707 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL F 709 " --> pdb=" O PHE F 736 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP F 738 " --> pdb=" O VAL F 709 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ILE F 672 " --> pdb=" O VAL F 637 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE F 674 " --> pdb=" O PRO F 639 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU F 641 " --> pdb=" O ILE F 674 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL F 676 " --> pdb=" O LEU F 641 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N HIS F 643 " --> pdb=" O VAL F 676 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU F 536 " --> pdb=" O VAL F 638 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU F 640 " --> pdb=" O GLU F 536 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL F 538 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU F 642 " --> pdb=" O VAL F 538 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY F 540 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N GLY F 644 " --> pdb=" O GLY F 540 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N VAL F 537 " --> pdb=" O GLU F 598 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS F 600 " --> pdb=" O VAL F 537 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE F 539 " --> pdb=" O LYS F 600 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER F 602 " --> pdb=" O ILE F 539 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 939 through 944 removed outlier: 3.513A pdb=" N GLY F 900 " --> pdb=" O TYR F 943 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE F 967 " --> pdb=" O ARG F 897 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ALA F 899 " --> pdb=" O ILE F 967 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA F 969 " --> pdb=" O ALA F 899 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE F1003 " --> pdb=" O TRP F 970 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA F 972 " --> pdb=" O ILE F1003 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU F1005 " --> pdb=" O ALA F 972 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU F1061 " --> pdb=" O LEU F1004 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU F1006 " --> pdb=" O LEU F1061 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE F1063 " --> pdb=" O LEU F1006 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR F1035 " --> pdb=" O VAL F1062 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N PHE F1064 " --> pdb=" O THR F1035 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA F1037 " --> pdb=" O PHE F1064 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 1129 through 1133 removed outlier: 6.800A pdb=" N LYS F1105 " --> pdb=" O ALA F1130 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL F1132 " --> pdb=" O LYS F1105 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N MET F1107 " --> pdb=" O VAL F1132 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU F1157 " --> pdb=" O VAL F1106 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU F1108 " --> pdb=" O GLU F1157 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU F1159 " --> pdb=" O LEU F1108 " (cutoff:3.500A) 1950 hydrogen bonds defined for protein. 5238 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: 18.03 Time building geometry restraints manager: 16.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 13531 1.33 - 1.47: 16769 1.47 - 1.60: 23016 1.60 - 1.73: 12 1.73 - 1.87: 438 Bond restraints: 53766 Sorted by residual: bond pdb=" C2 QSP D1303 " pdb=" N3 QSP D1303 " ideal model delta sigma weight residual 1.655 1.456 0.199 2.00e-02 2.50e+03 9.86e+01 bond pdb=" C2 QSP C1303 " pdb=" N3 QSP C1303 " ideal model delta sigma weight residual 1.655 1.457 0.198 2.00e-02 2.50e+03 9.82e+01 bond pdb=" C2 QSP A1303 " pdb=" N3 QSP A1303 " ideal model delta sigma weight residual 1.655 1.457 0.198 2.00e-02 2.50e+03 9.82e+01 bond pdb=" C2 QSP F1303 " pdb=" N3 QSP F1303 " ideal model delta sigma weight residual 1.655 1.457 0.198 2.00e-02 2.50e+03 9.81e+01 bond pdb=" C2 QSP B1303 " pdb=" N3 QSP B1303 " ideal model delta sigma weight residual 1.655 1.457 0.198 2.00e-02 2.50e+03 9.79e+01 ... (remaining 53761 not shown) Histogram of bond angle deviations from ideal: 92.24 - 101.66: 326 101.66 - 111.08: 19771 111.08 - 120.49: 33116 120.49 - 129.91: 19400 129.91 - 139.33: 317 Bond angle restraints: 72930 Sorted by residual: angle pdb=" C ACO D1302 " pdb=" S1P ACO D1302 " pdb=" C2P ACO D1302 " ideal model delta sigma weight residual 101.25 108.70 -7.45 1.00e+00 1.00e+00 5.55e+01 angle pdb=" C ACO B1302 " pdb=" S1P ACO B1302 " pdb=" C2P ACO B1302 " ideal model delta sigma weight residual 101.25 108.63 -7.38 1.00e+00 1.00e+00 5.44e+01 angle pdb=" C ACO E1302 " pdb=" S1P ACO E1302 " pdb=" C2P ACO E1302 " ideal model delta sigma weight residual 101.25 108.44 -7.19 1.00e+00 1.00e+00 5.17e+01 angle pdb=" C ACO F1302 " pdb=" S1P ACO F1302 " pdb=" C2P ACO F1302 " ideal model delta sigma weight residual 101.25 108.39 -7.14 1.00e+00 1.00e+00 5.10e+01 angle pdb=" C11 QSP F1303 " pdb=" C2 QSP F1303 " pdb=" N3 QSP F1303 " ideal model delta sigma weight residual 111.10 129.12 -18.02 3.00e+00 1.11e-01 3.61e+01 ... (remaining 72925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.93: 30658 21.93 - 43.86: 1246 43.86 - 65.79: 431 65.79 - 87.72: 55 87.72 - 109.65: 10 Dihedral angle restraints: 32400 sinusoidal: 13248 harmonic: 19152 Sorted by residual: dihedral pdb=" CA LEU B 307 " pdb=" C LEU B 307 " pdb=" N VAL B 308 " pdb=" CA VAL B 308 " ideal model delta harmonic sigma weight residual 180.00 153.40 26.60 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA LEU E 307 " pdb=" C LEU E 307 " pdb=" N VAL E 308 " pdb=" CA VAL E 308 " ideal model delta harmonic sigma weight residual 180.00 153.55 26.45 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA LEU C 307 " pdb=" C LEU C 307 " pdb=" N VAL C 308 " pdb=" CA VAL C 308 " ideal model delta harmonic sigma weight residual 180.00 153.59 26.41 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 32397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.345: 7938 0.345 - 0.691: 0 0.691 - 1.036: 0 1.036 - 1.381: 0 1.381 - 1.727: 6 Chirality restraints: 7944 Sorted by residual: chirality pdb=" C2 QSP E1303 " pdb=" C11 QSP E1303 " pdb=" N3 QSP E1303 " pdb=" S1 QSP E1303 " both_signs ideal model delta sigma weight residual False 3.26 1.53 1.73 2.00e-01 2.50e+01 7.45e+01 chirality pdb=" C2 QSP B1303 " pdb=" C11 QSP B1303 " pdb=" N3 QSP B1303 " pdb=" S1 QSP B1303 " both_signs ideal model delta sigma weight residual False 3.26 1.54 1.72 2.00e-01 2.50e+01 7.39e+01 chirality pdb=" C2 QSP A1303 " pdb=" C11 QSP A1303 " pdb=" N3 QSP A1303 " pdb=" S1 QSP A1303 " both_signs ideal model delta sigma weight residual False 3.26 1.54 1.72 2.00e-01 2.50e+01 7.38e+01 ... (remaining 7941 not shown) Planarity restraints: 9600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P ACO E1302 " -0.070 2.00e-02 2.50e+03 5.82e-02 4.24e+01 pdb=" C5P ACO E1302 " 0.016 2.00e-02 2.50e+03 pdb=" C6P ACO E1302 " -0.052 2.00e-02 2.50e+03 pdb=" N4P ACO E1302 " 0.094 2.00e-02 2.50e+03 pdb=" O5P ACO E1302 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO B1302 " 0.064 2.00e-02 2.50e+03 5.28e-02 3.48e+01 pdb=" C5P ACO B1302 " -0.014 2.00e-02 2.50e+03 pdb=" C6P ACO B1302 " 0.047 2.00e-02 2.50e+03 pdb=" N4P ACO B1302 " -0.085 2.00e-02 2.50e+03 pdb=" O5P ACO B1302 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO C1302 " -0.061 2.00e-02 2.50e+03 5.03e-02 3.17e+01 pdb=" C5P ACO C1302 " 0.014 2.00e-02 2.50e+03 pdb=" C6P ACO C1302 " -0.045 2.00e-02 2.50e+03 pdb=" N4P ACO C1302 " 0.081 2.00e-02 2.50e+03 pdb=" O5P ACO C1302 " 0.011 2.00e-02 2.50e+03 ... (remaining 9597 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 638 2.67 - 3.23: 46872 3.23 - 3.79: 73428 3.79 - 4.34: 111574 4.34 - 4.90: 180255 Nonbonded interactions: 412767 Sorted by model distance: nonbonded pdb="MG MG B1301 " pdb=" O3B QSP B1303 " model vdw 2.114 2.170 nonbonded pdb="MG MG E1301 " pdb=" O3B QSP E1303 " model vdw 2.117 2.170 nonbonded pdb="MG MG D1301 " pdb=" O3B QSP D1303 " model vdw 2.123 2.170 nonbonded pdb=" OD1 ASN F 678 " pdb="MG MG F1301 " model vdw 2.127 2.170 nonbonded pdb=" OD1 ASN C 678 " pdb="MG MG C1301 " model vdw 2.130 2.170 ... (remaining 412762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 3.460 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: 0.060 Extract box with map and model: 18.530 Check model and map are aligned: 0.720 Set scattering table: 0.380 Process input model: 103.990 Find NCS groups from input model: 2.550 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:9.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 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 : 0.009 0.199 53766 Z= 0.623 Angle : 1.176 18.022 72930 Z= 0.774 Chirality : 0.085 1.727 7944 Planarity : 0.007 0.165 9600 Dihedral : 14.020 109.654 20148 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.67 % Favored : 97.24 % Rotamer: Outliers : 0.11 % Allowed : 2.29 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.09), residues: 6702 helix: -0.78 (0.08), residues: 2688 sheet: 0.07 (0.14), residues: 1092 loop : -1.79 (0.09), residues: 2922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP A 466 HIS 0.013 0.003 HIS C 643 PHE 0.027 0.003 PHE F1046 TYR 0.046 0.005 TYR E 761 ARG 0.019 0.002 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1216 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1210 time to evaluate : 4.446 Fit side-chains revert: symmetry clash REVERT: A 118 MET cc_start: 0.8805 (mmp) cc_final: 0.8361 (mmt) REVERT: A 165 TYR cc_start: 0.8979 (t80) cc_final: 0.8758 (t80) REVERT: A 760 MET cc_start: 0.9093 (ttt) cc_final: 0.8855 (ttm) REVERT: A 838 GLU cc_start: 0.8501 (mp0) cc_final: 0.8243 (mp0) REVERT: B 190 LEU cc_start: 0.8853 (tp) cc_final: 0.8610 (tp) REVERT: B 405 ARG cc_start: 0.8650 (mtm180) cc_final: 0.8329 (mtm180) REVERT: B 410 GLU cc_start: 0.8337 (mp0) cc_final: 0.8120 (mp0) REVERT: B 598 GLU cc_start: 0.8550 (tt0) cc_final: 0.8240 (tt0) REVERT: B 629 ASP cc_start: 0.8651 (t0) cc_final: 0.8443 (t0) REVERT: B 781 ARG cc_start: 0.8915 (mtm180) cc_final: 0.8704 (mtm180) REVERT: B 816 GLU cc_start: 0.8700 (tt0) cc_final: 0.8486 (tt0) REVERT: B 1034 MET cc_start: 0.8873 (ptt) cc_final: 0.8599 (ptt) REVERT: C 290 GLU cc_start: 0.8572 (pm20) cc_final: 0.8233 (pm20) REVERT: C 410 GLU cc_start: 0.8350 (mp0) cc_final: 0.8137 (mp0) REVERT: C 566 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8342 (mm-30) REVERT: C 682 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8353 (t80) REVERT: C 1188 MET cc_start: 0.9018 (mtm) cc_final: 0.8790 (mtp) REVERT: D 410 GLU cc_start: 0.8352 (mp0) cc_final: 0.8147 (mp0) REVERT: D 760 MET cc_start: 0.9091 (ttt) cc_final: 0.8844 (ttm) REVERT: E 190 LEU cc_start: 0.8952 (tp) cc_final: 0.8691 (tp) REVERT: E 405 ARG cc_start: 0.8675 (mtm180) cc_final: 0.8403 (mtm180) REVERT: E 410 GLU cc_start: 0.8320 (mp0) cc_final: 0.8091 (mp0) REVERT: E 434 MET cc_start: 0.9013 (ttm) cc_final: 0.8752 (mtt) REVERT: E 682 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8507 (t80) REVERT: E 816 GLU cc_start: 0.8671 (tt0) cc_final: 0.8422 (tt0) REVERT: E 1185 MET cc_start: 0.9103 (ttp) cc_final: 0.8887 (ttm) REVERT: F 118 MET cc_start: 0.8673 (mmp) cc_final: 0.8201 (mmt) REVERT: F 172 MET cc_start: 0.8879 (mtt) cc_final: 0.8666 (mtm) REVERT: F 760 MET cc_start: 0.9087 (ttt) cc_final: 0.8765 (ttm) outliers start: 6 outliers final: 4 residues processed: 1213 average time/residue: 1.6765 time to fit residues: 2440.7806 Evaluate side-chains 1106 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1100 time to evaluate : 4.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain E residue 682 PHE Chi-restraints excluded: chain F residue 682 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 562 optimal weight: 0.9980 chunk 504 optimal weight: 1.9990 chunk 280 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 340 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 chunk 522 optimal weight: 0.7980 chunk 202 optimal weight: 2.9990 chunk 317 optimal weight: 0.2980 chunk 388 optimal weight: 1.9990 chunk 604 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1096 ASN B 117 ASN B 148 GLN B 251 GLN B 413 ASN B 589 GLN B 590 HIS B 805 ASN B 849 ASN B1096 ASN C 104 GLN C 148 GLN C 501 GLN C 589 GLN C1096 ASN D 498 ASN D 501 GLN D 573 GLN D 590 HIS D 805 ASN D 849 ASN D 973 GLN D1096 ASN E 148 GLN E 251 GLN E 498 ASN E1096 ASN F 722 GLN F1096 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 53766 Z= 0.202 Angle : 0.524 8.142 72930 Z= 0.275 Chirality : 0.044 0.213 7944 Planarity : 0.005 0.039 9600 Dihedral : 8.254 91.485 7704 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.36 % Allowed : 9.03 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.10), residues: 6702 helix: 0.86 (0.10), residues: 2706 sheet: 0.49 (0.15), residues: 1104 loop : -1.38 (0.10), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 466 HIS 0.005 0.001 HIS F 543 PHE 0.026 0.001 PHE D1046 TYR 0.013 0.001 TYR A 761 ARG 0.008 0.000 ARG C 837 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1193 time to evaluate : 4.376 Fit side-chains revert: symmetry clash REVERT: A 118 MET cc_start: 0.8788 (mmp) cc_final: 0.8147 (mmt) REVERT: A 165 TYR cc_start: 0.8840 (t80) cc_final: 0.8594 (t80) REVERT: A 760 MET cc_start: 0.9102 (ttt) cc_final: 0.8853 (ttm) REVERT: B 190 LEU cc_start: 0.8763 (tp) cc_final: 0.8521 (tp) REVERT: B 410 GLU cc_start: 0.8263 (mp0) cc_final: 0.8047 (mp0) REVERT: B 1084 GLU cc_start: 0.8601 (mp0) cc_final: 0.8222 (mp0) REVERT: C 290 GLU cc_start: 0.8495 (pm20) cc_final: 0.8161 (pm20) REVERT: C 410 GLU cc_start: 0.8292 (mp0) cc_final: 0.8073 (mp0) REVERT: C 866 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8428 (tmtm) REVERT: C 1027 GLN cc_start: 0.8389 (mt0) cc_final: 0.8090 (mt0) REVERT: D 113 SER cc_start: 0.8488 (m) cc_final: 0.8253 (p) REVERT: D 290 GLU cc_start: 0.8556 (pm20) cc_final: 0.8304 (pm20) REVERT: D 410 GLU cc_start: 0.8253 (mp0) cc_final: 0.8050 (mp0) REVERT: D 760 MET cc_start: 0.9025 (ttt) cc_final: 0.8814 (ttt) REVERT: D 1027 GLN cc_start: 0.8308 (mt0) cc_final: 0.7991 (tt0) REVERT: E 118 MET cc_start: 0.8685 (mmp) cc_final: 0.8153 (mmt) REVERT: E 405 ARG cc_start: 0.8592 (mtm180) cc_final: 0.8372 (mtm180) REVERT: E 410 GLU cc_start: 0.8242 (mp0) cc_final: 0.8027 (mp0) REVERT: E 819 THR cc_start: 0.8949 (p) cc_final: 0.8744 (p) REVERT: E 1027 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8028 (mt0) REVERT: F 118 MET cc_start: 0.8704 (mmp) cc_final: 0.8155 (mmt) REVERT: F 760 MET cc_start: 0.9063 (ttt) cc_final: 0.8759 (ttm) REVERT: F 1027 GLN cc_start: 0.8324 (mt0) cc_final: 0.8095 (tt0) outliers start: 75 outliers final: 16 residues processed: 1212 average time/residue: 1.6841 time to fit residues: 2449.6855 Evaluate side-chains 1109 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1091 time to evaluate : 4.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 866 LYS Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 1027 GLN Chi-restraints excluded: chain E residue 1209 LEU Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 505 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 336 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 503 optimal weight: 0.9990 chunk 411 optimal weight: 3.9990 chunk 166 optimal weight: 0.0570 chunk 605 optimal weight: 5.9990 chunk 654 optimal weight: 0.3980 chunk 539 optimal weight: 1.9990 chunk 600 optimal weight: 0.4980 chunk 206 optimal weight: 2.9990 chunk 486 optimal weight: 0.6980 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 148 GLN A 292 GLN A 404 HIS A1027 GLN A1096 ASN B 117 ASN B 148 GLN B 251 GLN B 404 HIS B 413 ASN B 677 ASN B1027 GLN B1096 ASN C 104 GLN C 677 ASN C 849 ASN C1096 ASN D 501 GLN D 573 GLN D 677 ASN D 722 GLN D1096 ASN E 148 GLN E 251 GLN E 404 HIS E 413 ASN E 677 ASN E 773 GLN E1096 ASN F 148 GLN F 404 HIS ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1096 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 53766 Z= 0.150 Angle : 0.469 8.600 72930 Z= 0.243 Chirality : 0.042 0.180 7944 Planarity : 0.004 0.039 9600 Dihedral : 7.747 80.493 7694 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.22 % Allowed : 11.04 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.10), residues: 6702 helix: 1.49 (0.10), residues: 2700 sheet: 0.73 (0.15), residues: 1044 loop : -1.13 (0.10), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 466 HIS 0.004 0.001 HIS E1045 PHE 0.023 0.001 PHE D1046 TYR 0.011 0.001 TYR B 233 ARG 0.009 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1173 time to evaluate : 4.466 Fit side-chains revert: symmetry clash REVERT: A 118 MET cc_start: 0.8761 (mmp) cc_final: 0.8329 (mmt) REVERT: A 165 TYR cc_start: 0.8802 (t80) cc_final: 0.8563 (t80) REVERT: A 760 MET cc_start: 0.9064 (ttt) cc_final: 0.8802 (ttm) REVERT: B 410 GLU cc_start: 0.8241 (mp0) cc_final: 0.8021 (mp0) REVERT: C 290 GLU cc_start: 0.8483 (pm20) cc_final: 0.8163 (pm20) REVERT: C 410 GLU cc_start: 0.8259 (mp0) cc_final: 0.8040 (mp0) REVERT: C 866 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8429 (tmtm) REVERT: D 290 GLU cc_start: 0.8513 (pm20) cc_final: 0.8260 (pm20) REVERT: E 149 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8391 (mp) REVERT: E 410 GLU cc_start: 0.8220 (mp0) cc_final: 0.7999 (mp0) REVERT: E 819 THR cc_start: 0.8926 (p) cc_final: 0.8687 (p) REVERT: E 1084 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: F 118 MET cc_start: 0.8662 (mmp) cc_final: 0.8091 (mmt) REVERT: F 760 MET cc_start: 0.9026 (ttt) cc_final: 0.8771 (ttm) outliers start: 67 outliers final: 31 residues processed: 1192 average time/residue: 1.7193 time to fit residues: 2453.5373 Evaluate side-chains 1157 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1123 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 1211 GLU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 589 GLN Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1123 LYS Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 866 LYS Chi-restraints excluded: chain C residue 1187 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 976 ASP Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 816 GLU Chi-restraints excluded: chain E residue 1034 MET Chi-restraints excluded: chain E residue 1084 GLU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 505 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 598 optimal weight: 0.9980 chunk 455 optimal weight: 7.9990 chunk 314 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 406 optimal weight: 2.9990 chunk 608 optimal weight: 3.9990 chunk 643 optimal weight: 0.6980 chunk 317 optimal weight: 0.9980 chunk 576 optimal weight: 1.9990 chunk 173 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 404 HIS A 677 ASN A1096 ASN B 148 GLN B 251 GLN B 404 HIS B 413 ASN B 677 ASN B1096 ASN C 104 GLN C 349 ASN C 677 ASN C1045 HIS C1096 ASN D 501 GLN D 573 GLN D 677 ASN D 799 GLN D 818 GLN D1045 HIS D1096 ASN E 148 GLN E 404 HIS E 413 ASN E 677 ASN E1027 GLN E1096 ASN F 148 GLN F 404 HIS F 748 ASN F 932 GLN F1027 GLN F1045 HIS F1096 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 53766 Z= 0.181 Angle : 0.471 9.266 72930 Z= 0.244 Chirality : 0.043 0.179 7944 Planarity : 0.004 0.041 9600 Dihedral : 7.659 77.942 7694 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.61 % Allowed : 11.82 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.10), residues: 6702 helix: 1.68 (0.10), residues: 2700 sheet: 0.91 (0.16), residues: 1044 loop : -1.06 (0.10), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 466 HIS 0.005 0.001 HIS A 643 PHE 0.024 0.001 PHE D1046 TYR 0.011 0.001 TYR F 761 ARG 0.010 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1246 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1157 time to evaluate : 4.414 Fit side-chains revert: symmetry clash REVERT: A 118 MET cc_start: 0.8744 (mmp) cc_final: 0.8280 (mmt) REVERT: A 760 MET cc_start: 0.9043 (ttt) cc_final: 0.8774 (ttm) REVERT: A 838 GLU cc_start: 0.8321 (mp0) cc_final: 0.8118 (mp0) REVERT: B 190 LEU cc_start: 0.8810 (tp) cc_final: 0.8605 (tp) REVERT: B 410 GLU cc_start: 0.8231 (mp0) cc_final: 0.8011 (mp0) REVERT: B 1084 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: C 290 GLU cc_start: 0.8500 (pm20) cc_final: 0.8163 (pm20) REVERT: C 410 GLU cc_start: 0.8265 (mp0) cc_final: 0.8046 (mp0) REVERT: C 1104 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8881 (mttm) REVERT: D 290 GLU cc_start: 0.8555 (pm20) cc_final: 0.8339 (pm20) REVERT: E 149 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8417 (mp) REVERT: E 410 GLU cc_start: 0.8224 (mp0) cc_final: 0.8008 (mp0) REVERT: E 819 THR cc_start: 0.8912 (p) cc_final: 0.8660 (p) REVERT: E 1104 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8845 (mttp) REVERT: F 118 MET cc_start: 0.8640 (mmp) cc_final: 0.8113 (mmt) outliers start: 89 outliers final: 43 residues processed: 1188 average time/residue: 1.6798 time to fit residues: 2398.3273 Evaluate side-chains 1178 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1131 time to evaluate : 5.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1211 GLU Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 837 ARG Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1084 GLU Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 1104 LYS Chi-restraints excluded: chain C residue 1187 LYS Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 976 ASP Chi-restraints excluded: chain D residue 1163 ASP Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 816 GLU Chi-restraints excluded: chain E residue 837 ARG Chi-restraints excluded: chain E residue 976 ASP Chi-restraints excluded: chain E residue 1034 MET Chi-restraints excluded: chain E residue 1104 LYS Chi-restraints excluded: chain E residue 1209 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 1027 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 536 optimal weight: 0.9980 chunk 365 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 479 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 549 optimal weight: 3.9990 chunk 444 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 328 optimal weight: 0.1980 chunk 577 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 404 HIS A1096 ASN B 148 GLN B 251 GLN B 404 HIS B 413 ASN B 677 ASN B1096 ASN C 104 GLN C 349 ASN C 677 ASN C1096 ASN D 501 GLN D 573 GLN D 677 ASN D 799 GLN D1045 HIS D1096 ASN E 148 GLN E 404 HIS E 413 ASN E 677 ASN ** E1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1096 ASN F 148 GLN F 404 HIS F 932 GLN F1096 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 53766 Z= 0.266 Angle : 0.514 9.881 72930 Z= 0.267 Chirality : 0.045 0.199 7944 Planarity : 0.004 0.043 9600 Dihedral : 7.788 78.572 7694 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.94 % Allowed : 12.30 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.10), residues: 6702 helix: 1.62 (0.10), residues: 2700 sheet: 0.96 (0.15), residues: 1104 loop : -1.11 (0.10), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 466 HIS 0.006 0.001 HIS A 643 PHE 0.024 0.001 PHE C1046 TYR 0.015 0.001 TYR A 761 ARG 0.010 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1272 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1165 time to evaluate : 4.435 Fit side-chains REVERT: A 118 MET cc_start: 0.8735 (mmp) cc_final: 0.8264 (mmt) REVERT: A 307 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8251 (mp) REVERT: A 760 MET cc_start: 0.8988 (ttt) cc_final: 0.8753 (ttm) REVERT: A 838 GLU cc_start: 0.8336 (mp0) cc_final: 0.8097 (mp0) REVERT: B 190 LEU cc_start: 0.8829 (tp) cc_final: 0.8619 (tp) REVERT: B 410 GLU cc_start: 0.8247 (mp0) cc_final: 0.8027 (mp0) REVERT: B 1084 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: C 290 GLU cc_start: 0.8552 (pm20) cc_final: 0.8167 (pm20) REVERT: C 410 GLU cc_start: 0.8281 (mp0) cc_final: 0.8066 (mp0) REVERT: C 1104 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8884 (mttm) REVERT: D 290 GLU cc_start: 0.8613 (pm20) cc_final: 0.8363 (pm20) REVERT: E 410 GLU cc_start: 0.8247 (mp0) cc_final: 0.8032 (mp0) REVERT: E 819 THR cc_start: 0.8901 (p) cc_final: 0.8656 (p) REVERT: E 1104 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8826 (mttp) REVERT: F 118 MET cc_start: 0.8613 (mmp) cc_final: 0.8131 (mmt) REVERT: F 497 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: F 569 MET cc_start: 0.8527 (mmm) cc_final: 0.8290 (mmm) REVERT: F 1027 GLN cc_start: 0.8192 (mt0) cc_final: 0.7962 (tt0) outliers start: 107 outliers final: 59 residues processed: 1199 average time/residue: 1.7057 time to fit residues: 2456.5935 Evaluate side-chains 1195 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1131 time to evaluate : 4.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 1211 GLU Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1084 GLU Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain C residue 880 TRP Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1104 LYS Chi-restraints excluded: chain C residue 1187 LYS Chi-restraints excluded: chain C residue 1211 GLU Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 692 MET Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 837 ARG Chi-restraints excluded: chain D residue 880 TRP Chi-restraints excluded: chain D residue 976 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 566 GLU Chi-restraints excluded: chain E residue 816 GLU Chi-restraints excluded: chain E residue 837 ARG Chi-restraints excluded: chain E residue 976 ASP Chi-restraints excluded: chain E residue 1034 MET Chi-restraints excluded: chain E residue 1104 LYS Chi-restraints excluded: chain E residue 1209 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 377 GLU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 497 GLU Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 837 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 216 optimal weight: 0.0020 chunk 579 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 377 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 644 optimal weight: 2.9990 chunk 534 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 338 optimal weight: 1.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 404 HIS A 932 GLN A1096 ASN B 148 GLN B 404 HIS B 413 ASN B 677 ASN B1096 ASN C 104 GLN C 349 ASN C 677 ASN C1096 ASN D 501 GLN D 573 GLN D 677 ASN D 799 GLN D1045 HIS D1096 ASN E 148 GLN E 404 HIS E 413 ASN E 677 ASN ** E1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1045 HIS E1096 ASN F 148 GLN F 404 HIS F 932 GLN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1096 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 53766 Z= 0.183 Angle : 0.476 9.654 72930 Z= 0.247 Chirality : 0.043 0.174 7944 Planarity : 0.004 0.040 9600 Dihedral : 7.600 78.085 7694 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.67 % Allowed : 13.46 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.10), residues: 6702 helix: 1.74 (0.10), residues: 2700 sheet: 0.97 (0.16), residues: 1092 loop : -0.98 (0.10), residues: 2910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 466 HIS 0.004 0.001 HIS E1045 PHE 0.024 0.001 PHE C1046 TYR 0.011 0.001 TYR F 761 ARG 0.009 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1155 time to evaluate : 4.473 Fit side-chains REVERT: A 118 MET cc_start: 0.8721 (mmp) cc_final: 0.8264 (mmt) REVERT: A 760 MET cc_start: 0.8986 (ttt) cc_final: 0.8767 (ttm) REVERT: A 838 GLU cc_start: 0.8322 (mp0) cc_final: 0.8092 (mp0) REVERT: B 190 LEU cc_start: 0.8813 (tp) cc_final: 0.8597 (tp) REVERT: C 290 GLU cc_start: 0.8523 (pm20) cc_final: 0.8233 (pm20) REVERT: C 410 GLU cc_start: 0.8281 (mp0) cc_final: 0.8062 (mp0) REVERT: C 1104 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8860 (mttm) REVERT: D 290 GLU cc_start: 0.8585 (pm20) cc_final: 0.8335 (pm20) REVERT: E 149 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8442 (mp) REVERT: E 410 GLU cc_start: 0.8244 (mp0) cc_final: 0.8032 (mp0) REVERT: E 569 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8208 (mmm) REVERT: E 819 THR cc_start: 0.8866 (p) cc_final: 0.8609 (p) REVERT: E 1027 GLN cc_start: 0.8220 (mt0) cc_final: 0.7960 (mt0) REVERT: F 118 MET cc_start: 0.8614 (mmp) cc_final: 0.8016 (mmt) outliers start: 92 outliers final: 51 residues processed: 1184 average time/residue: 1.6479 time to fit residues: 2348.0190 Evaluate side-chains 1185 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1131 time to evaluate : 4.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 1187 LYS Chi-restraints excluded: chain A residue 1211 GLU Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1104 LYS Chi-restraints excluded: chain C residue 1187 LYS Chi-restraints excluded: chain C residue 1211 GLU Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 837 ARG Chi-restraints excluded: chain D residue 880 TRP Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 603 LEU Chi-restraints excluded: chain E residue 800 MET Chi-restraints excluded: chain E residue 816 GLU Chi-restraints excluded: chain E residue 976 ASP Chi-restraints excluded: chain E residue 1034 MET Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 172 MET Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 505 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 621 optimal weight: 2.9990 chunk 72 optimal weight: 0.0060 chunk 367 optimal weight: 0.9980 chunk 470 optimal weight: 0.0870 chunk 364 optimal weight: 3.9990 chunk 542 optimal weight: 0.7980 chunk 359 optimal weight: 0.6980 chunk 641 optimal weight: 1.9990 chunk 401 optimal weight: 3.9990 chunk 391 optimal weight: 2.9990 chunk 296 optimal weight: 0.0030 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 404 HIS A 583 HIS A1045 HIS A1096 ASN B 148 GLN B 404 HIS B 413 ASN B 677 ASN B1096 ASN C 104 GLN C 349 ASN C 677 ASN C1096 ASN D 501 GLN D 573 GLN D 614 ASN D 677 ASN D1045 HIS D1096 ASN E 148 GLN E 404 HIS E 413 ASN E 677 ASN E1027 GLN E1096 ASN F 148 GLN F 404 HIS F 614 ASN F 932 GLN F1096 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 53766 Z= 0.125 Angle : 0.445 9.434 72930 Z= 0.228 Chirality : 0.041 0.150 7944 Planarity : 0.004 0.040 9600 Dihedral : 7.318 75.919 7694 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.05 % Allowed : 14.35 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.10), residues: 6702 helix: 1.83 (0.10), residues: 2742 sheet: 1.23 (0.16), residues: 1146 loop : -0.92 (0.10), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 466 HIS 0.002 0.000 HIS A1045 PHE 0.021 0.001 PHE C1046 TYR 0.009 0.001 TYR E 233 ARG 0.010 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1182 time to evaluate : 4.359 Fit side-chains revert: symmetry clash REVERT: A 118 MET cc_start: 0.8720 (mmp) cc_final: 0.8260 (mmt) REVERT: A 307 LEU cc_start: 0.8395 (mp) cc_final: 0.7930 (mt) REVERT: B 190 LEU cc_start: 0.8710 (tp) cc_final: 0.8483 (tp) REVERT: C 290 GLU cc_start: 0.8521 (pm20) cc_final: 0.8143 (pm20) REVERT: C 410 GLU cc_start: 0.8255 (mp0) cc_final: 0.8031 (mp0) REVERT: C 806 GLU cc_start: 0.8208 (tt0) cc_final: 0.7960 (tp30) REVERT: E 149 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8363 (mp) REVERT: E 410 GLU cc_start: 0.8231 (mp0) cc_final: 0.8015 (mp0) REVERT: E 569 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8176 (mmm) REVERT: E 819 THR cc_start: 0.8825 (p) cc_final: 0.8562 (p) REVERT: F 118 MET cc_start: 0.8624 (mmp) cc_final: 0.8028 (mmt) outliers start: 58 outliers final: 35 residues processed: 1198 average time/residue: 1.6832 time to fit residues: 2442.5338 Evaluate side-chains 1198 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1161 time to evaluate : 4.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 944 ASN Chi-restraints excluded: chain A residue 1187 LYS Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain B residue 892 SER Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1187 LYS Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 976 ASP Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 976 ASP Chi-restraints excluded: chain E residue 1034 MET Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 505 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 397 optimal weight: 1.9990 chunk 256 optimal weight: 0.6980 chunk 383 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 408 optimal weight: 0.9990 chunk 437 optimal weight: 1.9990 chunk 317 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 504 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 404 HIS A 583 HIS A 677 ASN A 773 GLN A1096 ASN B 148 GLN B 251 GLN B 404 HIS B 413 ASN B 677 ASN B 944 ASN B1096 ASN C 104 GLN C 349 ASN C 404 HIS C 583 HIS C 677 ASN C1096 ASN D 349 ASN D 404 HIS D 677 ASN D1096 ASN E 148 GLN E 404 HIS E 413 ASN E 677 ASN E 849 ASN E1096 ASN F 148 GLN F 404 HIS F 583 HIS F 677 ASN F 932 GLN F1096 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 53766 Z= 0.245 Angle : 0.509 10.146 72930 Z= 0.263 Chirality : 0.044 0.194 7944 Planarity : 0.004 0.042 9600 Dihedral : 7.564 79.069 7692 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.32 % Allowed : 14.91 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.10), residues: 6702 helix: 1.79 (0.10), residues: 2700 sheet: 1.09 (0.15), residues: 1158 loop : -0.93 (0.10), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 466 HIS 0.007 0.001 HIS A 643 PHE 0.024 0.001 PHE C1046 TYR 0.014 0.001 TYR F 761 ARG 0.010 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1174 time to evaluate : 4.512 Fit side-chains REVERT: A 118 MET cc_start: 0.8732 (mmp) cc_final: 0.8326 (mmt) REVERT: A 307 LEU cc_start: 0.8482 (mp) cc_final: 0.8100 (mp) REVERT: A 838 GLU cc_start: 0.8344 (mp0) cc_final: 0.8108 (mp0) REVERT: B 190 LEU cc_start: 0.8761 (tp) cc_final: 0.8531 (tp) REVERT: C 290 GLU cc_start: 0.8559 (pm20) cc_final: 0.8177 (pm20) REVERT: C 410 GLU cc_start: 0.8282 (mp0) cc_final: 0.8062 (mp0) REVERT: C 1104 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8877 (mttm) REVERT: E 190 LEU cc_start: 0.8930 (tp) cc_final: 0.8711 (tp) REVERT: E 410 GLU cc_start: 0.8254 (mp0) cc_final: 0.8037 (mp0) REVERT: E 569 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8190 (mmm) REVERT: E 819 THR cc_start: 0.8848 (p) cc_final: 0.8593 (p) REVERT: F 118 MET cc_start: 0.8616 (mmp) cc_final: 0.8012 (mmt) outliers start: 73 outliers final: 49 residues processed: 1197 average time/residue: 1.6784 time to fit residues: 2417.0484 Evaluate side-chains 1210 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1159 time to evaluate : 4.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 852 GLU Chi-restraints excluded: chain A residue 1187 LYS Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1104 LYS Chi-restraints excluded: chain C residue 1187 LYS Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 976 ASP Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 603 LEU Chi-restraints excluded: chain E residue 816 GLU Chi-restraints excluded: chain E residue 837 ARG Chi-restraints excluded: chain E residue 976 ASP Chi-restraints excluded: chain E residue 1034 MET Chi-restraints excluded: chain E residue 1197 SER Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 247 MET Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 377 GLU Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 768 GLU Chi-restraints excluded: chain F residue 852 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 583 optimal weight: 0.1980 chunk 614 optimal weight: 0.7980 chunk 561 optimal weight: 0.7980 chunk 598 optimal weight: 0.8980 chunk 360 optimal weight: 1.9990 chunk 260 optimal weight: 0.7980 chunk 469 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 540 optimal weight: 3.9990 chunk 565 optimal weight: 0.7980 chunk 596 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 404 HIS A 583 HIS A 932 GLN A1045 HIS A1096 ASN B 251 GLN B 404 HIS B 413 ASN B 944 ASN B1096 ASN C 104 GLN C 349 ASN C 404 HIS C 677 ASN C1096 ASN D 404 HIS D 501 GLN D 583 HIS D1096 ASN E 104 GLN E 148 GLN E 404 HIS E 413 ASN E 677 ASN E1096 ASN F 148 GLN F 404 HIS F 932 GLN F1096 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 53766 Z= 0.175 Angle : 0.475 9.745 72930 Z= 0.246 Chirality : 0.042 0.170 7944 Planarity : 0.004 0.039 9600 Dihedral : 7.427 78.336 7692 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.07 % Allowed : 15.34 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.10), residues: 6702 helix: 1.74 (0.10), residues: 2736 sheet: 1.15 (0.16), residues: 1158 loop : -0.94 (0.10), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 466 HIS 0.004 0.001 HIS A 643 PHE 0.023 0.001 PHE C1046 TYR 0.011 0.001 TYR F 761 ARG 0.010 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1158 time to evaluate : 4.432 Fit side-chains REVERT: A 118 MET cc_start: 0.8717 (mmp) cc_final: 0.8251 (mmt) REVERT: A 307 LEU cc_start: 0.8398 (mp) cc_final: 0.8036 (mp) REVERT: B 190 LEU cc_start: 0.8751 (tp) cc_final: 0.8524 (tp) REVERT: C 290 GLU cc_start: 0.8546 (pm20) cc_final: 0.8175 (pm20) REVERT: C 410 GLU cc_start: 0.8279 (mp0) cc_final: 0.8061 (mp0) REVERT: E 410 GLU cc_start: 0.8252 (mp0) cc_final: 0.8034 (mp0) REVERT: E 569 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8180 (mmm) REVERT: E 819 THR cc_start: 0.8832 (p) cc_final: 0.8575 (p) REVERT: F 118 MET cc_start: 0.8625 (mmp) cc_final: 0.8016 (mmt) outliers start: 59 outliers final: 48 residues processed: 1174 average time/residue: 1.7065 time to fit residues: 2417.4631 Evaluate side-chains 1197 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1148 time to evaluate : 4.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 1187 LYS Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1187 LYS Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 837 ARG Chi-restraints excluded: chain D residue 947 LEU Chi-restraints excluded: chain D residue 976 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 569 MET Chi-restraints excluded: chain E residue 603 LEU Chi-restraints excluded: chain E residue 837 ARG Chi-restraints excluded: chain E residue 976 ASP Chi-restraints excluded: chain E residue 1034 MET Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 247 MET Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 768 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 392 optimal weight: 1.9990 chunk 632 optimal weight: 1.9990 chunk 386 optimal weight: 0.0000 chunk 300 optimal weight: 2.9990 chunk 439 optimal weight: 0.0570 chunk 663 optimal weight: 4.9990 chunk 610 optimal weight: 0.9980 chunk 528 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 408 optimal weight: 0.9980 chunk 323 optimal weight: 0.2980 overall best weight: 0.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 404 HIS A 583 HIS A 932 GLN A 944 ASN A1096 ASN B 251 GLN B 404 HIS B 413 ASN B 677 ASN B 944 ASN B1045 HIS B1096 ASN C 104 GLN C 349 ASN C 404 HIS C 677 ASN C1096 ASN D 404 HIS D 501 GLN D1096 ASN E 104 GLN E 148 GLN E 404 HIS E 413 ASN E 677 ASN E1096 ASN F 148 GLN F 404 HIS F 583 HIS F 932 GLN F1096 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 53766 Z= 0.147 Angle : 0.462 9.768 72930 Z= 0.238 Chirality : 0.042 0.159 7944 Planarity : 0.004 0.040 9600 Dihedral : 7.277 77.413 7692 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.03 % Allowed : 15.54 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.10), residues: 6702 helix: 1.83 (0.10), residues: 2742 sheet: 1.22 (0.16), residues: 1158 loop : -0.88 (0.11), residues: 2802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 466 HIS 0.005 0.001 HIS C 404 PHE 0.022 0.001 PHE C1046 TYR 0.009 0.001 TYR F 233 ARG 0.010 0.000 ARG C 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13404 Ramachandran restraints generated. 6702 Oldfield, 0 Emsley, 6702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1216 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1159 time to evaluate : 4.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8713 (mmp) cc_final: 0.8249 (mmt) REVERT: A 307 LEU cc_start: 0.8446 (mp) cc_final: 0.8124 (mp) REVERT: A 569 MET cc_start: 0.8436 (mmm) cc_final: 0.8188 (mmt) REVERT: B 190 LEU cc_start: 0.8729 (tp) cc_final: 0.8497 (tp) REVERT: C 290 GLU cc_start: 0.8546 (pm20) cc_final: 0.8203 (pm20) REVERT: C 410 GLU cc_start: 0.8271 (mp0) cc_final: 0.8058 (mp0) REVERT: C 1104 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8854 (mttm) REVERT: C 1190 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8113 (ttm170) REVERT: D 1163 ASP cc_start: 0.8373 (t0) cc_final: 0.8172 (t0) REVERT: E 410 GLU cc_start: 0.8246 (mp0) cc_final: 0.8028 (mp0) REVERT: E 819 THR cc_start: 0.8836 (p) cc_final: 0.8566 (p) REVERT: F 118 MET cc_start: 0.8627 (mmp) cc_final: 0.8024 (mmt) REVERT: F 569 MET cc_start: 0.8456 (mmm) cc_final: 0.8169 (mmm) outliers start: 57 outliers final: 41 residues processed: 1172 average time/residue: 1.6811 time to fit residues: 2375.2852 Evaluate side-chains 1190 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1147 time to evaluate : 4.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 1187 LYS Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 768 GLU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1104 LYS Chi-restraints excluded: chain C residue 1187 LYS Chi-restraints excluded: chain C residue 1190 ARG Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 947 LEU Chi-restraints excluded: chain D residue 976 ASP Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 603 LEU Chi-restraints excluded: chain E residue 837 ARG Chi-restraints excluded: chain E residue 1034 MET Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 247 MET Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 768 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 419 optimal weight: 4.9990 chunk 562 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 487 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 529 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 chunk 543 optimal weight: 0.0030 chunk 67 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 404 HIS A 583 HIS A1096 ASN B 251 GLN B 404 HIS B 413 ASN B 944 ASN B1045 HIS B1096 ASN C 104 GLN C 349 ASN C 404 HIS C 677 ASN C1096 ASN D 404 HIS D 501 GLN D 583 HIS D1096 ASN E 104 GLN E 148 GLN E 195 HIS E 404 HIS E 413 ASN E 677 ASN E1096 ASN F 148 GLN F 195 HIS F 404 HIS F 932 GLN F 944 ASN F1096 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.108386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.098433 restraints weight = 71373.944| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.32 r_work: 0.3338 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 53766 Z= 0.265 Angle : 0.523 10.055 72930 Z= 0.271 Chirality : 0.045 0.193 7944 Planarity : 0.004 0.041 9600 Dihedral : 7.531 79.345 7692 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.09 % Allowed : 15.49 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.10), residues: 6702 helix: 1.77 (0.10), residues: 2694 sheet: 1.01 (0.15), residues: 1176 loop : -0.90 (0.10), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 466 HIS 0.007 0.001 HIS A 643 PHE 0.024 0.001 PHE F1046 TYR 0.015 0.001 TYR F 761 ARG 0.010 0.000 ARG C 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30493.29 seconds wall clock time: 520 minutes 56.86 seconds (31256.86 seconds total)