Starting phenix.real_space_refine on Fri Dec 8 17:59:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jv2_9889/12_2023/6jv2_9889.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jv2_9889/12_2023/6jv2_9889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jv2_9889/12_2023/6jv2_9889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jv2_9889/12_2023/6jv2_9889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jv2_9889/12_2023/6jv2_9889.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jv2_9889/12_2023/6jv2_9889.pdb" } resolution = 4.4 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= 0.001 sd= 0.004 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 Ca 20 9.91 5 Zn 4 6.06 5 S 668 5.16 5 C 70684 2.51 5 N 18976 2.21 5 O 20728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 458": "OD1" <-> "OD2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A ASP 728": "OD1" <-> "OD2" Residue "A PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 909": "OD1" <-> "OD2" Residue "A TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1266": "OE1" <-> "OE2" Residue "A TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1640": "OD1" <-> "OD2" Residue "A TYR 1693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1807": "NH1" <-> "NH2" Residue "A TYR 1913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1916": "OD1" <-> "OD2" Residue "A PHE 1929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1932": "OD1" <-> "OD2" Residue "A ARG 1942": "NH1" <-> "NH2" Residue "A PHE 1943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2149": "OD1" <-> "OD2" Residue "A ASP 2250": "OD1" <-> "OD2" Residue "A GLU 2264": "OE1" <-> "OE2" Residue "A PHE 2305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2323": "NH1" <-> "NH2" Residue "A PHE 2461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2519": "NH1" <-> "NH2" Residue "A ASP 2708": "OD1" <-> "OD2" Residue "A GLU 2716": "OE1" <-> "OE2" Residue "A TYR 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2766": "OE1" <-> "OE2" Residue "A GLU 2770": "OE1" <-> "OE2" Residue "A TYR 2822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2882": "OE1" <-> "OE2" Residue "A ASP 2892": "OD1" <-> "OD2" Residue "A TYR 2902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3616": "NH1" <-> "NH2" Residue "A ASP 3644": "OD1" <-> "OD2" Residue "A ASP 3663": "OD1" <-> "OD2" Residue "A TYR 3689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3721": "OE1" <-> "OE2" Residue "A TYR 3781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3839": "OD1" <-> "OD2" Residue "A ASP 3854": "OD1" <-> "OD2" Residue "A GLU 4006": "OE1" <-> "OE2" Residue "A ASP 4026": "OD1" <-> "OD2" Residue "A ASP 4074": "OD1" <-> "OD2" Residue "A GLU 4108": "OE1" <-> "OE2" Residue "A GLU 4121": "OE1" <-> "OE2" Residue "A ARG 4148": "NH1" <-> "NH2" Residue "A ARG 4158": "NH1" <-> "NH2" Residue "A ARG 4498": "NH1" <-> "NH2" Residue "A ARG 4504": "NH1" <-> "NH2" Residue "A PHE 4789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 4791": "NH1" <-> "NH2" Residue "A PHE 4871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4884": "OD1" <-> "OD2" Residue "A TYR 4919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "B ASP 119": "OD1" <-> "OD2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 458": "OD1" <-> "OD2" Residue "C PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 500": "OE1" <-> "OE2" Residue "C GLU 535": "OE1" <-> "OE2" Residue "C GLU 689": "OE1" <-> "OE2" Residue "C ASP 728": "OD1" <-> "OD2" Residue "C PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 909": "OD1" <-> "OD2" Residue "C TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1266": "OE1" <-> "OE2" Residue "C TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1640": "OD1" <-> "OD2" Residue "C TYR 1693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1807": "NH1" <-> "NH2" Residue "C TYR 1913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1916": "OD1" <-> "OD2" Residue "C PHE 1929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1932": "OD1" <-> "OD2" Residue "C ARG 1942": "NH1" <-> "NH2" Residue "C PHE 1943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2149": "OD1" <-> "OD2" Residue "C ASP 2250": "OD1" <-> "OD2" Residue "C GLU 2264": "OE1" <-> "OE2" Residue "C PHE 2305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2323": "NH1" <-> "NH2" Residue "C PHE 2461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2519": "NH1" <-> "NH2" Residue "C ASP 2708": "OD1" <-> "OD2" Residue "C GLU 2716": "OE1" <-> "OE2" Residue "C TYR 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2766": "OE1" <-> "OE2" Residue "C GLU 2770": "OE1" <-> "OE2" Residue "C TYR 2822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2882": "OE1" <-> "OE2" Residue "C ASP 2892": "OD1" <-> "OD2" Residue "C TYR 2902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3616": "NH1" <-> "NH2" Residue "C ASP 3644": "OD1" <-> "OD2" Residue "C ASP 3663": "OD1" <-> "OD2" Residue "C TYR 3689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3721": "OE1" <-> "OE2" Residue "C TYR 3781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3839": "OD1" <-> "OD2" Residue "C ASP 3854": "OD1" <-> "OD2" Residue "C GLU 4006": "OE1" <-> "OE2" Residue "C ASP 4026": "OD1" <-> "OD2" Residue "C ASP 4074": "OD1" <-> "OD2" Residue "C GLU 4108": "OE1" <-> "OE2" Residue "C GLU 4121": "OE1" <-> "OE2" Residue "C ARG 4148": "NH1" <-> "NH2" Residue "C ARG 4158": "NH1" <-> "NH2" Residue "C ARG 4498": "NH1" <-> "NH2" Residue "C ARG 4504": "NH1" <-> "NH2" Residue "C PHE 4789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 4791": "NH1" <-> "NH2" Residue "C PHE 4871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4884": "OD1" <-> "OD2" Residue "C TYR 4919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 96": "OD1" <-> "OD2" Residue "D ASP 119": "OD1" <-> "OD2" Residue "E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 257": "NH1" <-> "NH2" Residue "E TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 414": "NH1" <-> "NH2" Residue "E PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 458": "OD1" <-> "OD2" Residue "E PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 500": "OE1" <-> "OE2" Residue "E GLU 535": "OE1" <-> "OE2" Residue "E GLU 689": "OE1" <-> "OE2" Residue "E ASP 728": "OD1" <-> "OD2" Residue "E PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 909": "OD1" <-> "OD2" Residue "E TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1266": "OE1" <-> "OE2" Residue "E TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1640": "OD1" <-> "OD2" Residue "E TYR 1693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1807": "NH1" <-> "NH2" Residue "E TYR 1913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1916": "OD1" <-> "OD2" Residue "E PHE 1929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1932": "OD1" <-> "OD2" Residue "E ARG 1942": "NH1" <-> "NH2" Residue "E PHE 1943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 2149": "OD1" <-> "OD2" Residue "E ASP 2250": "OD1" <-> "OD2" Residue "E GLU 2264": "OE1" <-> "OE2" Residue "E PHE 2305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2323": "NH1" <-> "NH2" Residue "E PHE 2461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2519": "NH1" <-> "NH2" Residue "E ASP 2708": "OD1" <-> "OD2" Residue "E GLU 2716": "OE1" <-> "OE2" Residue "E TYR 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 2766": "OE1" <-> "OE2" Residue "E GLU 2770": "OE1" <-> "OE2" Residue "E TYR 2822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 2882": "OE1" <-> "OE2" Residue "E ASP 2892": "OD1" <-> "OD2" Residue "E TYR 2902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 3610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 3616": "NH1" <-> "NH2" Residue "E ASP 3644": "OD1" <-> "OD2" Residue "E ASP 3663": "OD1" <-> "OD2" Residue "E TYR 3689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 3692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 3721": "OE1" <-> "OE2" Residue "E TYR 3781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 3839": "OD1" <-> "OD2" Residue "E ASP 3854": "OD1" <-> "OD2" Residue "E GLU 4006": "OE1" <-> "OE2" Residue "E ASP 4026": "OD1" <-> "OD2" Residue "E ASP 4074": "OD1" <-> "OD2" Residue "E GLU 4108": "OE1" <-> "OE2" Residue "E GLU 4121": "OE1" <-> "OE2" Residue "E ARG 4148": "NH1" <-> "NH2" Residue "E ARG 4158": "NH1" <-> "NH2" Residue "E ARG 4498": "NH1" <-> "NH2" Residue "E ARG 4504": "NH1" <-> "NH2" Residue "E PHE 4789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 4790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 4791": "NH1" <-> "NH2" Residue "E PHE 4871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 4884": "OD1" <-> "OD2" Residue "E TYR 4919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 4952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 96": "OD1" <-> "OD2" Residue "F ASP 119": "OD1" <-> "OD2" Residue "G PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 190": "NH1" <-> "NH2" Residue "G TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 257": "NH1" <-> "NH2" Residue "G TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 414": "NH1" <-> "NH2" Residue "G PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 458": "OD1" <-> "OD2" Residue "G PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 500": "OE1" <-> "OE2" Residue "G GLU 535": "OE1" <-> "OE2" Residue "G GLU 689": "OE1" <-> "OE2" Residue "G ASP 728": "OD1" <-> "OD2" Residue "G PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 909": "OD1" <-> "OD2" Residue "G TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1266": "OE1" <-> "OE2" Residue "G TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1640": "OD1" <-> "OD2" Residue "G TYR 1693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1807": "NH1" <-> "NH2" Residue "G TYR 1913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1916": "OD1" <-> "OD2" Residue "G PHE 1929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1932": "OD1" <-> "OD2" Residue "G ARG 1942": "NH1" <-> "NH2" Residue "G PHE 1943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 2149": "OD1" <-> "OD2" Residue "G ASP 2250": "OD1" <-> "OD2" Residue "G GLU 2264": "OE1" <-> "OE2" Residue "G PHE 2305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 2323": "NH1" <-> "NH2" Residue "G PHE 2461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 2477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 2519": "NH1" <-> "NH2" Residue "G ASP 2708": "OD1" <-> "OD2" Residue "G GLU 2716": "OE1" <-> "OE2" Residue "G TYR 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 2766": "OE1" <-> "OE2" Residue "G GLU 2770": "OE1" <-> "OE2" Residue "G TYR 2822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 2882": "OE1" <-> "OE2" Residue "G ASP 2892": "OD1" <-> "OD2" Residue "G TYR 2902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 3610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 3616": "NH1" <-> "NH2" Residue "G ASP 3644": "OD1" <-> "OD2" Residue "G ASP 3663": "OD1" <-> "OD2" Residue "G TYR 3689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 3692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 3721": "OE1" <-> "OE2" Residue "G TYR 3781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 3839": "OD1" <-> "OD2" Residue "G ASP 3854": "OD1" <-> "OD2" Residue "G GLU 4006": "OE1" <-> "OE2" Residue "G ASP 4026": "OD1" <-> "OD2" Residue "G ASP 4074": "OD1" <-> "OD2" Residue "G GLU 4108": "OE1" <-> "OE2" Residue "G GLU 4121": "OE1" <-> "OE2" Residue "G ARG 4148": "NH1" <-> "NH2" Residue "G ARG 4158": "NH1" <-> "NH2" Residue "G ARG 4498": "NH1" <-> "NH2" Residue "G ARG 4504": "NH1" <-> "NH2" Residue "G PHE 4789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 4790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 4791": "NH1" <-> "NH2" Residue "G PHE 4871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 4884": "OD1" <-> "OD2" Residue "G TYR 4919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 4952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 96": "OD1" <-> "OD2" Residue "H ASP 119": "OD1" <-> "OD2" Time to flip residues: 0.34s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 111080 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 26722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3509, 26722 Classifications: {'peptide': 3509} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 370} Link IDs: {'PTRANS': 121, 'TRANS': 3387} Chain breaks: 60 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1526 Unresolved non-hydrogen angles: 1939 Unresolved non-hydrogen dihedrals: 1270 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 20, 'TYR:plan': 15, 'ASN:plan1': 19, 'TRP:plan': 3, 'ASP:plan': 25, 'PHE:plan': 18, 'GLU:plan': 38, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 849 Chain: "B" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1042 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "C" Number of atoms: 26722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3509, 26722 Classifications: {'peptide': 3509} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 370} Link IDs: {'PTRANS': 121, 'TRANS': 3387} Chain breaks: 60 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1526 Unresolved non-hydrogen angles: 1939 Unresolved non-hydrogen dihedrals: 1270 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 20, 'TYR:plan': 15, 'ASN:plan1': 19, 'TRP:plan': 3, 'ASP:plan': 25, 'PHE:plan': 18, 'GLU:plan': 38, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 849 Chain: "D" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1042 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "E" Number of atoms: 26722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3509, 26722 Classifications: {'peptide': 3509} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 370} Link IDs: {'PTRANS': 121, 'TRANS': 3387} Chain breaks: 60 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1526 Unresolved non-hydrogen angles: 1939 Unresolved non-hydrogen dihedrals: 1269 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 20, 'TYR:plan': 15, 'ASN:plan1': 19, 'TRP:plan': 3, 'ASP:plan': 25, 'PHE:plan': 18, 'GLU:plan': 38, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 849 Chain: "F" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1042 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "G" Number of atoms: 26722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3509, 26722 Classifications: {'peptide': 3509} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 370} Link IDs: {'PTRANS': 121, 'TRANS': 3387} Chain breaks: 60 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1526 Unresolved non-hydrogen angles: 1939 Unresolved non-hydrogen dihedrals: 1270 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 20, 'TYR:plan': 15, 'ASN:plan1': 19, 'TRP:plan': 3, 'ASP:plan': 25, 'PHE:plan': 18, 'GLU:plan': 38, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 849 Chain: "H" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1042 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26085 SG CYS A4889 205.589 204.860 86.779 1.00194.74 S ATOM 26110 SG CYS A4892 204.653 203.206 90.389 1.00197.16 S ATOM 53849 SG CYS C4889 204.868 178.440 86.782 1.00194.74 S ATOM 53874 SG CYS C4892 203.214 179.376 90.393 1.00197.16 S ATOM 81613 SG CYS E4889 178.452 179.172 86.781 1.00194.74 S ATOM 81638 SG CYS E4892 179.388 180.825 90.391 1.00197.16 S ATOM A078H SG CYS G4889 179.176 205.593 86.777 1.00194.74 S ATOM A0796 SG CYS G4892 180.830 204.658 90.387 1.00197.16 S Time building chain proxies: 41.48, per 1000 atoms: 0.37 Number of scatterers: 111080 At special positions: 0 Unit cell: (385.123, 385.123, 207.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Ca 20 19.99 S 668 16.00 O 20728 8.00 N 18976 7.00 C 70684 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: 33.82 Conformation dependent library (CDL) restraints added in 14.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A6000 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4914 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4889 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4892 " pdb=" ZN C6000 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4914 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4889 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4892 " pdb=" ZN E6000 " pdb="ZN ZN E6000 " - pdb=" NE2 HIS E4914 " pdb="ZN ZN E6000 " - pdb=" SG CYS E4889 " pdb="ZN ZN E6000 " - pdb=" SG CYS E4892 " pdb=" ZN G6000 " pdb="ZN ZN G6000 " - pdb=" NE2 HIS G4914 " pdb="ZN ZN G6000 " - pdb=" SG CYS G4889 " pdb="ZN ZN G6000 " - pdb=" SG CYS G4892 " 28120 Ramachandran restraints generated. 14060 Oldfield, 0 Emsley, 14060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 27352 Finding SS restraints... Secondary structure from input PDB file: 633 helices and 108 sheets defined 53.1% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.49 Creating SS restraints... Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 155 through 158 removed outlier: 4.040A pdb=" N CYS A 158 " --> pdb=" O GLY A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 158' Processing helix chain 'A' and resid 409 through 436 removed outlier: 3.859A pdb=" N VAL A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 3.562A pdb=" N ILE A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 461 " --> pdb=" O GLN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 491 removed outlier: 3.859A pdb=" N ARG A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN A 490 " --> pdb=" O GLN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 506 removed outlier: 4.100A pdb=" N GLU A 500 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS A 501 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 542 removed outlier: 4.316A pdb=" N LEU A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A 538 " --> pdb=" O TYR A 534 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 551 removed outlier: 4.119A pdb=" N CYS A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 removed outlier: 4.255A pdb=" N TRP A 557 " --> pdb=" O GLY A 553 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 removed outlier: 4.236A pdb=" N VAL A 574 " --> pdb=" O GLY A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 588 Processing helix chain 'A' and resid 590 through 604 removed outlier: 3.515A pdb=" N LEU A 600 " --> pdb=" O SER A 596 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP A 602 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 619 removed outlier: 3.619A pdb=" N VAL A 619 " --> pdb=" O CYS A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 removed outlier: 3.906A pdb=" N CYS A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP A 634 " --> pdb=" O HIS A 630 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 640 removed outlier: 3.526A pdb=" N ARG A 640 " --> pdb=" O LEU A 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 637 through 640' Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 878 through 898 removed outlier: 3.544A pdb=" N GLU A 887 " --> pdb=" O GLU A 883 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A 892 " --> pdb=" O ASN A 888 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A 897 " --> pdb=" O TRP A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 removed outlier: 4.280A pdb=" N GLU A 938 " --> pdb=" O GLN A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1011 removed outlier: 3.973A pdb=" N ASN A1005 " --> pdb=" O GLU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1060 removed outlier: 3.791A pdb=" N LYS A1043 " --> pdb=" O ASP A1039 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A1057 " --> pdb=" O ALA A1053 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A1058 " --> pdb=" O VAL A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1095 removed outlier: 3.548A pdb=" N ALA A1095 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1230 removed outlier: 3.589A pdb=" N ILE A1229 " --> pdb=" O LYS A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1570 through 1576 removed outlier: 4.201A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1646 removed outlier: 5.260A pdb=" N THR A1645 " --> pdb=" O LEU A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1665 removed outlier: 3.623A pdb=" N PHE A1653 " --> pdb=" O GLU A1649 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1681 removed outlier: 3.815A pdb=" N ALA A1675 " --> pdb=" O ARG A1671 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A1676 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS A1677 " --> pdb=" O ALA A1673 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1690 removed outlier: 3.624A pdb=" N LEU A1685 " --> pdb=" O ASP A1681 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A1686 " --> pdb=" O GLU A1682 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A1687 " --> pdb=" O PRO A1683 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1711 removed outlier: 3.661A pdb=" N ASP A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE A1707 " --> pdb=" O TYR A1703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1711 through 1721 removed outlier: 3.525A pdb=" N MET A1720 " --> pdb=" O THR A1716 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET A1721 " --> pdb=" O ALA A1717 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1724 No H-bonds generated for 'chain 'A' and resid 1722 through 1724' Processing helix chain 'A' and resid 1771 through 1776 removed outlier: 4.289A pdb=" N TYR A1776 " --> pdb=" O ASN A1772 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1802 removed outlier: 4.410A pdb=" N LEU A1787 " --> pdb=" O PRO A1783 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A1788 " --> pdb=" O LEU A1784 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A1789 " --> pdb=" O ASP A1785 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A1792 " --> pdb=" O LYS A1788 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A1797 " --> pdb=" O GLN A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1831 removed outlier: 3.587A pdb=" N VAL A1819 " --> pdb=" O GLU A1815 " (cutoff:3.500A) Proline residue: A1820 - end of helix removed outlier: 3.711A pdb=" N LYS A1823 " --> pdb=" O VAL A1819 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A1824 " --> pdb=" O PRO A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1847 Processing helix chain 'A' and resid 1900 through 1953 removed outlier: 4.128A pdb=" N LYS A1904 " --> pdb=" O PRO A1900 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A1905 " --> pdb=" O GLU A1901 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU A1909 " --> pdb=" O LEU A1905 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A1910 " --> pdb=" O GLN A1906 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A1911 " --> pdb=" O MET A1907 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS A1917 " --> pdb=" O TYR A1913 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A1926 " --> pdb=" O ARG A1922 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A1927 " --> pdb=" O ILE A1923 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A1928 " --> pdb=" O GLU A1924 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A1929 " --> pdb=" O ALA A1925 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP A1932 " --> pdb=" O ALA A1928 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A1933 " --> pdb=" O PHE A1929 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A1942 " --> pdb=" O GLN A1938 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N PHE A1943 " --> pdb=" O ASP A1939 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A1951 " --> pdb=" O GLU A1947 " (cutoff:3.500A) Processing helix chain 'A' and resid 1991 through 1996 removed outlier: 3.790A pdb=" N GLN A1996 " --> pdb=" O GLU A1992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1999 through 2010 removed outlier: 3.675A pdb=" N THR A2006 " --> pdb=" O GLU A2002 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS A2007 " --> pdb=" O ASP A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2011 through 2013 No H-bonds generated for 'chain 'A' and resid 2011 through 2013' Processing helix chain 'A' and resid 2024 through 2025 No H-bonds generated for 'chain 'A' and resid 2024 through 2025' Processing helix chain 'A' and resid 2026 through 2037 removed outlier: 3.881A pdb=" N LEU A2030 " --> pdb=" O ILE A2026 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A2035 " --> pdb=" O LEU A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2059 through 2074 removed outlier: 4.069A pdb=" N SER A2064 " --> pdb=" O GLN A2060 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A2067 " --> pdb=" O ILE A2063 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP A2070 " --> pdb=" O THR A2066 " (cutoff:3.500A) Processing helix chain 'A' and resid 2078 through 2094 removed outlier: 3.589A pdb=" N PHE A2086 " --> pdb=" O VAL A2082 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A2087 " --> pdb=" O ARG A2083 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A2088 " --> pdb=" O ALA A2084 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2103 removed outlier: 3.748A pdb=" N LEU A2099 " --> pdb=" O GLY A2095 " (cutoff:3.500A) Processing helix chain 'A' and resid 2104 through 2106 No H-bonds generated for 'chain 'A' and resid 2104 through 2106' Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 3.539A pdb=" N ILE A2118 " --> pdb=" O VAL A2114 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A2120 " --> pdb=" O ASP A2116 " (cutoff:3.500A) Processing helix chain 'A' and resid 2140 through 2152 removed outlier: 3.661A pdb=" N ILE A2144 " --> pdb=" O GLU A2140 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG A2145 " --> pdb=" O LYS A2141 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY A2146 " --> pdb=" O LEU A2142 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A2148 " --> pdb=" O ILE A2144 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A2149 " --> pdb=" O ARG A2145 " (cutoff:3.500A) Processing helix chain 'A' and resid 2159 through 2167 removed outlier: 3.745A pdb=" N MET A2163 " --> pdb=" O HIS A2159 " (cutoff:3.500A) Processing helix chain 'A' and resid 2167 through 2180 removed outlier: 3.681A pdb=" N VAL A2175 " --> pdb=" O THR A2171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2193 through 2206 removed outlier: 4.212A pdb=" N CYS A2197 " --> pdb=" O MET A2193 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG A2206 " --> pdb=" O CYS A2202 " (cutoff:3.500A) Processing helix chain 'A' and resid 2208 through 2215 removed outlier: 3.674A pdb=" N MET A2215 " --> pdb=" O ASN A2211 " (cutoff:3.500A) Processing helix chain 'A' and resid 2218 through 2223 Processing helix chain 'A' and resid 2240 through 2247 Processing helix chain 'A' and resid 2251 through 2258 Processing helix chain 'A' and resid 2260 through 2272 removed outlier: 3.507A pdb=" N GLU A2264 " --> pdb=" O GLU A2260 " (cutoff:3.500A) Processing helix chain 'A' and resid 2296 through 2309 removed outlier: 3.751A pdb=" N LEU A2300 " --> pdb=" O GLY A2296 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A2301 " --> pdb=" O GLU A2297 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS A2309 " --> pdb=" O PHE A2305 " (cutoff:3.500A) Processing helix chain 'A' and resid 2314 through 2327 removed outlier: 4.602A pdb=" N VAL A2322 " --> pdb=" O ALA A2318 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG A2323 " --> pdb=" O ASN A2319 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A2324 " --> pdb=" O VAL A2320 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A2325 " --> pdb=" O VAL A2321 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A2327 " --> pdb=" O ARG A2323 " (cutoff:3.500A) Processing helix chain 'A' and resid 2343 through 2345 No H-bonds generated for 'chain 'A' and resid 2343 through 2345' Processing helix chain 'A' and resid 2346 through 2351 removed outlier: 3.951A pdb=" N GLU A2350 " --> pdb=" O ALA A2346 " (cutoff:3.500A) Processing helix chain 'A' and resid 2387 through 2403 removed outlier: 3.621A pdb=" N THR A2391 " --> pdb=" O ASN A2387 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A2393 " --> pdb=" O ILE A2389 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A2396 " --> pdb=" O PHE A2392 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY A2401 " --> pdb=" O ILE A2397 " (cutoff:3.500A) Processing helix chain 'A' and resid 2408 through 2413 Processing helix chain 'A' and resid 2416 through 2427 removed outlier: 3.542A pdb=" N LEU A2427 " --> pdb=" O ILE A2423 " (cutoff:3.500A) Processing helix chain 'A' and resid 2431 through 2435 Processing helix chain 'A' and resid 2462 through 2476 removed outlier: 4.388A pdb=" N LYS A2466 " --> pdb=" O CYS A2462 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA A2467 " --> pdb=" O PRO A2463 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A2471 " --> pdb=" O ALA A2467 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N PHE A2472 " --> pdb=" O ALA A2468 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2488 removed outlier: 4.217A pdb=" N LEU A2486 " --> pdb=" O GLN A2482 " (cutoff:3.500A) Processing helix chain 'A' and resid 2492 through 2497 removed outlier: 3.732A pdb=" N LEU A2497 " --> pdb=" O PHE A2493 " (cutoff:3.500A) Processing helix chain 'A' and resid 2498 through 2502 removed outlier: 4.527A pdb=" N ALA A2501 " --> pdb=" O ARG A2498 " (cutoff:3.500A) Processing helix chain 'A' and resid 2512 through 2516 Processing helix chain 'A' and resid 2517 through 2521 Processing helix chain 'A' and resid 2537 through 2552 removed outlier: 3.519A pdb=" N ASP A2547 " --> pdb=" O ALA A2543 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER A2548 " --> pdb=" O SER A2544 " (cutoff:3.500A) Processing helix chain 'A' and resid 2559 through 2576 removed outlier: 3.514A pdb=" N ASP A2568 " --> pdb=" O LYS A2564 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A2569 " --> pdb=" O ALA A2565 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A2570 " --> pdb=" O GLN A2566 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A2571 " --> pdb=" O ARG A2567 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A2572 " --> pdb=" O ASP A2568 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A2574 " --> pdb=" O ILE A2570 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A2575 " --> pdb=" O GLU A2571 " (cutoff:3.500A) Processing helix chain 'A' and resid 2583 through 2595 removed outlier: 4.211A pdb=" N GLN A2587 " --> pdb=" O PRO A2583 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A2591 " --> pdb=" O GLN A2587 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG A2592 " --> pdb=" O HIS A2588 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A2593 " --> pdb=" O LEU A2589 " (cutoff:3.500A) Processing helix chain 'A' and resid 2606 through 2622 removed outlier: 3.910A pdb=" N ASN A2613 " --> pdb=" O LYS A2609 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS A2614 " --> pdb=" O LEU A2610 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A2617 " --> pdb=" O ASN A2613 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS A2618 " --> pdb=" O HIS A2614 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP A2619 " --> pdb=" O TYR A2615 " (cutoff:3.500A) Processing helix chain 'A' and resid 2622 through 2627 Processing helix chain 'A' and resid 2635 through 2651 Processing helix chain 'A' and resid 2660 through 2665 Processing helix chain 'A' and resid 2665 through 2676 Processing helix chain 'A' and resid 2718 through 2732 removed outlier: 4.425A pdb=" N LYS A2724 " --> pdb=" O TYR A2720 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A2732 " --> pdb=" O HIS A2728 " (cutoff:3.500A) Processing helix chain 'A' and resid 2735 through 2739 removed outlier: 3.844A pdb=" N LEU A2738 " --> pdb=" O MET A2735 " (cutoff:3.500A) Processing helix chain 'A' and resid 2749 through 2753 removed outlier: 3.937A pdb=" N SER A2752 " --> pdb=" O SER A2749 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A2753 " --> pdb=" O ASP A2750 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2749 through 2753' Processing helix chain 'A' and resid 2767 through 2772 removed outlier: 3.629A pdb=" N GLU A2770 " --> pdb=" O LYS A2767 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A2771 " --> pdb=" O GLU A2768 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A2772 " --> pdb=" O LYS A2769 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2767 through 2772' Processing helix chain 'A' and resid 2773 through 2778 Processing helix chain 'A' and resid 2838 through 2862 removed outlier: 3.977A pdb=" N MET A2844 " --> pdb=" O ALA A2840 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A2847 " --> pdb=" O GLU A2843 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A2851 " --> pdb=" O GLU A2847 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA A2854 " --> pdb=" O HIS A2850 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A2859 " --> pdb=" O LYS A2855 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU A2860 " --> pdb=" O LYS A2856 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A2861 " --> pdb=" O LYS A2857 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A2862 " --> pdb=" O LYS A2858 " (cutoff:3.500A) Processing helix chain 'A' and resid 2874 through 2878 removed outlier: 4.201A pdb=" N LEU A2878 " --> pdb=" O TYR A2875 " (cutoff:3.500A) Processing helix chain 'A' and resid 2882 through 2886 removed outlier: 3.528A pdb=" N LYS A2885 " --> pdb=" O GLU A2882 " (cutoff:3.500A) Processing helix chain 'A' and resid 2891 through 2900 removed outlier: 3.905A pdb=" N LYS A2895 " --> pdb=" O GLN A2891 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE A2896 " --> pdb=" O ASP A2892 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A2897 " --> pdb=" O ILE A2893 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN A2898 " --> pdb=" O LEU A2894 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A2899 " --> pdb=" O LYS A2895 " (cutoff:3.500A) Processing helix chain 'A' and resid 2982 through 2986 Processing helix chain 'A' and resid 2988 through 2999 Processing helix chain 'A' and resid 3000 through 3003 Processing helix chain 'A' and resid 3012 through 3028 removed outlier: 3.863A pdb=" N SER A3021 " --> pdb=" O ARG A3017 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU A3022 " --> pdb=" O HIS A3018 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE A3023 " --> pdb=" O ARG A3019 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY A3024 " --> pdb=" O ILE A3020 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN A3025 " --> pdb=" O SER A3021 " (cutoff:3.500A) Processing helix chain 'A' and resid 3035 through 3050 removed outlier: 3.974A pdb=" N LYS A3048 " --> pdb=" O ARG A3044 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY A3050 " --> pdb=" O VAL A3046 " (cutoff:3.500A) Processing helix chain 'A' and resid 3062 through 3067 Processing helix chain 'A' and resid 3067 through 3080 removed outlier: 3.674A pdb=" N LYS A3071 " --> pdb=" O GLU A3067 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A3074 " --> pdb=" O GLU A3070 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A3075 " --> pdb=" O LYS A3071 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A3076 " --> pdb=" O THR A3072 " (cutoff:3.500A) Processing helix chain 'A' and resid 3103 through 3115 removed outlier: 3.578A pdb=" N GLU A3111 " --> pdb=" O SER A3107 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N HIS A3112 " --> pdb=" O SER A3108 " (cutoff:3.500A) Processing helix chain 'A' and resid 3116 through 3118 No H-bonds generated for 'chain 'A' and resid 3116 through 3118' Processing helix chain 'A' and resid 3128 through 3133 Processing helix chain 'A' and resid 3136 through 3142 Processing helix chain 'A' and resid 3152 through 3162 removed outlier: 3.621A pdb=" N LEU A3160 " --> pdb=" O LEU A3156 " (cutoff:3.500A) Processing helix chain 'A' and resid 3171 through 3178 Processing helix chain 'A' and resid 3586 through 3605 removed outlier: 3.777A pdb=" N ARG A3605 " --> pdb=" O VAL A3601 " (cutoff:3.500A) Processing helix chain 'A' and resid 3613 through 3630 removed outlier: 4.155A pdb=" N ILE A3630 " --> pdb=" O GLU A3626 " (cutoff:3.500A) Processing helix chain 'A' and resid 3637 through 3646 Processing helix chain 'A' and resid 3663 through 3677 Processing helix chain 'A' and resid 3688 through 3699 removed outlier: 5.083A pdb=" N ASP A3694 " --> pdb=" O MET A3690 " (cutoff:3.500A) Processing helix chain 'A' and resid 3715 through 3734 Processing helix chain 'A' and resid 3736 through 3748 removed outlier: 4.605A pdb=" N MET A3740 " --> pdb=" O GLY A3736 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A3741 " --> pdb=" O ALA A3737 " (cutoff:3.500A) Processing helix chain 'A' and resid 3753 through 3767 Processing helix chain 'A' and resid 3771 through 3785 removed outlier: 3.601A pdb=" N GLN A3775 " --> pdb=" O ASN A3771 " (cutoff:3.500A) Processing helix chain 'A' and resid 3787 through 3800 removed outlier: 3.627A pdb=" N PHE A3791 " --> pdb=" O ASP A3787 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A3800 " --> pdb=" O GLY A3796 " (cutoff:3.500A) Processing helix chain 'A' and resid 3805 through 3819 removed outlier: 3.551A pdb=" N PHE A3809 " --> pdb=" O ASP A3805 " (cutoff:3.500A) Processing helix chain 'A' and resid 3833 through 3849 removed outlier: 3.884A pdb=" N THR A3837 " --> pdb=" O ASP A3833 " (cutoff:3.500A) Processing helix chain 'A' and resid 3852 through 3862 Processing helix chain 'A' and resid 3870 through 3894 removed outlier: 3.725A pdb=" N SER A3874 " --> pdb=" O ASN A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3900 through 3926 Processing helix chain 'A' and resid 3929 through 3938 removed outlier: 4.265A pdb=" N GLN A3933 " --> pdb=" O CYS A3929 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS A3938 " --> pdb=" O GLN A3934 " (cutoff:3.500A) Processing helix chain 'A' and resid 3940 through 3960 removed outlier: 4.269A pdb=" N ALA A3944 " --> pdb=" O ARG A3940 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS A3954 " --> pdb=" O HIS A3950 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A3957 " --> pdb=" O ALA A3953 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A3958 " --> pdb=" O HIS A3954 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3988 removed outlier: 3.629A pdb=" N LEU A3983 " --> pdb=" O MET A3979 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A3988 " --> pdb=" O LEU A3984 " (cutoff:3.500A) Processing helix chain 'A' and resid 3994 through 4006 Processing helix chain 'A' and resid 4007 through 4028 removed outlier: 3.994A pdb=" N PHE A4021 " --> pdb=" O PHE A4017 " (cutoff:3.500A) Processing helix chain 'A' and resid 4046 through 4055 Processing helix chain 'A' and resid 4060 through 4068 removed outlier: 3.929A pdb=" N THR A4064 " --> pdb=" O THR A4060 " (cutoff:3.500A) Processing helix chain 'A' and resid 4082 through 4090 removed outlier: 4.277A pdb=" N GLU A4090 " --> pdb=" O LYS A4086 " (cutoff:3.500A) Processing helix chain 'A' and resid 4093 through 4110 Processing helix chain 'A' and resid 4113 through 4123 removed outlier: 3.833A pdb=" N ALA A4123 " --> pdb=" O PHE A4119 " (cutoff:3.500A) Processing helix chain 'A' and resid 4123 through 4131 removed outlier: 3.932A pdb=" N LEU A4127 " --> pdb=" O ALA A4123 " (cutoff:3.500A) Processing helix chain 'A' and resid 4154 through 4162 removed outlier: 3.808A pdb=" N ARG A4158 " --> pdb=" O SER A4154 " (cutoff:3.500A) Processing helix chain 'A' and resid 4163 through 4179 removed outlier: 3.585A pdb=" N ASN A4179 " --> pdb=" O PHE A4175 " (cutoff:3.500A) Processing helix chain 'A' and resid 4185 through 4206 removed outlier: 3.774A pdb=" N GLN A4206 " --> pdb=" O GLN A4202 " (cutoff:3.500A) Processing helix chain 'A' and resid 4487 through 4499 removed outlier: 3.578A pdb=" N TYR A4495 " --> pdb=" O LYS A4491 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A4496 " --> pdb=" O LEU A4492 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4518 removed outlier: 3.648A pdb=" N ALA A4507 " --> pdb=" O MET A4503 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A4508 " --> pdb=" O ARG A4504 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A4509 " --> pdb=" O MET A4505 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA A4513 " --> pdb=" O PHE A4509 " (cutoff:3.500A) Processing helix chain 'A' and resid 4569 through 4614 removed outlier: 4.392A pdb=" N ILE A4578 " --> pdb=" O ARG A4574 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A4586 " --> pdb=" O VAL A4582 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS A4587 " --> pdb=" O ILE A4583 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE A4588 " --> pdb=" O SER A4584 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A4596 " --> pdb=" O TYR A4592 " (cutoff:3.500A) Proline residue: A4597 - end of helix removed outlier: 3.608A pdb=" N ARG A4603 " --> pdb=" O VAL A4599 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A4612 " --> pdb=" O ALA A4608 " (cutoff:3.500A) Processing helix chain 'A' and resid 4626 through 4632 Processing helix chain 'A' and resid 4633 through 4638 removed outlier: 4.386A pdb=" N ILE A4636 " --> pdb=" O ARG A4633 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN A4637 " --> pdb=" O LEU A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4649 through 4658 removed outlier: 3.588A pdb=" N VAL A4654 " --> pdb=" O VAL A4650 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N MET A4655 " --> pdb=" O LYS A4651 " (cutoff:3.500A) Processing helix chain 'A' and resid 4663 through 4669 Processing helix chain 'A' and resid 4696 through 4701 removed outlier: 3.550A pdb=" N LEU A4699 " --> pdb=" O SER A4696 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A4701 " --> pdb=" O VAL A4698 " (cutoff:3.500A) Processing helix chain 'A' and resid 4703 through 4715 removed outlier: 4.199A pdb=" N GLY A4712 " --> pdb=" O MET A4708 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A4713 " --> pdb=" O TRP A4709 " (cutoff:3.500A) Processing helix chain 'A' and resid 4717 through 4736 removed outlier: 3.676A pdb=" N LEU A4732 " --> pdb=" O THR A4728 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A4733 " --> pdb=" O MET A4729 " (cutoff:3.500A) Processing helix chain 'A' and resid 4741 through 4748 removed outlier: 3.681A pdb=" N ILE A4747 " --> pdb=" O LEU A4744 " (cutoff:3.500A) Processing helix chain 'A' and resid 4751 through 4763 removed outlier: 3.623A pdb=" N ARG A4755 " --> pdb=" O PHE A4751 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A4756 " --> pdb=" O LYS A4752 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE A4757 " --> pdb=" O THR A4753 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A4758 " --> pdb=" O LEU A4754 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A4761 " --> pdb=" O ILE A4757 " (cutoff:3.500A) Processing helix chain 'A' and resid 4767 through 4790 removed outlier: 3.861A pdb=" N THR A4771 " --> pdb=" O GLN A4767 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A4772 " --> pdb=" O LEU A4768 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL A4777 " --> pdb=" O GLY A4773 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A4779 " --> pdb=" O LEU A4775 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A4784 " --> pdb=" O TYR A4780 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A4785 " --> pdb=" O LEU A4781 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA A4786 " --> pdb=" O TYR A4782 " (cutoff:3.500A) Processing helix chain 'A' and resid 4791 through 4794 Processing helix chain 'A' and resid 4812 through 4825 removed outlier: 3.950A pdb=" N VAL A4822 " --> pdb=" O MET A4818 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A4823 " --> pdb=" O TYR A4819 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A4825 " --> pdb=" O GLY A4821 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4868 removed outlier: 3.960A pdb=" N TYR A4843 " --> pdb=" O GLU A4839 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A4849 " --> pdb=" O ILE A4845 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE A4858 " --> pdb=" O PHE A4854 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A4861 " --> pdb=" O VAL A4857 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLY A4865 " --> pdb=" O ALA A4861 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A4866 " --> pdb=" O ILE A4862 " (cutoff:3.500A) Processing helix chain 'A' and resid 4868 through 4881 removed outlier: 4.346A pdb=" N GLU A4873 " --> pdb=" O ASP A4869 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A4874 " --> pdb=" O ALA A4870 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A4881 " --> pdb=" O GLN A4877 " (cutoff:3.500A) Processing helix chain 'A' and resid 4895 through 4900 removed outlier: 4.183A pdb=" N PHE A4899 " --> pdb=" O GLY A4895 " (cutoff:3.500A) Processing helix chain 'A' and resid 4904 through 4910 removed outlier: 3.939A pdb=" N THR A4908 " --> pdb=" O HIS A4904 " (cutoff:3.500A) Processing helix chain 'A' and resid 4916 through 4929 removed outlier: 3.900A pdb=" N LEU A4920 " --> pdb=" O LEU A4916 " (cutoff:3.500A) Processing helix chain 'A' and resid 4935 through 4947 removed outlier: 3.915A pdb=" N TRP A4942 " --> pdb=" O GLU A4938 " (cutoff:3.500A) Processing helix chain 'A' and resid 4959 through 4963 Processing helix chain 'B' and resid 10 through 21 removed outlier: 3.574A pdb=" N PHE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.639A pdb=" N LEU B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 4.355A pdb=" N ASP B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.568A pdb=" N THR B 71 " --> pdb=" O PRO B 67 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 Processing helix chain 'B' and resid 102 through 110 removed outlier: 3.790A pdb=" N MET B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 removed outlier: 4.712A pdb=" N VAL B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.881A pdb=" N GLN B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 155 through 158 removed outlier: 4.040A pdb=" N CYS C 158 " --> pdb=" O GLY C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 158' Processing helix chain 'C' and resid 409 through 436 removed outlier: 3.860A pdb=" N VAL C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 423 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 463 removed outlier: 3.562A pdb=" N ILE C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY C 461 " --> pdb=" O GLN C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 491 removed outlier: 3.859A pdb=" N ARG C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE C 489 " --> pdb=" O ARG C 485 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN C 490 " --> pdb=" O GLN C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 506 removed outlier: 4.100A pdb=" N GLU C 500 " --> pdb=" O ASN C 496 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS C 501 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP C 503 " --> pdb=" O LEU C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 542 removed outlier: 4.316A pdb=" N LEU C 536 " --> pdb=" O SER C 532 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU C 537 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA C 538 " --> pdb=" O TYR C 534 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 551 removed outlier: 4.119A pdb=" N CYS C 548 " --> pdb=" O ASN C 544 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 549 " --> pdb=" O ARG C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 563 removed outlier: 4.255A pdb=" N TRP C 557 " --> pdb=" O GLY C 553 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 580 removed outlier: 4.236A pdb=" N VAL C 574 " --> pdb=" O GLY C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 588 Processing helix chain 'C' and resid 590 through 604 removed outlier: 3.515A pdb=" N LEU C 600 " --> pdb=" O SER C 596 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP C 602 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 619 removed outlier: 3.619A pdb=" N VAL C 619 " --> pdb=" O CYS C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 removed outlier: 3.906A pdb=" N CYS C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP C 634 " --> pdb=" O HIS C 630 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN C 635 " --> pdb=" O LEU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 640 removed outlier: 3.526A pdb=" N ARG C 640 " --> pdb=" O LEU C 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 637 through 640' Processing helix chain 'C' and resid 821 through 826 Processing helix chain 'C' and resid 875 through 877 No H-bonds generated for 'chain 'C' and resid 875 through 877' Processing helix chain 'C' and resid 878 through 898 removed outlier: 3.544A pdb=" N GLU C 887 " --> pdb=" O GLU C 883 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU C 892 " --> pdb=" O ASN C 888 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS C 897 " --> pdb=" O TRP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 removed outlier: 4.279A pdb=" N GLU C 938 " --> pdb=" O GLN C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1011 removed outlier: 3.973A pdb=" N ASN C1005 " --> pdb=" O GLU C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1060 removed outlier: 3.791A pdb=" N LYS C1043 " --> pdb=" O ASP C1039 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU C1057 " --> pdb=" O ALA C1053 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C1058 " --> pdb=" O VAL C1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1095 removed outlier: 3.548A pdb=" N ALA C1095 " --> pdb=" O LYS C1092 " (cutoff:3.500A) Processing helix chain 'C' and resid 1224 through 1230 removed outlier: 3.589A pdb=" N ILE C1229 " --> pdb=" O LYS C1225 " (cutoff:3.500A) Processing helix chain 'C' and resid 1570 through 1576 removed outlier: 4.201A pdb=" N GLU C1574 " --> pdb=" O LEU C1570 " (cutoff:3.500A) Processing helix chain 'C' and resid 1642 through 1646 removed outlier: 5.260A pdb=" N THR C1645 " --> pdb=" O LEU C1642 " (cutoff:3.500A) Processing helix chain 'C' and resid 1647 through 1665 removed outlier: 3.623A pdb=" N PHE C1653 " --> pdb=" O GLU C1649 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1681 removed outlier: 3.815A pdb=" N ALA C1675 " --> pdb=" O ARG C1671 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C1676 " --> pdb=" O VAL C1672 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS C1677 " --> pdb=" O ALA C1673 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1690 removed outlier: 3.624A pdb=" N LEU C1685 " --> pdb=" O ASP C1681 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C1686 " --> pdb=" O GLU C1682 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR C1687 " --> pdb=" O PRO C1683 " (cutoff:3.500A) Processing helix chain 'C' and resid 1695 through 1711 removed outlier: 3.661A pdb=" N ASP C1704 " --> pdb=" O ALA C1700 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE C1707 " --> pdb=" O TYR C1703 " (cutoff:3.500A) Processing helix chain 'C' and resid 1711 through 1721 removed outlier: 3.524A pdb=" N MET C1720 " --> pdb=" O THR C1716 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET C1721 " --> pdb=" O ALA C1717 " (cutoff:3.500A) Processing helix chain 'C' and resid 1722 through 1724 No H-bonds generated for 'chain 'C' and resid 1722 through 1724' Processing helix chain 'C' and resid 1771 through 1776 removed outlier: 4.289A pdb=" N TYR C1776 " --> pdb=" O ASN C1772 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1802 removed outlier: 4.410A pdb=" N LEU C1787 " --> pdb=" O PRO C1783 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS C1788 " --> pdb=" O LEU C1784 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C1789 " --> pdb=" O ASP C1785 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE C1792 " --> pdb=" O LYS C1788 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU C1797 " --> pdb=" O GLN C1793 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1831 removed outlier: 3.587A pdb=" N VAL C1819 " --> pdb=" O GLU C1815 " (cutoff:3.500A) Proline residue: C1820 - end of helix removed outlier: 3.711A pdb=" N LYS C1823 " --> pdb=" O VAL C1819 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C1824 " --> pdb=" O PRO C1820 " (cutoff:3.500A) Processing helix chain 'C' and resid 1836 through 1847 Processing helix chain 'C' and resid 1900 through 1953 removed outlier: 4.128A pdb=" N LYS C1904 " --> pdb=" O PRO C1900 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C1905 " --> pdb=" O GLU C1901 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU C1909 " --> pdb=" O LEU C1905 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C1910 " --> pdb=" O GLN C1906 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C1911 " --> pdb=" O MET C1907 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS C1917 " --> pdb=" O TYR C1913 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C1926 " --> pdb=" O ARG C1922 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C1927 " --> pdb=" O ILE C1923 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C1928 " --> pdb=" O GLU C1924 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C1929 " --> pdb=" O ALA C1925 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP C1932 " --> pdb=" O ALA C1928 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C1933 " --> pdb=" O PHE C1929 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG C1942 " --> pdb=" O GLN C1938 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N PHE C1943 " --> pdb=" O ASP C1939 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA C1951 " --> pdb=" O GLU C1947 " (cutoff:3.500A) Processing helix chain 'C' and resid 1991 through 1996 removed outlier: 3.790A pdb=" N GLN C1996 " --> pdb=" O GLU C1992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1999 through 2010 removed outlier: 3.675A pdb=" N THR C2006 " --> pdb=" O GLU C2002 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS C2007 " --> pdb=" O ASP C2003 " (cutoff:3.500A) Processing helix chain 'C' and resid 2011 through 2013 No H-bonds generated for 'chain 'C' and resid 2011 through 2013' Processing helix chain 'C' and resid 2024 through 2025 No H-bonds generated for 'chain 'C' and resid 2024 through 2025' Processing helix chain 'C' and resid 2026 through 2037 removed outlier: 3.881A pdb=" N LEU C2030 " --> pdb=" O ILE C2026 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU C2035 " --> pdb=" O LEU C2031 " (cutoff:3.500A) Processing helix chain 'C' and resid 2059 through 2074 removed outlier: 4.069A pdb=" N SER C2064 " --> pdb=" O GLN C2060 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET C2067 " --> pdb=" O ILE C2063 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP C2070 " --> pdb=" O THR C2066 " (cutoff:3.500A) Processing helix chain 'C' and resid 2078 through 2094 removed outlier: 3.588A pdb=" N PHE C2086 " --> pdb=" O VAL C2082 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C2087 " --> pdb=" O ARG C2083 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C2088 " --> pdb=" O ALA C2084 " (cutoff:3.500A) Processing helix chain 'C' and resid 2095 through 2103 removed outlier: 3.747A pdb=" N LEU C2099 " --> pdb=" O GLY C2095 " (cutoff:3.500A) Processing helix chain 'C' and resid 2104 through 2106 No H-bonds generated for 'chain 'C' and resid 2104 through 2106' Processing helix chain 'C' and resid 2113 through 2130 removed outlier: 3.540A pdb=" N ILE C2118 " --> pdb=" O VAL C2114 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU C2120 " --> pdb=" O ASP C2116 " (cutoff:3.500A) Processing helix chain 'C' and resid 2140 through 2152 removed outlier: 3.662A pdb=" N ILE C2144 " --> pdb=" O GLU C2140 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG C2145 " --> pdb=" O LYS C2141 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY C2146 " --> pdb=" O LEU C2142 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY C2148 " --> pdb=" O ILE C2144 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP C2149 " --> pdb=" O ARG C2145 " (cutoff:3.500A) Processing helix chain 'C' and resid 2159 through 2167 removed outlier: 3.745A pdb=" N MET C2163 " --> pdb=" O HIS C2159 " (cutoff:3.500A) Processing helix chain 'C' and resid 2167 through 2180 removed outlier: 3.681A pdb=" N VAL C2175 " --> pdb=" O THR C2171 " (cutoff:3.500A) Processing helix chain 'C' and resid 2193 through 2206 removed outlier: 4.212A pdb=" N CYS C2197 " --> pdb=" O MET C2193 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG C2206 " --> pdb=" O CYS C2202 " (cutoff:3.500A) Processing helix chain 'C' and resid 2208 through 2215 removed outlier: 3.674A pdb=" N MET C2215 " --> pdb=" O ASN C2211 " (cutoff:3.500A) Processing helix chain 'C' and resid 2218 through 2223 Processing helix chain 'C' and resid 2240 through 2247 Processing helix chain 'C' and resid 2251 through 2258 Processing helix chain 'C' and resid 2260 through 2272 removed outlier: 3.507A pdb=" N GLU C2264 " --> pdb=" O GLU C2260 " (cutoff:3.500A) Processing helix chain 'C' and resid 2296 through 2309 removed outlier: 3.752A pdb=" N LEU C2300 " --> pdb=" O GLY C2296 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP C2301 " --> pdb=" O GLU C2297 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS C2309 " --> pdb=" O PHE C2305 " (cutoff:3.500A) Processing helix chain 'C' and resid 2314 through 2327 removed outlier: 4.602A pdb=" N VAL C2322 " --> pdb=" O ALA C2318 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG C2323 " --> pdb=" O ASN C2319 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU C2324 " --> pdb=" O VAL C2320 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU C2325 " --> pdb=" O VAL C2321 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG C2327 " --> pdb=" O ARG C2323 " (cutoff:3.500A) Processing helix chain 'C' and resid 2343 through 2345 No H-bonds generated for 'chain 'C' and resid 2343 through 2345' Processing helix chain 'C' and resid 2346 through 2351 removed outlier: 3.951A pdb=" N GLU C2350 " --> pdb=" O ALA C2346 " (cutoff:3.500A) Processing helix chain 'C' and resid 2387 through 2403 removed outlier: 3.621A pdb=" N THR C2391 " --> pdb=" O ASN C2387 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR C2393 " --> pdb=" O ILE C2389 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C2396 " --> pdb=" O PHE C2392 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C2401 " --> pdb=" O ILE C2397 " (cutoff:3.500A) Processing helix chain 'C' and resid 2408 through 2413 Processing helix chain 'C' and resid 2416 through 2427 removed outlier: 3.542A pdb=" N LEU C2427 " --> pdb=" O ILE C2423 " (cutoff:3.500A) Processing helix chain 'C' and resid 2431 through 2435 Processing helix chain 'C' and resid 2462 through 2476 removed outlier: 4.388A pdb=" N LYS C2466 " --> pdb=" O CYS C2462 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA C2467 " --> pdb=" O PRO C2463 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU C2471 " --> pdb=" O ALA C2467 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE C2472 " --> pdb=" O ALA C2468 " (cutoff:3.500A) Processing helix chain 'C' and resid 2482 through 2488 removed outlier: 4.217A pdb=" N LEU C2486 " --> pdb=" O GLN C2482 " (cutoff:3.500A) Processing helix chain 'C' and resid 2492 through 2497 removed outlier: 3.732A pdb=" N LEU C2497 " --> pdb=" O PHE C2493 " (cutoff:3.500A) Processing helix chain 'C' and resid 2498 through 2502 removed outlier: 4.527A pdb=" N ALA C2501 " --> pdb=" O ARG C2498 " (cutoff:3.500A) Processing helix chain 'C' and resid 2512 through 2516 Processing helix chain 'C' and resid 2517 through 2521 Processing helix chain 'C' and resid 2537 through 2552 removed outlier: 3.519A pdb=" N ASP C2547 " --> pdb=" O ALA C2543 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER C2548 " --> pdb=" O SER C2544 " (cutoff:3.500A) Processing helix chain 'C' and resid 2559 through 2576 removed outlier: 3.514A pdb=" N ASP C2568 " --> pdb=" O LYS C2564 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C2569 " --> pdb=" O ALA C2565 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE C2570 " --> pdb=" O GLN C2566 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C2571 " --> pdb=" O ARG C2567 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL C2572 " --> pdb=" O ASP C2568 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C2574 " --> pdb=" O ILE C2570 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C2575 " --> pdb=" O GLU C2571 " (cutoff:3.500A) Processing helix chain 'C' and resid 2583 through 2595 removed outlier: 4.211A pdb=" N GLN C2587 " --> pdb=" O PRO C2583 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG C2591 " --> pdb=" O GLN C2587 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG C2592 " --> pdb=" O HIS C2588 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C2593 " --> pdb=" O LEU C2589 " (cutoff:3.500A) Processing helix chain 'C' and resid 2606 through 2622 removed outlier: 3.910A pdb=" N ASN C2613 " --> pdb=" O LYS C2609 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS C2614 " --> pdb=" O LEU C2610 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG C2617 " --> pdb=" O ASN C2613 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS C2618 " --> pdb=" O HIS C2614 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP C2619 " --> pdb=" O TYR C2615 " (cutoff:3.500A) Processing helix chain 'C' and resid 2622 through 2627 Processing helix chain 'C' and resid 2635 through 2651 Processing helix chain 'C' and resid 2660 through 2665 Processing helix chain 'C' and resid 2665 through 2676 Processing helix chain 'C' and resid 2718 through 2732 removed outlier: 4.426A pdb=" N LYS C2724 " --> pdb=" O TYR C2720 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS C2732 " --> pdb=" O HIS C2728 " (cutoff:3.500A) Processing helix chain 'C' and resid 2735 through 2739 removed outlier: 3.843A pdb=" N LEU C2738 " --> pdb=" O MET C2735 " (cutoff:3.500A) Processing helix chain 'C' and resid 2749 through 2753 removed outlier: 3.937A pdb=" N SER C2752 " --> pdb=" O SER C2749 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS C2753 " --> pdb=" O ASP C2750 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2749 through 2753' Processing helix chain 'C' and resid 2767 through 2772 removed outlier: 3.629A pdb=" N GLU C2770 " --> pdb=" O LYS C2767 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C2771 " --> pdb=" O GLU C2768 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR C2772 " --> pdb=" O LYS C2769 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2767 through 2772' Processing helix chain 'C' and resid 2773 through 2778 Processing helix chain 'C' and resid 2838 through 2862 removed outlier: 3.977A pdb=" N MET C2844 " --> pdb=" O ALA C2840 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C2847 " --> pdb=" O GLU C2843 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN C2851 " --> pdb=" O GLU C2847 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA C2854 " --> pdb=" O HIS C2850 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C2859 " --> pdb=" O LYS C2855 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU C2860 " --> pdb=" O LYS C2856 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU C2861 " --> pdb=" O LYS C2857 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU C2862 " --> pdb=" O LYS C2858 " (cutoff:3.500A) Processing helix chain 'C' and resid 2874 through 2878 removed outlier: 4.201A pdb=" N LEU C2878 " --> pdb=" O TYR C2875 " (cutoff:3.500A) Processing helix chain 'C' and resid 2882 through 2886 removed outlier: 3.528A pdb=" N LYS C2885 " --> pdb=" O GLU C2882 " (cutoff:3.500A) Processing helix chain 'C' and resid 2891 through 2900 removed outlier: 3.905A pdb=" N LYS C2895 " --> pdb=" O GLN C2891 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE C2896 " --> pdb=" O ASP C2892 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU C2897 " --> pdb=" O ILE C2893 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN C2898 " --> pdb=" O LEU C2894 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C2899 " --> pdb=" O LYS C2895 " (cutoff:3.500A) Processing helix chain 'C' and resid 2982 through 2986 Processing helix chain 'C' and resid 2988 through 2999 Processing helix chain 'C' and resid 3000 through 3003 Processing helix chain 'C' and resid 3012 through 3028 removed outlier: 3.863A pdb=" N SER C3021 " --> pdb=" O ARG C3017 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU C3022 " --> pdb=" O HIS C3018 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE C3023 " --> pdb=" O ARG C3019 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY C3024 " --> pdb=" O ILE C3020 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN C3025 " --> pdb=" O SER C3021 " (cutoff:3.500A) Processing helix chain 'C' and resid 3035 through 3050 removed outlier: 3.974A pdb=" N LYS C3048 " --> pdb=" O ARG C3044 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY C3050 " --> pdb=" O VAL C3046 " (cutoff:3.500A) Processing helix chain 'C' and resid 3062 through 3067 Processing helix chain 'C' and resid 3067 through 3080 removed outlier: 3.674A pdb=" N LYS C3071 " --> pdb=" O GLU C3067 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU C3074 " --> pdb=" O GLU C3070 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN C3075 " --> pdb=" O LYS C3071 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C3076 " --> pdb=" O THR C3072 " (cutoff:3.500A) Processing helix chain 'C' and resid 3103 through 3115 removed outlier: 3.579A pdb=" N GLU C3111 " --> pdb=" O SER C3107 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N HIS C3112 " --> pdb=" O SER C3108 " (cutoff:3.500A) Processing helix chain 'C' and resid 3116 through 3118 No H-bonds generated for 'chain 'C' and resid 3116 through 3118' Processing helix chain 'C' and resid 3128 through 3133 Processing helix chain 'C' and resid 3136 through 3142 Processing helix chain 'C' and resid 3152 through 3162 removed outlier: 3.621A pdb=" N LEU C3160 " --> pdb=" O LEU C3156 " (cutoff:3.500A) Processing helix chain 'C' and resid 3171 through 3178 Processing helix chain 'C' and resid 3586 through 3605 removed outlier: 3.777A pdb=" N ARG C3605 " --> pdb=" O VAL C3601 " (cutoff:3.500A) Processing helix chain 'C' and resid 3613 through 3630 removed outlier: 4.156A pdb=" N ILE C3630 " --> pdb=" O GLU C3626 " (cutoff:3.500A) Processing helix chain 'C' and resid 3637 through 3646 Processing helix chain 'C' and resid 3663 through 3677 Processing helix chain 'C' and resid 3688 through 3699 removed outlier: 5.083A pdb=" N ASP C3694 " --> pdb=" O MET C3690 " (cutoff:3.500A) Processing helix chain 'C' and resid 3715 through 3734 Processing helix chain 'C' and resid 3736 through 3748 removed outlier: 4.606A pdb=" N MET C3740 " --> pdb=" O GLY C3736 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C3741 " --> pdb=" O ALA C3737 " (cutoff:3.500A) Processing helix chain 'C' and resid 3753 through 3767 Processing helix chain 'C' and resid 3771 through 3785 removed outlier: 3.601A pdb=" N GLN C3775 " --> pdb=" O ASN C3771 " (cutoff:3.500A) Processing helix chain 'C' and resid 3787 through 3800 removed outlier: 3.627A pdb=" N PHE C3791 " --> pdb=" O ASP C3787 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER C3800 " --> pdb=" O GLY C3796 " (cutoff:3.500A) Processing helix chain 'C' and resid 3805 through 3819 removed outlier: 3.552A pdb=" N PHE C3809 " --> pdb=" O ASP C3805 " (cutoff:3.500A) Processing helix chain 'C' and resid 3833 through 3849 removed outlier: 3.884A pdb=" N THR C3837 " --> pdb=" O ASP C3833 " (cutoff:3.500A) Processing helix chain 'C' and resid 3852 through 3862 Processing helix chain 'C' and resid 3870 through 3894 removed outlier: 3.725A pdb=" N SER C3874 " --> pdb=" O ASN C3870 " (cutoff:3.500A) Processing helix chain 'C' and resid 3900 through 3926 Processing helix chain 'C' and resid 3929 through 3938 removed outlier: 4.265A pdb=" N GLN C3933 " --> pdb=" O CYS C3929 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS C3938 " --> pdb=" O GLN C3934 " (cutoff:3.500A) Processing helix chain 'C' and resid 3940 through 3960 removed outlier: 4.269A pdb=" N ALA C3944 " --> pdb=" O ARG C3940 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS C3954 " --> pdb=" O HIS C3950 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET C3957 " --> pdb=" O ALA C3953 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C3958 " --> pdb=" O HIS C3954 " (cutoff:3.500A) Processing helix chain 'C' and resid 3965 through 3988 removed outlier: 3.628A pdb=" N LEU C3983 " --> pdb=" O MET C3979 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU C3988 " --> pdb=" O LEU C3984 " (cutoff:3.500A) Processing helix chain 'C' and resid 3994 through 4006 Processing helix chain 'C' and resid 4007 through 4028 removed outlier: 3.994A pdb=" N PHE C4021 " --> pdb=" O PHE C4017 " (cutoff:3.500A) Processing helix chain 'C' and resid 4046 through 4055 Processing helix chain 'C' and resid 4060 through 4068 removed outlier: 3.929A pdb=" N THR C4064 " --> pdb=" O THR C4060 " (cutoff:3.500A) Processing helix chain 'C' and resid 4082 through 4090 removed outlier: 4.277A pdb=" N GLU C4090 " --> pdb=" O LYS C4086 " (cutoff:3.500A) Processing helix chain 'C' and resid 4093 through 4110 Processing helix chain 'C' and resid 4113 through 4123 removed outlier: 3.833A pdb=" N ALA C4123 " --> pdb=" O PHE C4119 " (cutoff:3.500A) Processing helix chain 'C' and resid 4123 through 4131 removed outlier: 3.932A pdb=" N LEU C4127 " --> pdb=" O ALA C4123 " (cutoff:3.500A) Processing helix chain 'C' and resid 4154 through 4162 removed outlier: 3.808A pdb=" N ARG C4158 " --> pdb=" O SER C4154 " (cutoff:3.500A) Processing helix chain 'C' and resid 4163 through 4179 removed outlier: 3.585A pdb=" N ASN C4179 " --> pdb=" O PHE C4175 " (cutoff:3.500A) Processing helix chain 'C' and resid 4185 through 4206 removed outlier: 3.774A pdb=" N GLN C4206 " --> pdb=" O GLN C4202 " (cutoff:3.500A) Processing helix chain 'C' and resid 4487 through 4499 removed outlier: 3.578A pdb=" N TYR C4495 " --> pdb=" O LYS C4491 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C4496 " --> pdb=" O LEU C4492 " (cutoff:3.500A) Processing helix chain 'C' and resid 4500 through 4518 removed outlier: 3.648A pdb=" N ALA C4507 " --> pdb=" O MET C4503 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU C4508 " --> pdb=" O ARG C4504 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C4509 " --> pdb=" O MET C4505 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA C4513 " --> pdb=" O PHE C4509 " (cutoff:3.500A) Processing helix chain 'C' and resid 4519 through 4521 No H-bonds generated for 'chain 'C' and resid 4519 through 4521' Processing helix chain 'C' and resid 4569 through 4614 removed outlier: 4.392A pdb=" N ILE C4578 " --> pdb=" O ARG C4574 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE C4586 " --> pdb=" O VAL C4582 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS C4587 " --> pdb=" O ILE C4583 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE C4588 " --> pdb=" O SER C4584 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL C4596 " --> pdb=" O TYR C4592 " (cutoff:3.500A) Proline residue: C4597 - end of helix removed outlier: 3.608A pdb=" N ARG C4603 " --> pdb=" O VAL C4599 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C4612 " --> pdb=" O ALA C4608 " (cutoff:3.500A) Processing helix chain 'C' and resid 4626 through 4632 Processing helix chain 'C' and resid 4633 through 4638 removed outlier: 4.386A pdb=" N ILE C4636 " --> pdb=" O ARG C4633 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN C4637 " --> pdb=" O LEU C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4649 through 4658 removed outlier: 3.588A pdb=" N VAL C4654 " --> pdb=" O VAL C4650 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N MET C4655 " --> pdb=" O LYS C4651 " (cutoff:3.500A) Processing helix chain 'C' and resid 4663 through 4669 Processing helix chain 'C' and resid 4696 through 4701 removed outlier: 3.550A pdb=" N LEU C4699 " --> pdb=" O SER C4696 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C4701 " --> pdb=" O VAL C4698 " (cutoff:3.500A) Processing helix chain 'C' and resid 4703 through 4715 removed outlier: 4.199A pdb=" N GLY C4712 " --> pdb=" O MET C4708 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL C4713 " --> pdb=" O TRP C4709 " (cutoff:3.500A) Processing helix chain 'C' and resid 4717 through 4736 removed outlier: 3.675A pdb=" N LEU C4732 " --> pdb=" O THR C4728 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY C4733 " --> pdb=" O MET C4729 " (cutoff:3.500A) Processing helix chain 'C' and resid 4741 through 4748 removed outlier: 3.681A pdb=" N ILE C4747 " --> pdb=" O LEU C4744 " (cutoff:3.500A) Processing helix chain 'C' and resid 4751 through 4763 removed outlier: 3.623A pdb=" N ARG C4755 " --> pdb=" O PHE C4751 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR C4756 " --> pdb=" O LYS C4752 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE C4757 " --> pdb=" O THR C4753 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C4758 " --> pdb=" O LEU C4754 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C4761 " --> pdb=" O ILE C4757 " (cutoff:3.500A) Processing helix chain 'C' and resid 4767 through 4790 removed outlier: 3.861A pdb=" N THR C4771 " --> pdb=" O GLN C4767 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C4772 " --> pdb=" O LEU C4768 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C4777 " --> pdb=" O GLY C4773 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C4779 " --> pdb=" O LEU C4775 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C4784 " --> pdb=" O TYR C4780 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL C4785 " --> pdb=" O LEU C4781 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA C4786 " --> pdb=" O TYR C4782 " (cutoff:3.500A) Processing helix chain 'C' and resid 4791 through 4794 Processing helix chain 'C' and resid 4812 through 4825 removed outlier: 3.950A pdb=" N VAL C4822 " --> pdb=" O MET C4818 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG C4823 " --> pdb=" O TYR C4819 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY C4825 " --> pdb=" O GLY C4821 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4868 removed outlier: 3.961A pdb=" N TYR C4843 " --> pdb=" O GLU C4839 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE C4849 " --> pdb=" O ILE C4845 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE C4858 " --> pdb=" O PHE C4854 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA C4861 " --> pdb=" O VAL C4857 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLY C4865 " --> pdb=" O ALA C4861 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C4866 " --> pdb=" O ILE C4862 " (cutoff:3.500A) Processing helix chain 'C' and resid 4868 through 4881 removed outlier: 4.346A pdb=" N GLU C4873 " --> pdb=" O ASP C4869 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C4874 " --> pdb=" O ALA C4870 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C4881 " --> pdb=" O GLN C4877 " (cutoff:3.500A) Processing helix chain 'C' and resid 4895 through 4900 removed outlier: 4.184A pdb=" N PHE C4899 " --> pdb=" O GLY C4895 " (cutoff:3.500A) Processing helix chain 'C' and resid 4904 through 4910 removed outlier: 3.939A pdb=" N THR C4908 " --> pdb=" O HIS C4904 " (cutoff:3.500A) Processing helix chain 'C' and resid 4916 through 4929 removed outlier: 3.900A pdb=" N LEU C4920 " --> pdb=" O LEU C4916 " (cutoff:3.500A) Processing helix chain 'C' and resid 4935 through 4947 removed outlier: 3.915A pdb=" N TRP C4942 " --> pdb=" O GLU C4938 " (cutoff:3.500A) Processing helix chain 'C' and resid 4959 through 4963 Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.574A pdb=" N PHE D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 41 removed outlier: 3.639A pdb=" N LEU D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY D 34 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 54 removed outlier: 4.355A pdb=" N ASP D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 75 removed outlier: 3.568A pdb=" N THR D 71 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 94 Processing helix chain 'D' and resid 102 through 110 removed outlier: 3.790A pdb=" N MET D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 removed outlier: 4.712A pdb=" N VAL D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 removed outlier: 3.881A pdb=" N GLN D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 83 removed outlier: 3.534A pdb=" N LEU E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 158 removed outlier: 4.040A pdb=" N CYS E 158 " --> pdb=" O GLY E 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 155 through 158' Processing helix chain 'E' and resid 409 through 436 removed outlier: 3.859A pdb=" N VAL E 418 " --> pdb=" O ARG E 414 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER E 421 " --> pdb=" O ARG E 417 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 423 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU E 425 " --> pdb=" O SER E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 463 removed outlier: 3.562A pdb=" N ILE E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY E 461 " --> pdb=" O GLN E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 491 removed outlier: 3.859A pdb=" N ARG E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE E 489 " --> pdb=" O ARG E 485 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN E 490 " --> pdb=" O GLN E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 506 removed outlier: 4.100A pdb=" N GLU E 500 " --> pdb=" O ASN E 496 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS E 501 " --> pdb=" O LEU E 497 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP E 503 " --> pdb=" O LEU E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 542 removed outlier: 4.316A pdb=" N LEU E 536 " --> pdb=" O SER E 532 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU E 537 " --> pdb=" O LEU E 533 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA E 538 " --> pdb=" O TYR E 534 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA E 539 " --> pdb=" O GLU E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 551 removed outlier: 4.119A pdb=" N CYS E 548 " --> pdb=" O ASN E 544 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 549 " --> pdb=" O ARG E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 563 removed outlier: 4.255A pdb=" N TRP E 557 " --> pdb=" O GLY E 553 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU E 563 " --> pdb=" O ILE E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 580 removed outlier: 4.235A pdb=" N VAL E 574 " --> pdb=" O GLY E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 588 Processing helix chain 'E' and resid 590 through 604 removed outlier: 3.515A pdb=" N LEU E 600 " --> pdb=" O SER E 596 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU E 601 " --> pdb=" O ILE E 597 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP E 602 " --> pdb=" O ILE E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 619 removed outlier: 3.618A pdb=" N VAL E 619 " --> pdb=" O CYS E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 636 removed outlier: 3.906A pdb=" N CYS E 633 " --> pdb=" O GLN E 629 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP E 634 " --> pdb=" O HIS E 630 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN E 635 " --> pdb=" O LEU E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 640 removed outlier: 3.526A pdb=" N ARG E 640 " --> pdb=" O LEU E 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 637 through 640' Processing helix chain 'E' and resid 821 through 826 Processing helix chain 'E' and resid 875 through 877 No H-bonds generated for 'chain 'E' and resid 875 through 877' Processing helix chain 'E' and resid 878 through 898 removed outlier: 3.544A pdb=" N GLU E 887 " --> pdb=" O GLU E 883 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU E 892 " --> pdb=" O ASN E 888 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS E 897 " --> pdb=" O TRP E 893 " (cutoff:3.500A) Processing helix chain 'E' and resid 933 through 942 removed outlier: 4.280A pdb=" N GLU E 938 " --> pdb=" O GLN E 934 " (cutoff:3.500A) Processing helix chain 'E' and resid 994 through 1011 removed outlier: 3.973A pdb=" N ASN E1005 " --> pdb=" O GLU E1001 " (cutoff:3.500A) Processing helix chain 'E' and resid 1039 through 1060 removed outlier: 3.791A pdb=" N LYS E1043 " --> pdb=" O ASP E1039 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU E1057 " --> pdb=" O ALA E1053 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E1058 " --> pdb=" O VAL E1054 " (cutoff:3.500A) Processing helix chain 'E' and resid 1091 through 1095 removed outlier: 3.548A pdb=" N ALA E1095 " --> pdb=" O LYS E1092 " (cutoff:3.500A) Processing helix chain 'E' and resid 1224 through 1230 removed outlier: 3.589A pdb=" N ILE E1229 " --> pdb=" O LYS E1225 " (cutoff:3.500A) Processing helix chain 'E' and resid 1570 through 1576 removed outlier: 4.201A pdb=" N GLU E1574 " --> pdb=" O LEU E1570 " (cutoff:3.500A) Processing helix chain 'E' and resid 1642 through 1646 removed outlier: 5.260A pdb=" N THR E1645 " --> pdb=" O LEU E1642 " (cutoff:3.500A) Processing helix chain 'E' and resid 1647 through 1665 removed outlier: 3.623A pdb=" N PHE E1653 " --> pdb=" O GLU E1649 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N CYS E1665 " --> pdb=" O TYR E1661 " (cutoff:3.500A) Processing helix chain 'E' and resid 1669 through 1681 removed outlier: 3.814A pdb=" N ALA E1675 " --> pdb=" O ARG E1671 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU E1676 " --> pdb=" O VAL E1672 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS E1677 " --> pdb=" O ALA E1673 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER E1678 " --> pdb=" O HIS E1674 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS E1679 " --> pdb=" O ALA E1675 " (cutoff:3.500A) Processing helix chain 'E' and resid 1681 through 1690 removed outlier: 3.624A pdb=" N LEU E1685 " --> pdb=" O ASP E1681 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E1686 " --> pdb=" O GLU E1682 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR E1687 " --> pdb=" O PRO E1683 " (cutoff:3.500A) Processing helix chain 'E' and resid 1695 through 1711 removed outlier: 3.661A pdb=" N ASP E1704 " --> pdb=" O ALA E1700 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE E1707 " --> pdb=" O TYR E1703 " (cutoff:3.500A) Processing helix chain 'E' and resid 1711 through 1721 removed outlier: 3.525A pdb=" N MET E1720 " --> pdb=" O THR E1716 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET E1721 " --> pdb=" O ALA E1717 " (cutoff:3.500A) Processing helix chain 'E' and resid 1722 through 1724 No H-bonds generated for 'chain 'E' and resid 1722 through 1724' Processing helix chain 'E' and resid 1771 through 1776 removed outlier: 4.289A pdb=" N TYR E1776 " --> pdb=" O ASN E1772 " (cutoff:3.500A) Processing helix chain 'E' and resid 1783 through 1802 removed outlier: 4.410A pdb=" N LEU E1787 " --> pdb=" O PRO E1783 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS E1788 " --> pdb=" O LEU E1784 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA E1789 " --> pdb=" O ASP E1785 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE E1792 " --> pdb=" O LYS E1788 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU E1797 " --> pdb=" O GLN E1793 " (cutoff:3.500A) Processing helix chain 'E' and resid 1813 through 1831 removed outlier: 3.587A pdb=" N VAL E1819 " --> pdb=" O GLU E1815 " (cutoff:3.500A) Proline residue: E1820 - end of helix removed outlier: 3.711A pdb=" N LYS E1823 " --> pdb=" O VAL E1819 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU E1824 " --> pdb=" O PRO E1820 " (cutoff:3.500A) Processing helix chain 'E' and resid 1836 through 1847 Processing helix chain 'E' and resid 1900 through 1953 removed outlier: 4.128A pdb=" N LYS E1904 " --> pdb=" O PRO E1900 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E1905 " --> pdb=" O GLU E1901 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU E1909 " --> pdb=" O LEU E1905 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU E1910 " --> pdb=" O GLN E1906 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU E1911 " --> pdb=" O MET E1907 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS E1917 " --> pdb=" O TYR E1913 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE E1926 " --> pdb=" O ARG E1922 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL E1927 " --> pdb=" O ILE E1923 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA E1928 " --> pdb=" O GLU E1924 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE E1929 " --> pdb=" O ALA E1925 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP E1932 " --> pdb=" O ALA E1928 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE E1933 " --> pdb=" O PHE E1929 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG E1942 " --> pdb=" O GLN E1938 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N PHE E1943 " --> pdb=" O ASP E1939 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA E1951 " --> pdb=" O GLU E1947 " (cutoff:3.500A) Processing helix chain 'E' and resid 1991 through 1996 removed outlier: 3.790A pdb=" N GLN E1996 " --> pdb=" O GLU E1992 " (cutoff:3.500A) Processing helix chain 'E' and resid 1999 through 2010 removed outlier: 3.675A pdb=" N THR E2006 " --> pdb=" O GLU E2002 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS E2007 " --> pdb=" O ASP E2003 " (cutoff:3.500A) Processing helix chain 'E' and resid 2011 through 2013 No H-bonds generated for 'chain 'E' and resid 2011 through 2013' Processing helix chain 'E' and resid 2024 through 2025 No H-bonds generated for 'chain 'E' and resid 2024 through 2025' Processing helix chain 'E' and resid 2026 through 2037 removed outlier: 3.881A pdb=" N LEU E2030 " --> pdb=" O ILE E2026 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU E2035 " --> pdb=" O LEU E2031 " (cutoff:3.500A) Processing helix chain 'E' and resid 2059 through 2074 removed outlier: 4.069A pdb=" N SER E2064 " --> pdb=" O GLN E2060 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET E2067 " --> pdb=" O ILE E2063 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP E2070 " --> pdb=" O THR E2066 " (cutoff:3.500A) Processing helix chain 'E' and resid 2078 through 2094 removed outlier: 3.589A pdb=" N PHE E2086 " --> pdb=" O VAL E2082 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E2087 " --> pdb=" O ARG E2083 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU E2088 " --> pdb=" O ALA E2084 " (cutoff:3.500A) Processing helix chain 'E' and resid 2095 through 2103 removed outlier: 3.748A pdb=" N LEU E2099 " --> pdb=" O GLY E2095 " (cutoff:3.500A) Processing helix chain 'E' and resid 2104 through 2106 No H-bonds generated for 'chain 'E' and resid 2104 through 2106' Processing helix chain 'E' and resid 2113 through 2130 removed outlier: 3.539A pdb=" N ILE E2118 " --> pdb=" O VAL E2114 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU E2120 " --> pdb=" O ASP E2116 " (cutoff:3.500A) Processing helix chain 'E' and resid 2140 through 2152 removed outlier: 3.660A pdb=" N ILE E2144 " --> pdb=" O GLU E2140 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG E2145 " --> pdb=" O LYS E2141 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY E2146 " --> pdb=" O LEU E2142 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY E2148 " --> pdb=" O ILE E2144 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP E2149 " --> pdb=" O ARG E2145 " (cutoff:3.500A) Processing helix chain 'E' and resid 2159 through 2167 removed outlier: 3.745A pdb=" N MET E2163 " --> pdb=" O HIS E2159 " (cutoff:3.500A) Processing helix chain 'E' and resid 2167 through 2180 removed outlier: 3.681A pdb=" N VAL E2175 " --> pdb=" O THR E2171 " (cutoff:3.500A) Processing helix chain 'E' and resid 2193 through 2206 removed outlier: 4.213A pdb=" N CYS E2197 " --> pdb=" O MET E2193 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG E2206 " --> pdb=" O CYS E2202 " (cutoff:3.500A) Processing helix chain 'E' and resid 2208 through 2215 removed outlier: 3.674A pdb=" N MET E2215 " --> pdb=" O ASN E2211 " (cutoff:3.500A) Processing helix chain 'E' and resid 2218 through 2223 Processing helix chain 'E' and resid 2240 through 2247 Processing helix chain 'E' and resid 2251 through 2258 Processing helix chain 'E' and resid 2260 through 2272 removed outlier: 3.507A pdb=" N GLU E2264 " --> pdb=" O GLU E2260 " (cutoff:3.500A) Processing helix chain 'E' and resid 2296 through 2309 removed outlier: 3.751A pdb=" N LEU E2300 " --> pdb=" O GLY E2296 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP E2301 " --> pdb=" O GLU E2297 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS E2309 " --> pdb=" O PHE E2305 " (cutoff:3.500A) Processing helix chain 'E' and resid 2314 through 2327 removed outlier: 4.602A pdb=" N VAL E2322 " --> pdb=" O ALA E2318 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG E2323 " --> pdb=" O ASN E2319 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU E2324 " --> pdb=" O VAL E2320 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E2325 " --> pdb=" O VAL E2321 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG E2327 " --> pdb=" O ARG E2323 " (cutoff:3.500A) Processing helix chain 'E' and resid 2343 through 2345 No H-bonds generated for 'chain 'E' and resid 2343 through 2345' Processing helix chain 'E' and resid 2346 through 2351 removed outlier: 3.951A pdb=" N GLU E2350 " --> pdb=" O ALA E2346 " (cutoff:3.500A) Processing helix chain 'E' and resid 2387 through 2403 removed outlier: 3.621A pdb=" N THR E2391 " --> pdb=" O ASN E2387 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR E2393 " --> pdb=" O ILE E2389 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E2396 " --> pdb=" O PHE E2392 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY E2401 " --> pdb=" O ILE E2397 " (cutoff:3.500A) Processing helix chain 'E' and resid 2408 through 2413 Processing helix chain 'E' and resid 2416 through 2427 removed outlier: 3.542A pdb=" N LEU E2427 " --> pdb=" O ILE E2423 " (cutoff:3.500A) Processing helix chain 'E' and resid 2431 through 2435 Processing helix chain 'E' and resid 2462 through 2476 removed outlier: 4.389A pdb=" N LYS E2466 " --> pdb=" O CYS E2462 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA E2467 " --> pdb=" O PRO E2463 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU E2471 " --> pdb=" O ALA E2467 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N PHE E2472 " --> pdb=" O ALA E2468 " (cutoff:3.500A) Processing helix chain 'E' and resid 2482 through 2488 removed outlier: 4.217A pdb=" N LEU E2486 " --> pdb=" O GLN E2482 " (cutoff:3.500A) Processing helix chain 'E' and resid 2492 through 2497 removed outlier: 3.732A pdb=" N LEU E2497 " --> pdb=" O PHE E2493 " (cutoff:3.500A) Processing helix chain 'E' and resid 2498 through 2502 removed outlier: 4.527A pdb=" N ALA E2501 " --> pdb=" O ARG E2498 " (cutoff:3.500A) Processing helix chain 'E' and resid 2512 through 2516 Processing helix chain 'E' and resid 2517 through 2521 Processing helix chain 'E' and resid 2537 through 2552 removed outlier: 3.520A pdb=" N ASP E2547 " --> pdb=" O ALA E2543 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER E2548 " --> pdb=" O SER E2544 " (cutoff:3.500A) Processing helix chain 'E' and resid 2559 through 2576 removed outlier: 3.514A pdb=" N ASP E2568 " --> pdb=" O LYS E2564 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER E2569 " --> pdb=" O ALA E2565 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE E2570 " --> pdb=" O GLN E2566 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU E2571 " --> pdb=" O ARG E2567 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL E2572 " --> pdb=" O ASP E2568 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU E2574 " --> pdb=" O ILE E2570 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU E2575 " --> pdb=" O GLU E2571 " (cutoff:3.500A) Processing helix chain 'E' and resid 2583 through 2595 removed outlier: 4.212A pdb=" N GLN E2587 " --> pdb=" O PRO E2583 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG E2591 " --> pdb=" O GLN E2587 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG E2592 " --> pdb=" O HIS E2588 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU E2593 " --> pdb=" O LEU E2589 " (cutoff:3.500A) Processing helix chain 'E' and resid 2606 through 2622 removed outlier: 3.910A pdb=" N ASN E2613 " --> pdb=" O LYS E2609 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS E2614 " --> pdb=" O LEU E2610 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG E2617 " --> pdb=" O ASN E2613 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS E2618 " --> pdb=" O HIS E2614 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP E2619 " --> pdb=" O TYR E2615 " (cutoff:3.500A) Processing helix chain 'E' and resid 2622 through 2627 Processing helix chain 'E' and resid 2635 through 2651 Processing helix chain 'E' and resid 2660 through 2665 Processing helix chain 'E' and resid 2665 through 2676 Processing helix chain 'E' and resid 2718 through 2732 removed outlier: 4.425A pdb=" N LYS E2724 " --> pdb=" O TYR E2720 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS E2732 " --> pdb=" O HIS E2728 " (cutoff:3.500A) Processing helix chain 'E' and resid 2735 through 2739 removed outlier: 3.844A pdb=" N LEU E2738 " --> pdb=" O MET E2735 " (cutoff:3.500A) Processing helix chain 'E' and resid 2749 through 2753 removed outlier: 3.937A pdb=" N SER E2752 " --> pdb=" O SER E2749 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS E2753 " --> pdb=" O ASP E2750 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2749 through 2753' Processing helix chain 'E' and resid 2767 through 2772 removed outlier: 3.629A pdb=" N GLU E2770 " --> pdb=" O LYS E2767 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE E2771 " --> pdb=" O GLU E2768 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR E2772 " --> pdb=" O LYS E2769 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2767 through 2772' Processing helix chain 'E' and resid 2773 through 2778 Processing helix chain 'E' and resid 2838 through 2862 removed outlier: 3.977A pdb=" N MET E2844 " --> pdb=" O ALA E2840 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU E2847 " --> pdb=" O GLU E2843 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN E2851 " --> pdb=" O GLU E2847 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA E2854 " --> pdb=" O HIS E2850 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU E2859 " --> pdb=" O LYS E2855 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU E2860 " --> pdb=" O LYS E2856 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU E2861 " --> pdb=" O LYS E2857 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU E2862 " --> pdb=" O LYS E2858 " (cutoff:3.500A) Processing helix chain 'E' and resid 2874 through 2878 removed outlier: 4.201A pdb=" N LEU E2878 " --> pdb=" O TYR E2875 " (cutoff:3.500A) Processing helix chain 'E' and resid 2882 through 2886 removed outlier: 3.528A pdb=" N LYS E2885 " --> pdb=" O GLU E2882 " (cutoff:3.500A) Processing helix chain 'E' and resid 2891 through 2900 removed outlier: 3.906A pdb=" N LYS E2895 " --> pdb=" O GLN E2891 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE E2896 " --> pdb=" O ASP E2892 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU E2897 " --> pdb=" O ILE E2893 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN E2898 " --> pdb=" O LEU E2894 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE E2899 " --> pdb=" O LYS E2895 " (cutoff:3.500A) Processing helix chain 'E' and resid 2982 through 2986 Processing helix chain 'E' and resid 2988 through 2999 Processing helix chain 'E' and resid 3000 through 3003 Processing helix chain 'E' and resid 3012 through 3028 removed outlier: 3.863A pdb=" N SER E3021 " --> pdb=" O ARG E3017 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU E3022 " --> pdb=" O HIS E3018 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE E3023 " --> pdb=" O ARG E3019 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY E3024 " --> pdb=" O ILE E3020 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN E3025 " --> pdb=" O SER E3021 " (cutoff:3.500A) Processing helix chain 'E' and resid 3035 through 3050 removed outlier: 3.974A pdb=" N LYS E3048 " --> pdb=" O ARG E3044 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR E3049 " --> pdb=" O THR E3045 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY E3050 " --> pdb=" O VAL E3046 " (cutoff:3.500A) Processing helix chain 'E' and resid 3062 through 3067 Processing helix chain 'E' and resid 3067 through 3080 removed outlier: 3.674A pdb=" N LYS E3071 " --> pdb=" O GLU E3067 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU E3074 " --> pdb=" O GLU E3070 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN E3075 " --> pdb=" O LYS E3071 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU E3076 " --> pdb=" O THR E3072 " (cutoff:3.500A) Processing helix chain 'E' and resid 3103 through 3115 removed outlier: 3.578A pdb=" N GLU E3111 " --> pdb=" O SER E3107 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N HIS E3112 " --> pdb=" O SER E3108 " (cutoff:3.500A) Processing helix chain 'E' and resid 3116 through 3118 No H-bonds generated for 'chain 'E' and resid 3116 through 3118' Processing helix chain 'E' and resid 3128 through 3133 Processing helix chain 'E' and resid 3136 through 3142 Processing helix chain 'E' and resid 3152 through 3162 removed outlier: 3.621A pdb=" N LEU E3160 " --> pdb=" O LEU E3156 " (cutoff:3.500A) Processing helix chain 'E' and resid 3171 through 3178 Processing helix chain 'E' and resid 3586 through 3605 removed outlier: 3.777A pdb=" N ARG E3605 " --> pdb=" O VAL E3601 " (cutoff:3.500A) Processing helix chain 'E' and resid 3613 through 3630 removed outlier: 4.155A pdb=" N ILE E3630 " --> pdb=" O GLU E3626 " (cutoff:3.500A) Processing helix chain 'E' and resid 3637 through 3646 Processing helix chain 'E' and resid 3663 through 3677 Processing helix chain 'E' and resid 3688 through 3699 removed outlier: 5.083A pdb=" N ASP E3694 " --> pdb=" O MET E3690 " (cutoff:3.500A) Processing helix chain 'E' and resid 3715 through 3734 Processing helix chain 'E' and resid 3736 through 3748 removed outlier: 4.605A pdb=" N MET E3740 " --> pdb=" O GLY E3736 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL E3741 " --> pdb=" O ALA E3737 " (cutoff:3.500A) Processing helix chain 'E' and resid 3753 through 3767 Processing helix chain 'E' and resid 3771 through 3785 removed outlier: 3.601A pdb=" N GLN E3775 " --> pdb=" O ASN E3771 " (cutoff:3.500A) Processing helix chain 'E' and resid 3787 through 3800 removed outlier: 3.627A pdb=" N PHE E3791 " --> pdb=" O ASP E3787 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER E3800 " --> pdb=" O GLY E3796 " (cutoff:3.500A) Processing helix chain 'E' and resid 3805 through 3819 removed outlier: 3.552A pdb=" N PHE E3809 " --> pdb=" O ASP E3805 " (cutoff:3.500A) Processing helix chain 'E' and resid 3833 through 3849 removed outlier: 3.884A pdb=" N THR E3837 " --> pdb=" O ASP E3833 " (cutoff:3.500A) Processing helix chain 'E' and resid 3852 through 3862 Processing helix chain 'E' and resid 3870 through 3894 removed outlier: 3.725A pdb=" N SER E3874 " --> pdb=" O ASN E3870 " (cutoff:3.500A) Processing helix chain 'E' and resid 3900 through 3926 Processing helix chain 'E' and resid 3929 through 3938 removed outlier: 4.265A pdb=" N GLN E3933 " --> pdb=" O CYS E3929 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS E3938 " --> pdb=" O GLN E3934 " (cutoff:3.500A) Processing helix chain 'E' and resid 3940 through 3960 removed outlier: 4.269A pdb=" N ALA E3944 " --> pdb=" O ARG E3940 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS E3954 " --> pdb=" O HIS E3950 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET E3957 " --> pdb=" O ALA E3953 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS E3958 " --> pdb=" O HIS E3954 " (cutoff:3.500A) Processing helix chain 'E' and resid 3965 through 3988 removed outlier: 3.629A pdb=" N LEU E3983 " --> pdb=" O MET E3979 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU E3988 " --> pdb=" O LEU E3984 " (cutoff:3.500A) Processing helix chain 'E' and resid 3994 through 4006 Processing helix chain 'E' and resid 4007 through 4028 removed outlier: 3.994A pdb=" N PHE E4021 " --> pdb=" O PHE E4017 " (cutoff:3.500A) Processing helix chain 'E' and resid 4046 through 4055 Processing helix chain 'E' and resid 4060 through 4068 removed outlier: 3.929A pdb=" N THR E4064 " --> pdb=" O THR E4060 " (cutoff:3.500A) Processing helix chain 'E' and resid 4082 through 4090 removed outlier: 4.277A pdb=" N GLU E4090 " --> pdb=" O LYS E4086 " (cutoff:3.500A) Processing helix chain 'E' and resid 4093 through 4110 Processing helix chain 'E' and resid 4113 through 4123 removed outlier: 3.832A pdb=" N ALA E4123 " --> pdb=" O PHE E4119 " (cutoff:3.500A) Processing helix chain 'E' and resid 4123 through 4131 removed outlier: 3.932A pdb=" N LEU E4127 " --> pdb=" O ALA E4123 " (cutoff:3.500A) Processing helix chain 'E' and resid 4154 through 4162 removed outlier: 3.808A pdb=" N ARG E4158 " --> pdb=" O SER E4154 " (cutoff:3.500A) Processing helix chain 'E' and resid 4163 through 4179 removed outlier: 3.585A pdb=" N ASN E4179 " --> pdb=" O PHE E4175 " (cutoff:3.500A) Processing helix chain 'E' and resid 4185 through 4206 removed outlier: 3.774A pdb=" N GLN E4206 " --> pdb=" O GLN E4202 " (cutoff:3.500A) Processing helix chain 'E' and resid 4487 through 4499 removed outlier: 3.578A pdb=" N TYR E4495 " --> pdb=" O LYS E4491 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE E4496 " --> pdb=" O LEU E4492 " (cutoff:3.500A) Processing helix chain 'E' and resid 4500 through 4518 removed outlier: 3.648A pdb=" N ALA E4507 " --> pdb=" O MET E4503 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU E4508 " --> pdb=" O ARG E4504 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE E4509 " --> pdb=" O MET E4505 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA E4513 " --> pdb=" O PHE E4509 " (cutoff:3.500A) Processing helix chain 'E' and resid 4569 through 4614 removed outlier: 4.392A pdb=" N ILE E4578 " --> pdb=" O ARG E4574 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE E4586 " --> pdb=" O VAL E4582 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS E4587 " --> pdb=" O ILE E4583 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE E4588 " --> pdb=" O SER E4584 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL E4596 " --> pdb=" O TYR E4592 " (cutoff:3.500A) Proline residue: E4597 - end of helix removed outlier: 3.608A pdb=" N ARG E4603 " --> pdb=" O VAL E4599 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU E4612 " --> pdb=" O ALA E4608 " (cutoff:3.500A) Processing helix chain 'E' and resid 4626 through 4632 Processing helix chain 'E' and resid 4633 through 4638 removed outlier: 4.386A pdb=" N ILE E4636 " --> pdb=" O ARG E4633 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN E4637 " --> pdb=" O LEU E4634 " (cutoff:3.500A) Processing helix chain 'E' and resid 4649 through 4658 removed outlier: 3.588A pdb=" N VAL E4654 " --> pdb=" O VAL E4650 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N MET E4655 " --> pdb=" O LYS E4651 " (cutoff:3.500A) Processing helix chain 'E' and resid 4663 through 4669 Processing helix chain 'E' and resid 4696 through 4701 removed outlier: 3.551A pdb=" N LEU E4699 " --> pdb=" O SER E4696 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER E4701 " --> pdb=" O VAL E4698 " (cutoff:3.500A) Processing helix chain 'E' and resid 4703 through 4715 removed outlier: 4.199A pdb=" N GLY E4712 " --> pdb=" O MET E4708 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL E4713 " --> pdb=" O TRP E4709 " (cutoff:3.500A) Processing helix chain 'E' and resid 4717 through 4736 removed outlier: 3.676A pdb=" N LEU E4732 " --> pdb=" O THR E4728 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY E4733 " --> pdb=" O MET E4729 " (cutoff:3.500A) Processing helix chain 'E' and resid 4741 through 4748 removed outlier: 3.681A pdb=" N ILE E4747 " --> pdb=" O LEU E4744 " (cutoff:3.500A) Processing helix chain 'E' and resid 4751 through 4763 removed outlier: 3.624A pdb=" N ARG E4755 " --> pdb=" O PHE E4751 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR E4756 " --> pdb=" O LYS E4752 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE E4757 " --> pdb=" O THR E4753 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU E4758 " --> pdb=" O LEU E4754 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E4761 " --> pdb=" O ILE E4757 " (cutoff:3.500A) Processing helix chain 'E' and resid 4767 through 4790 removed outlier: 3.860A pdb=" N THR E4771 " --> pdb=" O GLN E4767 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL E4772 " --> pdb=" O LEU E4768 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL E4777 " --> pdb=" O GLY E4773 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E4779 " --> pdb=" O LEU E4775 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL E4784 " --> pdb=" O TYR E4780 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL E4785 " --> pdb=" O LEU E4781 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA E4786 " --> pdb=" O TYR E4782 " (cutoff:3.500A) Processing helix chain 'E' and resid 4791 through 4794 Processing helix chain 'E' and resid 4812 through 4825 removed outlier: 3.950A pdb=" N VAL E4822 " --> pdb=" O MET E4818 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG E4823 " --> pdb=" O TYR E4819 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY E4825 " --> pdb=" O GLY E4821 " (cutoff:3.500A) Processing helix chain 'E' and resid 4839 through 4868 removed outlier: 3.960A pdb=" N TYR E4843 " --> pdb=" O GLU E4839 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE E4849 " --> pdb=" O ILE E4845 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE E4858 " --> pdb=" O PHE E4854 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA E4861 " --> pdb=" O VAL E4857 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY E4865 " --> pdb=" O ALA E4861 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E4866 " --> pdb=" O ILE E4862 " (cutoff:3.500A) Processing helix chain 'E' and resid 4868 through 4881 removed outlier: 4.346A pdb=" N GLU E4873 " --> pdb=" O ASP E4869 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU E4874 " --> pdb=" O ALA E4870 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL E4881 " --> pdb=" O GLN E4877 " (cutoff:3.500A) Processing helix chain 'E' and resid 4895 through 4900 removed outlier: 4.183A pdb=" N PHE E4899 " --> pdb=" O GLY E4895 " (cutoff:3.500A) Processing helix chain 'E' and resid 4904 through 4910 removed outlier: 3.939A pdb=" N THR E4908 " --> pdb=" O HIS E4904 " (cutoff:3.500A) Processing helix chain 'E' and resid 4916 through 4929 removed outlier: 3.900A pdb=" N LEU E4920 " --> pdb=" O LEU E4916 " (cutoff:3.500A) Processing helix chain 'E' and resid 4935 through 4947 removed outlier: 3.915A pdb=" N TRP E4942 " --> pdb=" O GLU E4938 " (cutoff:3.500A) Processing helix chain 'E' and resid 4959 through 4963 Processing helix chain 'F' and resid 10 through 21 removed outlier: 3.574A pdb=" N PHE F 20 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 41 removed outlier: 3.639A pdb=" N LEU F 33 " --> pdb=" O THR F 29 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 54 removed outlier: 4.355A pdb=" N ASP F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 75 removed outlier: 3.567A pdb=" N THR F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 94 Processing helix chain 'F' and resid 102 through 110 removed outlier: 3.790A pdb=" N MET F 110 " --> pdb=" O LEU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 128 removed outlier: 4.712A pdb=" N VAL F 122 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 145 removed outlier: 3.881A pdb=" N GLN F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 83 removed outlier: 3.505A pdb=" N LEU G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 158 removed outlier: 4.040A pdb=" N CYS G 158 " --> pdb=" O GLY G 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 155 through 158' Processing helix chain 'G' and resid 409 through 436 removed outlier: 3.860A pdb=" N VAL G 418 " --> pdb=" O ARG G 414 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER G 421 " --> pdb=" O ARG G 417 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 423 " --> pdb=" O ILE G 419 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU G 425 " --> pdb=" O SER G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 463 removed outlier: 3.563A pdb=" N ILE G 460 " --> pdb=" O LEU G 456 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY G 461 " --> pdb=" O GLN G 457 " (cutoff:3.500A) Processing helix chain 'G' and resid 471 through 491 removed outlier: 3.859A pdb=" N ARG G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE G 489 " --> pdb=" O ARG G 485 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN G 490 " --> pdb=" O GLN G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 493 through 506 removed outlier: 4.100A pdb=" N GLU G 500 " --> pdb=" O ASN G 496 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS G 501 " --> pdb=" O LEU G 497 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP G 503 " --> pdb=" O LEU G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 542 removed outlier: 4.316A pdb=" N LEU G 536 " --> pdb=" O SER G 532 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU G 537 " --> pdb=" O LEU G 533 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA G 538 " --> pdb=" O TYR G 534 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA G 539 " --> pdb=" O GLU G 535 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 551 removed outlier: 4.119A pdb=" N CYS G 548 " --> pdb=" O ASN G 544 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA G 549 " --> pdb=" O ARG G 545 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 563 removed outlier: 4.255A pdb=" N TRP G 557 " --> pdb=" O GLY G 553 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU G 563 " --> pdb=" O ILE G 559 " (cutoff:3.500A) Processing helix chain 'G' and resid 567 through 580 removed outlier: 4.236A pdb=" N VAL G 574 " --> pdb=" O GLY G 570 " (cutoff:3.500A) Processing helix chain 'G' and resid 584 through 588 Processing helix chain 'G' and resid 590 through 604 removed outlier: 3.515A pdb=" N LEU G 600 " --> pdb=" O SER G 596 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU G 601 " --> pdb=" O ILE G 597 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP G 602 " --> pdb=" O ILE G 598 " (cutoff:3.500A) Processing helix chain 'G' and resid 607 through 619 removed outlier: 3.619A pdb=" N VAL G 619 " --> pdb=" O CYS G 615 " (cutoff:3.500A) Processing helix chain 'G' and resid 625 through 636 removed outlier: 3.906A pdb=" N CYS G 633 " --> pdb=" O GLN G 629 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP G 634 " --> pdb=" O HIS G 630 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN G 635 " --> pdb=" O LEU G 631 " (cutoff:3.500A) Processing helix chain 'G' and resid 637 through 640 removed outlier: 3.526A pdb=" N ARG G 640 " --> pdb=" O LEU G 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 637 through 640' Processing helix chain 'G' and resid 821 through 826 Processing helix chain 'G' and resid 875 through 877 No H-bonds generated for 'chain 'G' and resid 875 through 877' Processing helix chain 'G' and resid 878 through 898 removed outlier: 3.544A pdb=" N GLU G 887 " --> pdb=" O GLU G 883 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU G 892 " --> pdb=" O ASN G 888 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS G 897 " --> pdb=" O TRP G 893 " (cutoff:3.500A) Processing helix chain 'G' and resid 933 through 942 removed outlier: 4.280A pdb=" N GLU G 938 " --> pdb=" O GLN G 934 " (cutoff:3.500A) Processing helix chain 'G' and resid 994 through 1011 removed outlier: 3.974A pdb=" N ASN G1005 " --> pdb=" O GLU G1001 " (cutoff:3.500A) Processing helix chain 'G' and resid 1039 through 1060 removed outlier: 3.791A pdb=" N LYS G1043 " --> pdb=" O ASP G1039 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU G1057 " --> pdb=" O ALA G1053 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU G1058 " --> pdb=" O VAL G1054 " (cutoff:3.500A) Processing helix chain 'G' and resid 1091 through 1095 removed outlier: 3.548A pdb=" N ALA G1095 " --> pdb=" O LYS G1092 " (cutoff:3.500A) Processing helix chain 'G' and resid 1224 through 1230 removed outlier: 3.588A pdb=" N ILE G1229 " --> pdb=" O LYS G1225 " (cutoff:3.500A) Processing helix chain 'G' and resid 1570 through 1576 removed outlier: 4.202A pdb=" N GLU G1574 " --> pdb=" O LEU G1570 " (cutoff:3.500A) Processing helix chain 'G' and resid 1642 through 1646 removed outlier: 5.260A pdb=" N THR G1645 " --> pdb=" O LEU G1642 " (cutoff:3.500A) Processing helix chain 'G' and resid 1647 through 1665 removed outlier: 3.623A pdb=" N PHE G1653 " --> pdb=" O GLU G1649 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N CYS G1665 " --> pdb=" O TYR G1661 " (cutoff:3.500A) Processing helix chain 'G' and resid 1669 through 1681 removed outlier: 3.815A pdb=" N ALA G1675 " --> pdb=" O ARG G1671 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU G1676 " --> pdb=" O VAL G1672 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS G1677 " --> pdb=" O ALA G1673 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER G1678 " --> pdb=" O HIS G1674 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS G1679 " --> pdb=" O ALA G1675 " (cutoff:3.500A) Processing helix chain 'G' and resid 1681 through 1690 removed outlier: 3.624A pdb=" N LEU G1685 " --> pdb=" O ASP G1681 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU G1686 " --> pdb=" O GLU G1682 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR G1687 " --> pdb=" O PRO G1683 " (cutoff:3.500A) Processing helix chain 'G' and resid 1695 through 1711 removed outlier: 3.661A pdb=" N ASP G1704 " --> pdb=" O ALA G1700 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE G1707 " --> pdb=" O TYR G1703 " (cutoff:3.500A) Processing helix chain 'G' and resid 1711 through 1721 removed outlier: 3.526A pdb=" N MET G1720 " --> pdb=" O THR G1716 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET G1721 " --> pdb=" O ALA G1717 " (cutoff:3.500A) Processing helix chain 'G' and resid 1722 through 1724 No H-bonds generated for 'chain 'G' and resid 1722 through 1724' Processing helix chain 'G' and resid 1771 through 1776 removed outlier: 4.289A pdb=" N TYR G1776 " --> pdb=" O ASN G1772 " (cutoff:3.500A) Processing helix chain 'G' and resid 1783 through 1802 removed outlier: 4.410A pdb=" N LEU G1787 " --> pdb=" O PRO G1783 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS G1788 " --> pdb=" O LEU G1784 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G1789 " --> pdb=" O ASP G1785 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE G1792 " --> pdb=" O LYS G1788 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU G1797 " --> pdb=" O GLN G1793 " (cutoff:3.500A) Processing helix chain 'G' and resid 1813 through 1831 removed outlier: 3.587A pdb=" N VAL G1819 " --> pdb=" O GLU G1815 " (cutoff:3.500A) Proline residue: G1820 - end of helix removed outlier: 3.711A pdb=" N LYS G1823 " --> pdb=" O VAL G1819 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU G1824 " --> pdb=" O PRO G1820 " (cutoff:3.500A) Processing helix chain 'G' and resid 1836 through 1847 Processing helix chain 'G' and resid 1900 through 1953 removed outlier: 4.128A pdb=" N LYS G1904 " --> pdb=" O PRO G1900 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU G1905 " --> pdb=" O GLU G1901 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU G1909 " --> pdb=" O LEU G1905 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU G1910 " --> pdb=" O GLN G1906 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU G1911 " --> pdb=" O MET G1907 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS G1917 " --> pdb=" O TYR G1913 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE G1926 " --> pdb=" O ARG G1922 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL G1927 " --> pdb=" O ILE G1923 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA G1928 " --> pdb=" O GLU G1924 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE G1929 " --> pdb=" O ALA G1925 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP G1932 " --> pdb=" O ALA G1928 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE G1933 " --> pdb=" O PHE G1929 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG G1942 " --> pdb=" O GLN G1938 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N PHE G1943 " --> pdb=" O ASP G1939 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA G1951 " --> pdb=" O GLU G1947 " (cutoff:3.500A) Processing helix chain 'G' and resid 1991 through 1996 removed outlier: 3.790A pdb=" N GLN G1996 " --> pdb=" O GLU G1992 " (cutoff:3.500A) Processing helix chain 'G' and resid 1999 through 2010 removed outlier: 3.675A pdb=" N THR G2006 " --> pdb=" O GLU G2002 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS G2007 " --> pdb=" O ASP G2003 " (cutoff:3.500A) Processing helix chain 'G' and resid 2011 through 2013 No H-bonds generated for 'chain 'G' and resid 2011 through 2013' Processing helix chain 'G' and resid 2024 through 2025 No H-bonds generated for 'chain 'G' and resid 2024 through 2025' Processing helix chain 'G' and resid 2026 through 2037 removed outlier: 3.881A pdb=" N LEU G2030 " --> pdb=" O ILE G2026 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU G2035 " --> pdb=" O LEU G2031 " (cutoff:3.500A) Processing helix chain 'G' and resid 2059 through 2074 removed outlier: 4.069A pdb=" N SER G2064 " --> pdb=" O GLN G2060 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET G2067 " --> pdb=" O ILE G2063 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP G2070 " --> pdb=" O THR G2066 " (cutoff:3.500A) Processing helix chain 'G' and resid 2078 through 2094 removed outlier: 3.589A pdb=" N PHE G2086 " --> pdb=" O VAL G2082 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL G2087 " --> pdb=" O ARG G2083 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU G2088 " --> pdb=" O ALA G2084 " (cutoff:3.500A) Processing helix chain 'G' and resid 2095 through 2103 removed outlier: 3.748A pdb=" N LEU G2099 " --> pdb=" O GLY G2095 " (cutoff:3.500A) Processing helix chain 'G' and resid 2104 through 2106 No H-bonds generated for 'chain 'G' and resid 2104 through 2106' Processing helix chain 'G' and resid 2113 through 2130 removed outlier: 3.539A pdb=" N ILE G2118 " --> pdb=" O VAL G2114 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU G2120 " --> pdb=" O ASP G2116 " (cutoff:3.500A) Processing helix chain 'G' and resid 2140 through 2152 removed outlier: 3.661A pdb=" N ILE G2144 " --> pdb=" O GLU G2140 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG G2145 " --> pdb=" O LYS G2141 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY G2146 " --> pdb=" O LEU G2142 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY G2148 " --> pdb=" O ILE G2144 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP G2149 " --> pdb=" O ARG G2145 " (cutoff:3.500A) Processing helix chain 'G' and resid 2159 through 2167 removed outlier: 3.745A pdb=" N MET G2163 " --> pdb=" O HIS G2159 " (cutoff:3.500A) Processing helix chain 'G' and resid 2167 through 2180 removed outlier: 3.681A pdb=" N VAL G2175 " --> pdb=" O THR G2171 " (cutoff:3.500A) Processing helix chain 'G' and resid 2193 through 2206 removed outlier: 4.212A pdb=" N CYS G2197 " --> pdb=" O MET G2193 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG G2206 " --> pdb=" O CYS G2202 " (cutoff:3.500A) Processing helix chain 'G' and resid 2208 through 2215 removed outlier: 3.674A pdb=" N MET G2215 " --> pdb=" O ASN G2211 " (cutoff:3.500A) Processing helix chain 'G' and resid 2218 through 2223 Processing helix chain 'G' and resid 2240 through 2247 Processing helix chain 'G' and resid 2251 through 2258 Processing helix chain 'G' and resid 2260 through 2272 removed outlier: 3.507A pdb=" N GLU G2264 " --> pdb=" O GLU G2260 " (cutoff:3.500A) Processing helix chain 'G' and resid 2296 through 2309 removed outlier: 3.751A pdb=" N LEU G2300 " --> pdb=" O GLY G2296 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP G2301 " --> pdb=" O GLU G2297 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS G2309 " --> pdb=" O PHE G2305 " (cutoff:3.500A) Processing helix chain 'G' and resid 2314 through 2327 removed outlier: 4.602A pdb=" N VAL G2322 " --> pdb=" O ALA G2318 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG G2323 " --> pdb=" O ASN G2319 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU G2324 " --> pdb=" O VAL G2320 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU G2325 " --> pdb=" O VAL G2321 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG G2327 " --> pdb=" O ARG G2323 " (cutoff:3.500A) Processing helix chain 'G' and resid 2343 through 2345 No H-bonds generated for 'chain 'G' and resid 2343 through 2345' Processing helix chain 'G' and resid 2346 through 2351 removed outlier: 3.950A pdb=" N GLU G2350 " --> pdb=" O ALA G2346 " (cutoff:3.500A) Processing helix chain 'G' and resid 2387 through 2403 removed outlier: 3.621A pdb=" N THR G2391 " --> pdb=" O ASN G2387 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR G2393 " --> pdb=" O ILE G2389 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU G2396 " --> pdb=" O PHE G2392 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY G2401 " --> pdb=" O ILE G2397 " (cutoff:3.500A) Processing helix chain 'G' and resid 2408 through 2413 Processing helix chain 'G' and resid 2416 through 2427 removed outlier: 3.542A pdb=" N LEU G2427 " --> pdb=" O ILE G2423 " (cutoff:3.500A) Processing helix chain 'G' and resid 2431 through 2435 Processing helix chain 'G' and resid 2462 through 2476 removed outlier: 4.388A pdb=" N LYS G2466 " --> pdb=" O CYS G2462 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA G2467 " --> pdb=" O PRO G2463 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU G2471 " --> pdb=" O ALA G2467 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N PHE G2472 " --> pdb=" O ALA G2468 " (cutoff:3.500A) Processing helix chain 'G' and resid 2482 through 2488 removed outlier: 4.218A pdb=" N LEU G2486 " --> pdb=" O GLN G2482 " (cutoff:3.500A) Processing helix chain 'G' and resid 2492 through 2497 removed outlier: 3.732A pdb=" N LEU G2497 " --> pdb=" O PHE G2493 " (cutoff:3.500A) Processing helix chain 'G' and resid 2498 through 2502 removed outlier: 4.527A pdb=" N ALA G2501 " --> pdb=" O ARG G2498 " (cutoff:3.500A) Processing helix chain 'G' and resid 2512 through 2516 Processing helix chain 'G' and resid 2517 through 2521 Processing helix chain 'G' and resid 2537 through 2552 removed outlier: 3.519A pdb=" N ASP G2547 " --> pdb=" O ALA G2543 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER G2548 " --> pdb=" O SER G2544 " (cutoff:3.500A) Processing helix chain 'G' and resid 2559 through 2576 removed outlier: 3.514A pdb=" N ASP G2568 " --> pdb=" O LYS G2564 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G2569 " --> pdb=" O ALA G2565 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE G2570 " --> pdb=" O GLN G2566 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU G2571 " --> pdb=" O ARG G2567 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL G2572 " --> pdb=" O ASP G2568 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU G2574 " --> pdb=" O ILE G2570 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU G2575 " --> pdb=" O GLU G2571 " (cutoff:3.500A) Processing helix chain 'G' and resid 2583 through 2595 removed outlier: 4.211A pdb=" N GLN G2587 " --> pdb=" O PRO G2583 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG G2591 " --> pdb=" O GLN G2587 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG G2592 " --> pdb=" O HIS G2588 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU G2593 " --> pdb=" O LEU G2589 " (cutoff:3.500A) Processing helix chain 'G' and resid 2606 through 2622 removed outlier: 3.910A pdb=" N ASN G2613 " --> pdb=" O LYS G2609 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS G2614 " --> pdb=" O LEU G2610 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG G2617 " --> pdb=" O ASN G2613 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS G2618 " --> pdb=" O HIS G2614 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP G2619 " --> pdb=" O TYR G2615 " (cutoff:3.500A) Processing helix chain 'G' and resid 2622 through 2627 Processing helix chain 'G' and resid 2635 through 2651 Processing helix chain 'G' and resid 2660 through 2665 Processing helix chain 'G' and resid 2665 through 2676 Processing helix chain 'G' and resid 2718 through 2732 removed outlier: 4.425A pdb=" N LYS G2724 " --> pdb=" O TYR G2720 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS G2732 " --> pdb=" O HIS G2728 " (cutoff:3.500A) Processing helix chain 'G' and resid 2735 through 2739 removed outlier: 3.845A pdb=" N LEU G2738 " --> pdb=" O MET G2735 " (cutoff:3.500A) Processing helix chain 'G' and resid 2749 through 2753 removed outlier: 3.937A pdb=" N SER G2752 " --> pdb=" O SER G2749 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS G2753 " --> pdb=" O ASP G2750 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2749 through 2753' Processing helix chain 'G' and resid 2767 through 2772 removed outlier: 3.630A pdb=" N GLU G2770 " --> pdb=" O LYS G2767 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE G2771 " --> pdb=" O GLU G2768 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR G2772 " --> pdb=" O LYS G2769 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2767 through 2772' Processing helix chain 'G' and resid 2773 through 2778 Processing helix chain 'G' and resid 2838 through 2862 removed outlier: 3.977A pdb=" N MET G2844 " --> pdb=" O ALA G2840 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU G2847 " --> pdb=" O GLU G2843 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN G2851 " --> pdb=" O GLU G2847 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA G2854 " --> pdb=" O HIS G2850 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU G2859 " --> pdb=" O LYS G2855 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU G2860 " --> pdb=" O LYS G2856 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU G2861 " --> pdb=" O LYS G2857 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU G2862 " --> pdb=" O LYS G2858 " (cutoff:3.500A) Processing helix chain 'G' and resid 2874 through 2878 removed outlier: 4.201A pdb=" N LEU G2878 " --> pdb=" O TYR G2875 " (cutoff:3.500A) Processing helix chain 'G' and resid 2882 through 2886 removed outlier: 3.528A pdb=" N LYS G2885 " --> pdb=" O GLU G2882 " (cutoff:3.500A) Processing helix chain 'G' and resid 2891 through 2900 removed outlier: 3.905A pdb=" N LYS G2895 " --> pdb=" O GLN G2891 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE G2896 " --> pdb=" O ASP G2892 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU G2897 " --> pdb=" O ILE G2893 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN G2898 " --> pdb=" O LEU G2894 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE G2899 " --> pdb=" O LYS G2895 " (cutoff:3.500A) Processing helix chain 'G' and resid 2982 through 2986 Processing helix chain 'G' and resid 2988 through 2999 Processing helix chain 'G' and resid 3000 through 3003 Processing helix chain 'G' and resid 3012 through 3028 removed outlier: 3.863A pdb=" N SER G3021 " --> pdb=" O ARG G3017 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU G3022 " --> pdb=" O HIS G3018 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE G3023 " --> pdb=" O ARG G3019 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY G3024 " --> pdb=" O ILE G3020 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN G3025 " --> pdb=" O SER G3021 " (cutoff:3.500A) Processing helix chain 'G' and resid 3035 through 3050 removed outlier: 3.974A pdb=" N LYS G3048 " --> pdb=" O ARG G3044 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY G3050 " --> pdb=" O VAL G3046 " (cutoff:3.500A) Processing helix chain 'G' and resid 3062 through 3067 Processing helix chain 'G' and resid 3067 through 3080 removed outlier: 3.674A pdb=" N LYS G3071 " --> pdb=" O GLU G3067 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU G3074 " --> pdb=" O GLU G3070 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN G3075 " --> pdb=" O LYS G3071 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU G3076 " --> pdb=" O THR G3072 " (cutoff:3.500A) Processing helix chain 'G' and resid 3103 through 3115 removed outlier: 3.578A pdb=" N GLU G3111 " --> pdb=" O SER G3107 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N HIS G3112 " --> pdb=" O SER G3108 " (cutoff:3.500A) Processing helix chain 'G' and resid 3116 through 3118 No H-bonds generated for 'chain 'G' and resid 3116 through 3118' Processing helix chain 'G' and resid 3128 through 3133 Processing helix chain 'G' and resid 3136 through 3142 Processing helix chain 'G' and resid 3152 through 3162 removed outlier: 3.621A pdb=" N LEU G3160 " --> pdb=" O LEU G3156 " (cutoff:3.500A) Processing helix chain 'G' and resid 3171 through 3178 Processing helix chain 'G' and resid 3586 through 3605 removed outlier: 3.776A pdb=" N ARG G3605 " --> pdb=" O VAL G3601 " (cutoff:3.500A) Processing helix chain 'G' and resid 3613 through 3630 removed outlier: 4.156A pdb=" N ILE G3630 " --> pdb=" O GLU G3626 " (cutoff:3.500A) Processing helix chain 'G' and resid 3637 through 3646 Processing helix chain 'G' and resid 3663 through 3677 Processing helix chain 'G' and resid 3688 through 3699 removed outlier: 5.084A pdb=" N ASP G3694 " --> pdb=" O MET G3690 " (cutoff:3.500A) Processing helix chain 'G' and resid 3715 through 3734 Processing helix chain 'G' and resid 3736 through 3748 removed outlier: 4.606A pdb=" N MET G3740 " --> pdb=" O GLY G3736 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL G3741 " --> pdb=" O ALA G3737 " (cutoff:3.500A) Processing helix chain 'G' and resid 3753 through 3767 Processing helix chain 'G' and resid 3771 through 3785 removed outlier: 3.601A pdb=" N GLN G3775 " --> pdb=" O ASN G3771 " (cutoff:3.500A) Processing helix chain 'G' and resid 3787 through 3800 removed outlier: 3.627A pdb=" N PHE G3791 " --> pdb=" O ASP G3787 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER G3800 " --> pdb=" O GLY G3796 " (cutoff:3.500A) Processing helix chain 'G' and resid 3805 through 3819 removed outlier: 3.552A pdb=" N PHE G3809 " --> pdb=" O ASP G3805 " (cutoff:3.500A) Processing helix chain 'G' and resid 3833 through 3849 removed outlier: 3.884A pdb=" N THR G3837 " --> pdb=" O ASP G3833 " (cutoff:3.500A) Processing helix chain 'G' and resid 3852 through 3862 Processing helix chain 'G' and resid 3870 through 3894 removed outlier: 3.725A pdb=" N SER G3874 " --> pdb=" O ASN G3870 " (cutoff:3.500A) Processing helix chain 'G' and resid 3900 through 3926 Processing helix chain 'G' and resid 3929 through 3938 removed outlier: 4.265A pdb=" N GLN G3933 " --> pdb=" O CYS G3929 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS G3938 " --> pdb=" O GLN G3934 " (cutoff:3.500A) Processing helix chain 'G' and resid 3940 through 3960 removed outlier: 4.269A pdb=" N ALA G3944 " --> pdb=" O ARG G3940 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS G3954 " --> pdb=" O HIS G3950 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET G3957 " --> pdb=" O ALA G3953 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS G3958 " --> pdb=" O HIS G3954 " (cutoff:3.500A) Processing helix chain 'G' and resid 3965 through 3988 removed outlier: 3.629A pdb=" N LEU G3983 " --> pdb=" O MET G3979 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU G3988 " --> pdb=" O LEU G3984 " (cutoff:3.500A) Processing helix chain 'G' and resid 3994 through 4006 Processing helix chain 'G' and resid 4007 through 4028 removed outlier: 3.994A pdb=" N PHE G4021 " --> pdb=" O PHE G4017 " (cutoff:3.500A) Processing helix chain 'G' and resid 4046 through 4055 Processing helix chain 'G' and resid 4060 through 4068 removed outlier: 3.929A pdb=" N THR G4064 " --> pdb=" O THR G4060 " (cutoff:3.500A) Processing helix chain 'G' and resid 4082 through 4090 removed outlier: 4.278A pdb=" N GLU G4090 " --> pdb=" O LYS G4086 " (cutoff:3.500A) Processing helix chain 'G' and resid 4093 through 4110 Processing helix chain 'G' and resid 4113 through 4123 removed outlier: 3.833A pdb=" N ALA G4123 " --> pdb=" O PHE G4119 " (cutoff:3.500A) Processing helix chain 'G' and resid 4123 through 4131 removed outlier: 3.932A pdb=" N LEU G4127 " --> pdb=" O ALA G4123 " (cutoff:3.500A) Processing helix chain 'G' and resid 4154 through 4162 removed outlier: 3.808A pdb=" N ARG G4158 " --> pdb=" O SER G4154 " (cutoff:3.500A) Processing helix chain 'G' and resid 4163 through 4179 removed outlier: 3.584A pdb=" N ASN G4179 " --> pdb=" O PHE G4175 " (cutoff:3.500A) Processing helix chain 'G' and resid 4185 through 4206 removed outlier: 3.774A pdb=" N GLN G4206 " --> pdb=" O GLN G4202 " (cutoff:3.500A) Processing helix chain 'G' and resid 4487 through 4499 removed outlier: 3.578A pdb=" N TYR G4495 " --> pdb=" O LYS G4491 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE G4496 " --> pdb=" O LEU G4492 " (cutoff:3.500A) Processing helix chain 'G' and resid 4500 through 4518 removed outlier: 3.647A pdb=" N ALA G4507 " --> pdb=" O MET G4503 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU G4508 " --> pdb=" O ARG G4504 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE G4509 " --> pdb=" O MET G4505 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA G4513 " --> pdb=" O PHE G4509 " (cutoff:3.500A) Processing helix chain 'G' and resid 4569 through 4614 removed outlier: 4.392A pdb=" N ILE G4578 " --> pdb=" O ARG G4574 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE G4586 " --> pdb=" O VAL G4582 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS G4587 " --> pdb=" O ILE G4583 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE G4588 " --> pdb=" O SER G4584 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL G4596 " --> pdb=" O TYR G4592 " (cutoff:3.500A) Proline residue: G4597 - end of helix removed outlier: 3.609A pdb=" N ARG G4603 " --> pdb=" O VAL G4599 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU G4612 " --> pdb=" O ALA G4608 " (cutoff:3.500A) Processing helix chain 'G' and resid 4626 through 4632 Processing helix chain 'G' and resid 4633 through 4638 removed outlier: 4.386A pdb=" N ILE G4636 " --> pdb=" O ARG G4633 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN G4637 " --> pdb=" O LEU G4634 " (cutoff:3.500A) Processing helix chain 'G' and resid 4649 through 4658 removed outlier: 3.588A pdb=" N VAL G4654 " --> pdb=" O VAL G4650 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N MET G4655 " --> pdb=" O LYS G4651 " (cutoff:3.500A) Processing helix chain 'G' and resid 4663 through 4669 Processing helix chain 'G' and resid 4696 through 4701 removed outlier: 3.550A pdb=" N LEU G4699 " --> pdb=" O SER G4696 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER G4701 " --> pdb=" O VAL G4698 " (cutoff:3.500A) Processing helix chain 'G' and resid 4703 through 4715 removed outlier: 4.199A pdb=" N GLY G4712 " --> pdb=" O MET G4708 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL G4713 " --> pdb=" O TRP G4709 " (cutoff:3.500A) Processing helix chain 'G' and resid 4717 through 4736 removed outlier: 3.676A pdb=" N LEU G4732 " --> pdb=" O THR G4728 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY G4733 " --> pdb=" O MET G4729 " (cutoff:3.500A) Processing helix chain 'G' and resid 4741 through 4748 removed outlier: 3.681A pdb=" N ILE G4747 " --> pdb=" O LEU G4744 " (cutoff:3.500A) Processing helix chain 'G' and resid 4751 through 4763 removed outlier: 3.623A pdb=" N ARG G4755 " --> pdb=" O PHE G4751 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR G4756 " --> pdb=" O LYS G4752 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE G4757 " --> pdb=" O THR G4753 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU G4758 " --> pdb=" O LEU G4754 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL G4761 " --> pdb=" O ILE G4757 " (cutoff:3.500A) Processing helix chain 'G' and resid 4767 through 4790 removed outlier: 3.861A pdb=" N THR G4771 " --> pdb=" O GLN G4767 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL G4772 " --> pdb=" O LEU G4768 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL G4777 " --> pdb=" O GLY G4773 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL G4779 " --> pdb=" O LEU G4775 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL G4784 " --> pdb=" O TYR G4780 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL G4785 " --> pdb=" O LEU G4781 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA G4786 " --> pdb=" O TYR G4782 " (cutoff:3.500A) Processing helix chain 'G' and resid 4791 through 4794 Processing helix chain 'G' and resid 4812 through 4825 removed outlier: 3.949A pdb=" N VAL G4822 " --> pdb=" O MET G4818 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG G4823 " --> pdb=" O TYR G4819 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY G4825 " --> pdb=" O GLY G4821 " (cutoff:3.500A) Processing helix chain 'G' and resid 4839 through 4868 removed outlier: 3.960A pdb=" N TYR G4843 " --> pdb=" O GLU G4839 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE G4849 " --> pdb=" O ILE G4845 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE G4858 " --> pdb=" O PHE G4854 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA G4861 " --> pdb=" O VAL G4857 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY G4865 " --> pdb=" O ALA G4861 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G4866 " --> pdb=" O ILE G4862 " (cutoff:3.500A) Processing helix chain 'G' and resid 4868 through 4881 removed outlier: 4.346A pdb=" N GLU G4873 " --> pdb=" O ASP G4869 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU G4874 " --> pdb=" O ALA G4870 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL G4881 " --> pdb=" O GLN G4877 " (cutoff:3.500A) Processing helix chain 'G' and resid 4895 through 4900 removed outlier: 4.183A pdb=" N PHE G4899 " --> pdb=" O GLY G4895 " (cutoff:3.500A) Processing helix chain 'G' and resid 4904 through 4910 removed outlier: 3.939A pdb=" N THR G4908 " --> pdb=" O HIS G4904 " (cutoff:3.500A) Processing helix chain 'G' and resid 4916 through 4929 removed outlier: 3.900A pdb=" N LEU G4920 " --> pdb=" O LEU G4916 " (cutoff:3.500A) Processing helix chain 'G' and resid 4935 through 4947 removed outlier: 3.914A pdb=" N TRP G4942 " --> pdb=" O GLU G4938 " (cutoff:3.500A) Processing helix chain 'G' and resid 4959 through 4963 Processing helix chain 'H' and resid 10 through 21 removed outlier: 3.574A pdb=" N PHE H 20 " --> pdb=" O ALA H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 41 removed outlier: 3.639A pdb=" N LEU H 33 " --> pdb=" O THR H 29 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY H 34 " --> pdb=" O THR H 30 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 54 removed outlier: 4.355A pdb=" N ASP H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.568A pdb=" N THR H 71 " --> pdb=" O PRO H 67 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 94 Processing helix chain 'H' and resid 102 through 110 removed outlier: 3.789A pdb=" N MET H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 128 removed outlier: 4.712A pdb=" N VAL H 122 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP H 123 " --> pdb=" O ASP H 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 145 removed outlier: 3.881A pdb=" N GLN H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 23 removed outlier: 3.829A pdb=" N VAL A 20 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU A 69 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG A 122 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 71 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP A 160 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 181 " --> pdb=" O TRP A 212 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU A 19 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 133 Processing sheet with id=AA5, first strand: chain 'A' and resid 191 through 194 Processing sheet with id=AA6, first strand: chain 'A' and resid 296 through 299 removed outlier: 4.031A pdb=" N ARG A 298 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG A 276 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER A 406 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 244 through 246 Processing sheet with id=AA8, first strand: chain 'A' and resid 305 through 309 Processing sheet with id=AA9, first strand: chain 'A' and resid 329 through 332 removed outlier: 3.862A pdb=" N CYS A 361 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 403 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 371 through 374 Processing sheet with id=AB2, first strand: chain 'A' and resid 645 through 647 removed outlier: 3.668A pdb=" N GLN A 645 " --> pdb=" O HIS A1631 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A1630 " --> pdb=" O VAL A1639 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 653 through 654 Processing sheet with id=AB4, first strand: chain 'A' and resid 677 through 679 Processing sheet with id=AB5, first strand: chain 'A' and resid 732 through 733 Processing sheet with id=AB6, first strand: chain 'A' and resid 755 through 756 Processing sheet with id=AB7, first strand: chain 'A' and resid 765 through 766 removed outlier: 3.723A pdb=" N PHE A 779 " --> pdb=" O ILE A 766 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1086 through 1089 Processing sheet with id=AB9, first strand: chain 'A' and resid 1160 through 1161 removed outlier: 3.744A pdb=" N ASP A1160 " --> pdb=" O ALA A1107 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE A1103 " --> pdb=" O CYS A1164 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1160 through 1161 removed outlier: 3.744A pdb=" N ASP A1160 " --> pdb=" O ALA A1107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1257 through 1259 Processing sheet with id=AC3, first strand: chain 'A' and resid 1271 through 1273 removed outlier: 3.596A pdb=" N SER A1289 " --> pdb=" O THR A1271 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1300 through 1302 Processing sheet with id=AC5, first strand: chain 'A' and resid 1610 through 1611 Processing sheet with id=AC6, first strand: chain 'A' and resid 1727 through 1728 removed outlier: 7.004A pdb=" N VAL A1727 " --> pdb=" O ILE A2109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 2790 through 2791 removed outlier: 3.526A pdb=" N GLU A2791 " --> pdb=" O ALA A2903 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA A2903 " --> pdb=" O GLU A2791 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'A' and resid 4134 through 4139 Processing sheet with id=AC9, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AD1, first strand: chain 'C' and resid 19 through 23 removed outlier: 3.829A pdb=" N VAL C 20 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU C 69 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ARG C 122 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 71 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP C 160 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 181 " --> pdb=" O TRP C 212 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU C 19 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 26 through 28 Processing sheet with id=AD3, first strand: chain 'C' and resid 35 through 39 Processing sheet with id=AD4, first strand: chain 'C' and resid 129 through 133 Processing sheet with id=AD5, first strand: chain 'C' and resid 191 through 194 Processing sheet with id=AD6, first strand: chain 'C' and resid 296 through 299 removed outlier: 4.031A pdb=" N ARG C 298 " --> pdb=" O ARG C 276 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG C 276 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER C 406 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AD8, first strand: chain 'C' and resid 305 through 309 Processing sheet with id=AD9, first strand: chain 'C' and resid 329 through 332 removed outlier: 3.861A pdb=" N CYS C 361 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 403 " --> pdb=" O CYS C 361 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 371 through 374 Processing sheet with id=AE2, first strand: chain 'C' and resid 645 through 647 removed outlier: 3.668A pdb=" N GLN C 645 " --> pdb=" O HIS C1631 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C1630 " --> pdb=" O VAL C1639 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 653 through 654 Processing sheet with id=AE4, first strand: chain 'C' and resid 677 through 679 Processing sheet with id=AE5, first strand: chain 'C' and resid 732 through 733 Processing sheet with id=AE6, first strand: chain 'C' and resid 755 through 756 Processing sheet with id=AE7, first strand: chain 'C' and resid 765 through 766 removed outlier: 3.723A pdb=" N PHE C 779 " --> pdb=" O ILE C 766 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1086 through 1089 Processing sheet with id=AE9, first strand: chain 'C' and resid 1160 through 1161 removed outlier: 3.744A pdb=" N ASP C1160 " --> pdb=" O ALA C1107 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C1103 " --> pdb=" O CYS C1164 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1160 through 1161 removed outlier: 3.744A pdb=" N ASP C1160 " --> pdb=" O ALA C1107 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1257 through 1259 Processing sheet with id=AF3, first strand: chain 'C' and resid 1271 through 1273 removed outlier: 3.596A pdb=" N SER C1289 " --> pdb=" O THR C1271 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1300 through 1302 Processing sheet with id=AF5, first strand: chain 'C' and resid 1610 through 1611 Processing sheet with id=AF6, first strand: chain 'C' and resid 1727 through 1728 removed outlier: 7.004A pdb=" N VAL C1727 " --> pdb=" O ILE C2109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'C' and resid 2790 through 2791 removed outlier: 3.526A pdb=" N GLU C2791 " --> pdb=" O ALA C2903 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA C2903 " --> pdb=" O GLU C2791 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 4134 through 4139 Processing sheet with id=AF9, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AG1, first strand: chain 'E' and resid 19 through 23 removed outlier: 3.829A pdb=" N VAL E 20 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU E 69 " --> pdb=" O ARG E 122 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG E 122 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN E 71 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP E 160 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 181 " --> pdb=" O TRP E 212 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU E 19 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 26 through 28 Processing sheet with id=AG3, first strand: chain 'E' and resid 35 through 39 Processing sheet with id=AG4, first strand: chain 'E' and resid 129 through 133 Processing sheet with id=AG5, first strand: chain 'E' and resid 191 through 194 Processing sheet with id=AG6, first strand: chain 'E' and resid 296 through 299 removed outlier: 4.031A pdb=" N ARG E 298 " --> pdb=" O ARG E 276 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG E 276 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER E 406 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 244 through 246 Processing sheet with id=AG8, first strand: chain 'E' and resid 305 through 309 Processing sheet with id=AG9, first strand: chain 'E' and resid 329 through 332 removed outlier: 3.862A pdb=" N CYS E 361 " --> pdb=" O LEU E 403 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 403 " --> pdb=" O CYS E 361 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 371 through 374 Processing sheet with id=AH2, first strand: chain 'E' and resid 645 through 647 removed outlier: 3.668A pdb=" N GLN E 645 " --> pdb=" O HIS E1631 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E1630 " --> pdb=" O VAL E1639 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 653 through 654 Processing sheet with id=AH4, first strand: chain 'E' and resid 677 through 679 Processing sheet with id=AH5, first strand: chain 'E' and resid 732 through 733 Processing sheet with id=AH6, first strand: chain 'E' and resid 755 through 756 Processing sheet with id=AH7, first strand: chain 'E' and resid 765 through 766 removed outlier: 3.723A pdb=" N PHE E 779 " --> pdb=" O ILE E 766 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 1086 through 1089 Processing sheet with id=AH9, first strand: chain 'E' and resid 1160 through 1161 removed outlier: 3.744A pdb=" N ASP E1160 " --> pdb=" O ALA E1107 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE E1103 " --> pdb=" O CYS E1164 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 1160 through 1161 removed outlier: 3.744A pdb=" N ASP E1160 " --> pdb=" O ALA E1107 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 1257 through 1259 Processing sheet with id=AI3, first strand: chain 'E' and resid 1271 through 1273 removed outlier: 3.596A pdb=" N SER E1289 " --> pdb=" O THR E1271 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 1300 through 1302 Processing sheet with id=AI5, first strand: chain 'E' and resid 1610 through 1611 Processing sheet with id=AI6, first strand: chain 'E' and resid 1727 through 1728 removed outlier: 7.004A pdb=" N VAL E1727 " --> pdb=" O ILE E2109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'E' and resid 2790 through 2791 removed outlier: 3.526A pdb=" N GLU E2791 " --> pdb=" O ALA E2903 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA E2903 " --> pdb=" O GLU E2791 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'E' and resid 4134 through 4139 Processing sheet with id=AI9, first strand: chain 'F' and resid 100 through 101 Processing sheet with id=AJ1, first strand: chain 'G' and resid 19 through 23 removed outlier: 3.829A pdb=" N VAL G 20 " --> pdb=" O PHE G 67 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU G 69 " --> pdb=" O ARG G 122 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG G 122 " --> pdb=" O LEU G 69 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN G 71 " --> pdb=" O LEU G 120 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP G 160 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 181 " --> pdb=" O TRP G 212 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU G 19 " --> pdb=" O ILE G 217 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'G' and resid 26 through 28 Processing sheet with id=AJ3, first strand: chain 'G' and resid 35 through 39 Processing sheet with id=AJ4, first strand: chain 'G' and resid 129 through 133 Processing sheet with id=AJ5, first strand: chain 'G' and resid 191 through 194 Processing sheet with id=AJ6, first strand: chain 'G' and resid 296 through 299 removed outlier: 4.031A pdb=" N ARG G 298 " --> pdb=" O ARG G 276 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG G 276 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER G 406 " --> pdb=" O ARG G 235 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'G' and resid 244 through 246 Processing sheet with id=AJ8, first strand: chain 'G' and resid 305 through 309 Processing sheet with id=AJ9, first strand: chain 'G' and resid 329 through 332 removed outlier: 3.862A pdb=" N CYS G 361 " --> pdb=" O LEU G 403 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU G 403 " --> pdb=" O CYS G 361 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'G' and resid 371 through 374 Processing sheet with id=AK2, first strand: chain 'G' and resid 645 through 647 removed outlier: 3.668A pdb=" N GLN G 645 " --> pdb=" O HIS G1631 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU G1630 " --> pdb=" O VAL G1639 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'G' and resid 653 through 654 Processing sheet with id=AK4, first strand: chain 'G' and resid 677 through 679 Processing sheet with id=AK5, first strand: chain 'G' and resid 732 through 733 Processing sheet with id=AK6, first strand: chain 'G' and resid 755 through 756 Processing sheet with id=AK7, first strand: chain 'G' and resid 765 through 766 removed outlier: 3.723A pdb=" N PHE G 779 " --> pdb=" O ILE G 766 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'G' and resid 1086 through 1089 Processing sheet with id=AK9, first strand: chain 'G' and resid 1160 through 1161 removed outlier: 3.745A pdb=" N ASP G1160 " --> pdb=" O ALA G1107 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE G1103 " --> pdb=" O CYS G1164 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'G' and resid 1160 through 1161 removed outlier: 3.745A pdb=" N ASP G1160 " --> pdb=" O ALA G1107 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'G' and resid 1257 through 1259 Processing sheet with id=AL3, first strand: chain 'G' and resid 1271 through 1273 removed outlier: 3.596A pdb=" N SER G1289 " --> pdb=" O THR G1271 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'G' and resid 1300 through 1302 Processing sheet with id=AL5, first strand: chain 'G' and resid 1610 through 1611 Processing sheet with id=AL6, first strand: chain 'G' and resid 1727 through 1728 removed outlier: 7.004A pdb=" N VAL G1727 " --> pdb=" O ILE G2109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL6 Processing sheet with id=AL7, first strand: chain 'G' and resid 2790 through 2791 removed outlier: 3.526A pdb=" N GLU G2791 " --> pdb=" O ALA G2903 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA G2903 " --> pdb=" O GLU G2791 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL7 Processing sheet with id=AL8, first strand: chain 'G' and resid 4134 through 4139 Processing sheet with id=AL9, first strand: chain 'H' and resid 100 through 101 4779 hydrogen bonds defined for protein. 13581 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: 72.90 Time building geometry restraints manager: 37.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 33169 1.33 - 1.45: 24750 1.45 - 1.58: 54101 1.58 - 1.70: 4 1.70 - 1.82: 1080 Bond restraints: 113104 Sorted by residual: bond pdb=" CA LYS E1692 " pdb=" C LYS E1692 " ideal model delta sigma weight residual 1.522 1.448 0.075 1.38e-02 5.25e+03 2.92e+01 bond pdb=" CA LYS A1692 " pdb=" C LYS A1692 " ideal model delta sigma weight residual 1.522 1.448 0.075 1.38e-02 5.25e+03 2.92e+01 bond pdb=" CA LYS G1692 " pdb=" C LYS G1692 " ideal model delta sigma weight residual 1.522 1.448 0.075 1.38e-02 5.25e+03 2.92e+01 bond pdb=" CA LYS C1692 " pdb=" C LYS C1692 " ideal model delta sigma weight residual 1.522 1.448 0.075 1.38e-02 5.25e+03 2.92e+01 bond pdb=" CB TRP G4950 " pdb=" CG TRP G4950 " ideal model delta sigma weight residual 1.498 1.397 0.101 3.10e-02 1.04e+03 1.05e+01 ... (remaining 113099 not shown) Histogram of bond angle deviations from ideal: 91.61 - 100.39: 176 100.39 - 109.17: 13431 109.17 - 117.95: 72005 117.95 - 126.73: 65963 126.73 - 135.51: 1377 Bond angle restraints: 152952 Sorted by residual: angle pdb=" C LEU C4519 " pdb=" CA LEU C4519 " pdb=" CB LEU C4519 " ideal model delta sigma weight residual 110.72 91.61 19.11 1.77e+00 3.19e-01 1.17e+02 angle pdb=" N PHE C4520 " pdb=" CA PHE C4520 " pdb=" C PHE C4520 " ideal model delta sigma weight residual 113.61 101.45 12.16 1.50e+00 4.44e-01 6.58e+01 angle pdb=" C GLY C2431 " pdb=" N ASP C2432 " pdb=" CA ASP C2432 " ideal model delta sigma weight residual 120.99 131.81 -10.82 1.86e+00 2.89e-01 3.38e+01 angle pdb=" C GLY G2431 " pdb=" N ASP G2432 " pdb=" CA ASP G2432 " ideal model delta sigma weight residual 120.99 131.80 -10.81 1.86e+00 2.89e-01 3.38e+01 angle pdb=" C GLY E2431 " pdb=" N ASP E2432 " pdb=" CA ASP E2432 " ideal model delta sigma weight residual 120.99 131.80 -10.81 1.86e+00 2.89e-01 3.38e+01 ... (remaining 152947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 57753 17.45 - 34.90: 7773 34.90 - 52.35: 1506 52.35 - 69.79: 273 69.79 - 87.24: 128 Dihedral angle restraints: 67433 sinusoidal: 25301 harmonic: 42132 Sorted by residual: dihedral pdb=" CA GLU E1847 " pdb=" C GLU E1847 " pdb=" N PRO E1848 " pdb=" CA PRO E1848 " ideal model delta harmonic sigma weight residual -180.00 -111.46 -68.54 0 5.00e+00 4.00e-02 1.88e+02 dihedral pdb=" CA GLU A1847 " pdb=" C GLU A1847 " pdb=" N PRO A1848 " pdb=" CA PRO A1848 " ideal model delta harmonic sigma weight residual -180.00 -111.47 -68.53 0 5.00e+00 4.00e-02 1.88e+02 dihedral pdb=" CA GLU C1847 " pdb=" C GLU C1847 " pdb=" N PRO C1848 " pdb=" CA PRO C1848 " ideal model delta harmonic sigma weight residual -180.00 -111.47 -68.53 0 5.00e+00 4.00e-02 1.88e+02 ... (remaining 67430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 13797 0.077 - 0.155: 3052 0.155 - 0.232: 386 0.232 - 0.310: 49 0.310 - 0.387: 8 Chirality restraints: 17292 Sorted by residual: chirality pdb=" CB THR G 687 " pdb=" CA THR G 687 " pdb=" OG1 THR G 687 " pdb=" CG2 THR G 687 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CB THR C 687 " pdb=" CA THR C 687 " pdb=" OG1 THR C 687 " pdb=" CG2 THR C 687 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CB THR E 687 " pdb=" CA THR E 687 " pdb=" OG1 THR E 687 " pdb=" CG2 THR E 687 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 17289 not shown) Planarity restraints: 19704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C1579 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO C1580 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO C1580 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C1580 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1579 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO A1580 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO A1580 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A1580 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E1579 " -0.066 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO E1580 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO E1580 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO E1580 " -0.056 5.00e-02 4.00e+02 ... (remaining 19701 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 5192 2.67 - 3.23: 116841 3.23 - 3.79: 204867 3.79 - 4.34: 249750 4.34 - 4.90: 367504 Nonbonded interactions: 944154 Sorted by model distance: nonbonded pdb=" N CYS G4892 " pdb="ZN ZN G6000 " model vdw 2.116 2.310 nonbonded pdb=" N CYS C4892 " pdb="ZN ZN C6000 " model vdw 2.116 2.310 nonbonded pdb=" N CYS E4892 " pdb="ZN ZN E6000 " model vdw 2.116 2.310 nonbonded pdb=" N CYS A4892 " pdb="ZN ZN A6000 " model vdw 2.116 2.310 nonbonded pdb=" OG SER E1764 " pdb=" O SER E1779 " model vdw 2.206 2.440 ... (remaining 944149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 16.950 Check model and map are aligned: 1.190 Set scattering table: 0.730 Process input model: 269.970 Find NCS groups from input model: 4.810 Set up NCS constraints: 0.610 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 298.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 : 0.011 0.101 113104 Z= 0.717 Angle : 1.296 19.105 152952 Z= 0.713 Chirality : 0.064 0.387 17292 Planarity : 0.008 0.101 19704 Dihedral : 16.740 87.243 40081 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.26 % Allowed : 13.27 % Favored : 86.47 % Rotamer: Outliers : 1.92 % Allowed : 16.72 % Favored : 81.36 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.13 % Twisted General : 0.81 % 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: -4.61 (0.06), residues: 14060 helix: -2.87 (0.05), residues: 6112 sheet: -3.89 (0.12), residues: 1088 loop : -3.06 (0.07), residues: 6860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP A 275 HIS 0.021 0.004 HIS C 163 PHE 0.045 0.004 PHE A 426 TYR 0.032 0.004 TYR C2093 ARG 0.014 0.002 ARG A1303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28120 Ramachandran restraints generated. 14060 Oldfield, 0 Emsley, 14060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28120 Ramachandran restraints generated. 14060 Oldfield, 0 Emsley, 14060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 12804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 834 time to evaluate : 9.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 214 outliers final: 106 residues processed: 1030 average time/residue: 0.9081 time to fit residues: 1658.5731 Evaluate side-chains 762 residues out of total 12804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 656 time to evaluate : 9.804 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 11 residues processed: 106 average time/residue: 0.7570 time to fit residues: 167.0240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1452 random chunks: chunk 1226 optimal weight: 6.9990 chunk 1100 optimal weight: 6.9990 chunk 610 optimal weight: 10.0000 chunk 375 optimal weight: 9.9990 chunk 742 optimal weight: 30.0000 chunk 587 optimal weight: 50.0000 chunk 1138 optimal weight: 6.9990 chunk 440 optimal weight: 40.0000 chunk 692 optimal weight: 6.9990 chunk 847 optimal weight: 20.0000 chunk 1318 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 HIS ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 GLN A 84 ASN A 123 HIS A 394 HIS A 476 GLN A 531 ASN A 576 HIS A 587 ASN A 593 HIS A 628 ASN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS A 681 HIS ** A 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 HIS A1149 ASN A1440 ASN ** A1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1602 GLN A1654 HIS A1656 HIS A1691 ASN ** A1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1836 ASN ** A1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1938 GLN A1940 ASN A1941 GLN ** A2210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2251 ASN A2317 ASN A2839 HIS A3589 HIS ** A3729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3743 GLN ** A3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3851 HIS ** A3856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3954 HIS A3961 GLN A3993 ASN ** A4089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4117 GLN A4128 ASN A4131 GLN A4179 ASN A4499 ASN ** A4515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4643 ASN ** A4707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4763 HIS A4817 HIS ** A4918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4946 GLN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS C 57 ASN C 79 GLN C 123 HIS C 394 HIS C 476 GLN C 531 ASN C 576 HIS C 587 ASN C 593 HIS C 628 ASN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS C 681 HIS ** C 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 HIS C1149 ASN C1440 ASN ** C1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1602 GLN C1654 HIS C1656 HIS C1691 ASN ** C1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1836 ASN ** C1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1938 GLN C1940 ASN C1941 GLN ** C2210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2251 ASN C2317 ASN C2839 HIS C3589 HIS ** C3729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3743 GLN ** C3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3851 HIS ** C3856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3954 HIS C3961 GLN C3993 ASN ** C4089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4128 ASN C4131 GLN C4179 ASN C4499 ASN ** C4515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4643 ASN ** C4707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4763 HIS C4817 HIS ** C4918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4946 GLN ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS E 57 ASN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 HIS E 476 GLN E 531 ASN E 576 HIS E 587 ASN E 593 HIS E 628 ASN ** E 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 HIS E 681 HIS ** E 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 836 HIS E1440 ASN ** E1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1602 GLN E1654 HIS E1656 HIS E1691 ASN ** E1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1836 ASN ** E1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1938 GLN E1940 ASN E1941 GLN ** E2210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2251 ASN E2317 ASN E2839 HIS E3589 HIS ** E3729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E3743 GLN ** E3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E3851 HIS ** E3856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E3954 HIS E3961 GLN E3993 ASN ** E4089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4117 GLN E4128 ASN E4131 GLN E4179 ASN E4499 ASN ** E4515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4643 ASN ** E4707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4763 HIS E4817 HIS ** E4918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4946 GLN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 HIS G 57 ASN G 79 GLN G 123 HIS G 394 HIS G 476 GLN G 531 ASN ** G 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 576 HIS G 587 ASN G 593 HIS G 628 ASN ** G 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 651 HIS G 681 HIS ** G 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 836 HIS ** G 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1149 ASN G1440 ASN ** G1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1602 GLN G1654 HIS G1656 HIS G1691 ASN ** G1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1836 ASN ** G1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1938 GLN G1940 ASN G1941 GLN ** G2210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2251 ASN G2317 ASN G2839 HIS G3589 HIS ** G3729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G3743 GLN ** G3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G3851 HIS ** G3856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3954 HIS G3961 GLN G3993 ASN ** G4089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4117 GLN G4128 ASN G4131 GLN G4179 ASN G4499 ASN ** G4515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4643 ASN ** G4707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G4763 HIS G4817 HIS ** G4918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4946 GLN Total number of N/Q/H flips: 164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 113104 Z= 0.286 Angle : 0.774 10.182 152952 Z= 0.416 Chirality : 0.044 0.251 17292 Planarity : 0.006 0.088 19704 Dihedral : 7.705 59.716 15396 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 24.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.44 % Favored : 88.42 % Rotamer: Outliers : 0.50 % Allowed : 6.47 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.13 % Twisted General : 0.38 % 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: -3.54 (0.06), residues: 14060 helix: -1.55 (0.06), residues: 6960 sheet: -3.51 (0.13), residues: 1124 loop : -3.04 (0.08), residues: 5976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 893 HIS 0.019 0.002 HIS C4089 PHE 0.027 0.002 PHE B 20 TYR 0.031 0.002 TYR G2849 ARG 0.007 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28120 Ramachandran restraints generated. 14060 Oldfield, 0 Emsley, 14060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28120 Ramachandran restraints generated. 14060 Oldfield, 0 Emsley, 14060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 12804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 846 time to evaluate : 9.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 27 residues processed: 894 average time/residue: 0.9136 time to fit residues: 1454.9561 Evaluate side-chains 695 residues out of total 12804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 668 time to evaluate : 9.396 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 11 residues processed: 27 average time/residue: 0.7425 time to fit residues: 51.4856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1452 random chunks: chunk 732 optimal weight: 6.9990 chunk 409 optimal weight: 9.9990 chunk 1097 optimal weight: 20.0000 chunk 897 optimal weight: 20.0000 chunk 363 optimal weight: 30.0000 chunk 1320 optimal weight: 6.9990 chunk 1427 optimal weight: 7.9990 chunk 1176 optimal weight: 9.9990 chunk 1309 optimal weight: 50.0000 chunk 450 optimal weight: 10.0000 chunk 1059 optimal weight: 1.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 HIS ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN ** A1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 HIS ** A1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4743 HIS A4880 GLN ** A4918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN C 117 HIS ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN ** C1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1575 HIS ** C1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3595 GLN ** C3729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4743 HIS ** C4918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 635 ASN E1149 ASN ** E1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1575 HIS ** E1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3595 GLN ** E3729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4743 HIS E4880 GLN ** E4918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS ** G 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 635 ASN ** G1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1575 HIS ** G1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3595 GLN ** G3729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G4743 HIS G4880 GLN ** G4918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 113104 Z= 0.276 Angle : 0.731 9.787 152952 Z= 0.390 Chirality : 0.044 0.283 17292 Planarity : 0.005 0.091 19704 Dihedral : 7.128 58.127 15396 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 24.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.29 % Favored : 87.53 % Rotamer: Outliers : 0.21 % Allowed : 5.30 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.31 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.07), residues: 14060 helix: -0.88 (0.06), residues: 6944 sheet: -3.62 (0.13), residues: 1104 loop : -2.90 (0.08), residues: 6012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E3942 HIS 0.013 0.002 HIS E4089 PHE 0.033 0.002 PHE G4066 TYR 0.020 0.002 TYR E2849 ARG 0.005 0.001 ARG G4087 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28120 Ramachandran restraints generated. 14060 Oldfield, 0 Emsley, 14060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28120 Ramachandran restraints generated. 14060 Oldfield, 0 Emsley, 14060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 12804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 804 time to evaluate : 8.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 827 average time/residue: 0.9178 time to fit residues: 1348.7332 Evaluate side-chains 662 residues out of total 12804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 647 time to evaluate : 8.731 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 15 average time/residue: 0.7501 time to fit residues: 34.7017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1452 random chunks: chunk 1305 optimal weight: 7.9990 chunk 993 optimal weight: 1.9990 chunk 685 optimal weight: 20.0000 chunk 146 optimal weight: 30.0000 chunk 630 optimal weight: 9.9990 chunk 887 optimal weight: 0.9980 chunk 1325 optimal weight: 50.0000 chunk 1403 optimal weight: 20.0000 chunk 692 optimal weight: 20.0000 chunk 1256 optimal weight: 8.9990 chunk 378 optimal weight: 30.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 GLN A 163 HIS A 506 HIS ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1941 GLN ** A2211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2310 ASN A3635 HIS ** A3729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3919 ASN A3990 ASN ** A4089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4112 ASN A4179 ASN ** A4515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 163 HIS C 506 HIS ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1941 GLN ** C2211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2310 ASN C3635 HIS ** C3729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3919 ASN C3990 ASN ** C4089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4112 ASN ** C4515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 HIS E 506 HIS ** E 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1941 GLN ** E2211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2310 ASN E3635 HIS ** E3729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3919 ASN E3990 ASN ** E4089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E4112 ASN E4179 ASN ** E4515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 HIS G 506 HIS ** G 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1941 GLN ** G2210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2310 ASN G3635 HIS ** G3729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3919 ASN G3990 ASN ** G4089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G4112 ASN G4179 ASN ** G4515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 113104 Z= 0.248 Angle : 0.694 9.603 152952 Z= 0.368 Chirality : 0.043 0.243 17292 Planarity : 0.005 0.092 19704 Dihedral : 6.791 56.023 15396 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 24.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.72 % Favored : 88.15 % Rotamer: Outliers : 0.24 % Allowed : 5.27 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.31 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.07), residues: 14060 helix: -0.54 (0.06), residues: 6940 sheet: -3.38 (0.13), residues: 1144 loop : -2.81 (0.08), residues: 5976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 275 HIS 0.010 0.001 HIS C4934 PHE 0.032 0.002 PHE F 20 TYR 0.016 0.002 TYR E2093 ARG 0.007 0.000 ARG E 431 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28120 Ramachandran restraints generated. 14060 Oldfield, 0 Emsley, 14060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28120 Ramachandran restraints generated. 14060 Oldfield, 0 Emsley, 14060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 12804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 777 time to evaluate : 9.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 800 average time/residue: 0.9009 time to fit residues: 1293.3920 Evaluate side-chains 663 residues out of total 12804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 648 time to evaluate : 8.498 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 15 average time/residue: 0.7389 time to fit residues: 33.5301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1452 random chunks: chunk 1168 optimal weight: 20.0000 chunk 796 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 chunk 1045 optimal weight: 8.9990 chunk 579 optimal weight: 1.9990 chunk 1197 optimal weight: 9.9990 chunk 970 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 716 optimal weight: 20.0000 chunk 1259 optimal weight: 6.9990 chunk 354 optimal weight: 0.3980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS A 487 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2218 HIS A3595 GLN ** A3729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3976 GLN ** A4076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4179 ASN ** A4515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS C 487 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1722 ASN ** C1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2218 HIS ** C3729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4179 ASN ** C4515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 HIS E 487 ASN ** E 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1906 GLN ** E1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2218 HIS ** E3729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E4117 GLN ** E4515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 HIS G 487 ASN ** G 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1722 ASN ** G1912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2218 HIS ** G3729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 113104 Z= 0.194 Angle : 0.657 8.591 152952 Z= 0.343 Chirality : 0.043 0.298 17292 Planarity : 0.005 0.092 19704 Dihedral : 6.422 54.444 15396 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.94 % Favored : 88.95 % Rotamer: Outliers : 0.15 % Allowed : 3.15 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.48 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.07), residues: 14060 helix: -0.15 (0.06), residues: 6988 sheet: -3.22 (0.14), residues: 1120 loop : -2.72 (0.08), residues: 5952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A3942 HIS 0.009 0.001 HIS G4089 PHE 0.037 0.002 PHE D 69 TYR 0.015 0.001 TYR E1826 ARG 0.005 0.000 ARG E 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28120 Ramachandran restraints generated. 14060 Oldfield, 0 Emsley, 14060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28120 Ramachandran restraints generated. 14060 Oldfield, 0 Emsley, 14060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 12804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 846 time to evaluate : 8.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 294, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 600, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 180, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 131, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 99, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 209, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 196, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable