Starting phenix.real_space_refine on Fri Feb 23 06:59:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxm_4669/02_2024/6qxm_4669.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxm_4669/02_2024/6qxm_4669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxm_4669/02_2024/6qxm_4669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxm_4669/02_2024/6qxm_4669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxm_4669/02_2024/6qxm_4669.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxm_4669/02_2024/6qxm_4669.pdb" } resolution = 4.1 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= 0.003 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 23532 2.51 5 N 6264 2.21 5 O 7200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 23": "OD1" <-> "OD2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A ASP 326": "OD1" <-> "OD2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "B ASP 23": "OD1" <-> "OD2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 208": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B ASP 326": "OD1" <-> "OD2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B ASP 383": "OD1" <-> "OD2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C ASP 107": "OD1" <-> "OD2" Residue "C PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 208": "OD1" <-> "OD2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C ASP 241": "OD1" <-> "OD2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "C TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 318": "OD1" <-> "OD2" Residue "C GLU 325": "OE1" <-> "OE2" Residue "C ASP 326": "OD1" <-> "OD2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "C ASP 337": "OD1" <-> "OD2" Residue "C ARG 351": "NH1" <-> "NH2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "C GLU 382": "OE1" <-> "OE2" Residue "C ASP 383": "OD1" <-> "OD2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "D ASP 23": "OD1" <-> "OD2" Residue "D ASP 107": "OD1" <-> "OD2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 208": "OD1" <-> "OD2" Residue "D ASP 212": "OD1" <-> "OD2" Residue "D TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D ASP 241": "OD1" <-> "OD2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 266": "NH1" <-> "NH2" Residue "D TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 318": "OD1" <-> "OD2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D ASP 326": "OD1" <-> "OD2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "D ASP 337": "OD1" <-> "OD2" Residue "D ARG 351": "NH1" <-> "NH2" Residue "D GLU 380": "OE1" <-> "OE2" Residue "D GLU 382": "OE1" <-> "OE2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "E ASP 23": "OD1" <-> "OD2" Residue "E ASP 107": "OD1" <-> "OD2" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 208": "OD1" <-> "OD2" Residue "E ASP 212": "OD1" <-> "OD2" Residue "E TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "E GLU 236": "OE1" <-> "OE2" Residue "E ASP 241": "OD1" <-> "OD2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 266": "NH1" <-> "NH2" Residue "E TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 318": "OD1" <-> "OD2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "E ASP 326": "OD1" <-> "OD2" Residue "E GLU 333": "OE1" <-> "OE2" Residue "E ASP 337": "OD1" <-> "OD2" Residue "E ARG 351": "NH1" <-> "NH2" Residue "E GLU 380": "OE1" <-> "OE2" Residue "E GLU 382": "OE1" <-> "OE2" Residue "E ASP 383": "OD1" <-> "OD2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "F ASP 23": "OD1" <-> "OD2" Residue "F ASP 107": "OD1" <-> "OD2" Residue "F PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 208": "OD1" <-> "OD2" Residue "F ASP 212": "OD1" <-> "OD2" Residue "F TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 230": "OE1" <-> "OE2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "F ASP 241": "OD1" <-> "OD2" Residue "F TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 266": "NH1" <-> "NH2" Residue "F TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 318": "OD1" <-> "OD2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "F ASP 326": "OD1" <-> "OD2" Residue "F GLU 333": "OE1" <-> "OE2" Residue "F ASP 337": "OD1" <-> "OD2" Residue "F ARG 351": "NH1" <-> "NH2" Residue "F GLU 380": "OE1" <-> "OE2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F ASP 383": "OD1" <-> "OD2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "G ASP 23": "OD1" <-> "OD2" Residue "G ASP 107": "OD1" <-> "OD2" Residue "G PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 208": "OD1" <-> "OD2" Residue "G ASP 212": "OD1" <-> "OD2" Residue "G TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 230": "OE1" <-> "OE2" Residue "G GLU 236": "OE1" <-> "OE2" Residue "G ASP 241": "OD1" <-> "OD2" Residue "G TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 266": "NH1" <-> "NH2" Residue "G TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 318": "OD1" <-> "OD2" Residue "G GLU 325": "OE1" <-> "OE2" Residue "G ASP 326": "OD1" <-> "OD2" Residue "G GLU 333": "OE1" <-> "OE2" Residue "G ASP 337": "OD1" <-> "OD2" Residue "G ARG 351": "NH1" <-> "NH2" Residue "G GLU 380": "OE1" <-> "OE2" Residue "G GLU 382": "OE1" <-> "OE2" Residue "G ASP 383": "OD1" <-> "OD2" Residue "G GLU 395": "OE1" <-> "OE2" Residue "H ASP 23": "OD1" <-> "OD2" Residue "H ASP 107": "OD1" <-> "OD2" Residue "H PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 208": "OD1" <-> "OD2" Residue "H ASP 212": "OD1" <-> "OD2" Residue "H TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 230": "OE1" <-> "OE2" Residue "H GLU 236": "OE1" <-> "OE2" Residue "H ASP 241": "OD1" <-> "OD2" Residue "H TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 266": "NH1" <-> "NH2" Residue "H TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 318": "OD1" <-> "OD2" Residue "H GLU 325": "OE1" <-> "OE2" Residue "H ASP 326": "OD1" <-> "OD2" Residue "H GLU 333": "OE1" <-> "OE2" Residue "H ASP 337": "OD1" <-> "OD2" Residue "H ARG 351": "NH1" <-> "NH2" Residue "H GLU 380": "OE1" <-> "OE2" Residue "H GLU 382": "OE1" <-> "OE2" Residue "H ASP 383": "OD1" <-> "OD2" Residue "H GLU 395": "OE1" <-> "OE2" Residue "I ASP 23": "OD1" <-> "OD2" Residue "I ASP 107": "OD1" <-> "OD2" Residue "I PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 208": "OD1" <-> "OD2" Residue "I ASP 212": "OD1" <-> "OD2" Residue "I TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 230": "OE1" <-> "OE2" Residue "I GLU 236": "OE1" <-> "OE2" Residue "I ASP 241": "OD1" <-> "OD2" Residue "I TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 266": "NH1" <-> "NH2" Residue "I TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 318": "OD1" <-> "OD2" Residue "I GLU 325": "OE1" <-> "OE2" Residue "I ASP 326": "OD1" <-> "OD2" Residue "I GLU 333": "OE1" <-> "OE2" Residue "I ASP 337": "OD1" <-> "OD2" Residue "I ARG 351": "NH1" <-> "NH2" Residue "I GLU 380": "OE1" <-> "OE2" Residue "I GLU 382": "OE1" <-> "OE2" Residue "I ASP 383": "OD1" <-> "OD2" Residue "I GLU 395": "OE1" <-> "OE2" Residue "J ASP 23": "OD1" <-> "OD2" Residue "J ASP 107": "OD1" <-> "OD2" Residue "J PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 208": "OD1" <-> "OD2" Residue "J ASP 212": "OD1" <-> "OD2" Residue "J TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 230": "OE1" <-> "OE2" Residue "J GLU 236": "OE1" <-> "OE2" Residue "J ASP 241": "OD1" <-> "OD2" Residue "J TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 266": "NH1" <-> "NH2" Residue "J TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 318": "OD1" <-> "OD2" Residue "J GLU 325": "OE1" <-> "OE2" Residue "J ASP 326": "OD1" <-> "OD2" Residue "J GLU 333": "OE1" <-> "OE2" Residue "J ASP 337": "OD1" <-> "OD2" Residue "J ARG 351": "NH1" <-> "NH2" Residue "J GLU 380": "OE1" <-> "OE2" Residue "J GLU 382": "OE1" <-> "OE2" Residue "J ASP 383": "OD1" <-> "OD2" Residue "J GLU 395": "OE1" <-> "OE2" Residue "K ASP 23": "OD1" <-> "OD2" Residue "K ASP 107": "OD1" <-> "OD2" Residue "K PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 208": "OD1" <-> "OD2" Residue "K ASP 212": "OD1" <-> "OD2" Residue "K TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 230": "OE1" <-> "OE2" Residue "K GLU 236": "OE1" <-> "OE2" Residue "K ASP 241": "OD1" <-> "OD2" Residue "K TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 266": "NH1" <-> "NH2" Residue "K TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 318": "OD1" <-> "OD2" Residue "K GLU 325": "OE1" <-> "OE2" Residue "K ASP 326": "OD1" <-> "OD2" Residue "K GLU 333": "OE1" <-> "OE2" Residue "K ASP 337": "OD1" <-> "OD2" Residue "K ARG 351": "NH1" <-> "NH2" Residue "K GLU 380": "OE1" <-> "OE2" Residue "K GLU 382": "OE1" <-> "OE2" Residue "K ASP 383": "OD1" <-> "OD2" Residue "K GLU 395": "OE1" <-> "OE2" Residue "L ASP 23": "OD1" <-> "OD2" Residue "L ASP 107": "OD1" <-> "OD2" Residue "L PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 208": "OD1" <-> "OD2" Residue "L ASP 212": "OD1" <-> "OD2" Residue "L TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 230": "OE1" <-> "OE2" Residue "L GLU 236": "OE1" <-> "OE2" Residue "L ASP 241": "OD1" <-> "OD2" Residue "L TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 266": "NH1" <-> "NH2" Residue "L TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 318": "OD1" <-> "OD2" Residue "L GLU 325": "OE1" <-> "OE2" Residue "L ASP 326": "OD1" <-> "OD2" Residue "L GLU 333": "OE1" <-> "OE2" Residue "L ASP 337": "OD1" <-> "OD2" Residue "L ARG 351": "NH1" <-> "NH2" Residue "L GLU 380": "OE1" <-> "OE2" Residue "L GLU 382": "OE1" <-> "OE2" Residue "L ASP 383": "OD1" <-> "OD2" Residue "L GLU 395": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37164 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "B" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "C" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "D" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "E" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "F" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "G" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "H" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "I" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "J" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "K" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Chain: "L" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3097 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 19, 'TRANS': 372} Chain breaks: 2 Time building chain proxies: 19.14, per 1000 atoms: 0.52 Number of scatterers: 37164 At special positions: 0 Unit cell: (188.24, 188.24, 111.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 7200 8.00 N 6264 7.00 C 23532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.10 Conformation dependent library (CDL) restraints added in 6.7 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8808 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 48 sheets defined 41.9% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 removed outlier: 3.648A pdb=" N TYR A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 36 removed outlier: 3.570A pdb=" N ARG A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 78 " --> pdb=" O MET A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 396 through 407 removed outlier: 3.714A pdb=" N VAL A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 24 through 36 removed outlier: 3.570A pdb=" N ARG B 30 " --> pdb=" O PRO B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 75 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 124 removed outlier: 3.523A pdb=" N VAL B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 123 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN B 124 " --> pdb=" O TYR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR B 129 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 132 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA B 285 " --> pdb=" O ASN B 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS B 313 " --> pdb=" O ARG B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 removed outlier: 4.069A pdb=" N TYR B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 386 " --> pdb=" O GLU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 392 Processing helix chain 'B' and resid 396 through 407 removed outlier: 3.716A pdb=" N VAL B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE C 78 " --> pdb=" O MET C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL C 113 " --> pdb=" O GLY C 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C 122 " --> pdb=" O MET C 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C 123 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 124 " --> pdb=" O TYR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 132 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU C 311 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS C 313 " --> pdb=" O ARG C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR C 339 " --> pdb=" O GLN C 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG D 30 " --> pdb=" O PRO D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU D 75 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D 78 " --> pdb=" O MET D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU D 132 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL D 198 " --> pdb=" O ILE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA D 285 " --> pdb=" O ASN D 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D 295 " --> pdb=" O MET D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 313 removed outlier: 3.792A pdb=" N LEU D 311 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR D 339 " --> pdb=" O GLN D 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA D 341 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY D 386 " --> pdb=" O GLU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 392 Processing helix chain 'D' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL D 401 " --> pdb=" O GLN D 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG E 30 " --> pdb=" O PRO E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN E 67 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE E 78 " --> pdb=" O MET E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU E 122 " --> pdb=" O MET E 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN E 124 " --> pdb=" O TYR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR E 129 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE E 131 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU E 132 " --> pdb=" O VAL E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA E 285 " --> pdb=" O ASN E 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU E 311 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS E 313 " --> pdb=" O ARG E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 356 removed outlier: 3.504A pdb=" N THR E 339 " --> pdb=" O GLN E 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA E 341 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR E 376 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY E 386 " --> pdb=" O GLU E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 392 Processing helix chain 'E' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL E 401 " --> pdb=" O GLN E 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG F 30 " --> pdb=" O PRO F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU F 75 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE F 78 " --> pdb=" O MET F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE F 117 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU F 122 " --> pdb=" O MET F 118 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER F 123 " --> pdb=" O ASN F 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN F 124 " --> pdb=" O TYR F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR F 129 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE F 131 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU F 132 " --> pdb=" O VAL F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL F 198 " --> pdb=" O ILE F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA F 285 " --> pdb=" O ASN F 281 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS F 295 " --> pdb=" O MET F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU F 311 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS F 313 " --> pdb=" O ARG F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 356 removed outlier: 3.504A pdb=" N THR F 339 " --> pdb=" O GLN F 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA F 341 " --> pdb=" O ASP F 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE F 354 " --> pdb=" O ALA F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR F 376 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY F 386 " --> pdb=" O GLU F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 392 Processing helix chain 'F' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL F 401 " --> pdb=" O GLN F 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 21 Processing helix chain 'G' and resid 24 through 36 removed outlier: 3.570A pdb=" N ARG G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU G 75 " --> pdb=" O SER G 71 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE G 78 " --> pdb=" O MET G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 124 removed outlier: 3.521A pdb=" N VAL G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE G 117 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET G 118 " --> pdb=" O GLU G 114 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU G 122 " --> pdb=" O MET G 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER G 123 " --> pdb=" O ASN G 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN G 124 " --> pdb=" O TYR G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 138 removed outlier: 4.227A pdb=" N THR G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE G 131 " --> pdb=" O ARG G 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU G 132 " --> pdb=" O VAL G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL G 198 " --> pdb=" O ILE G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA G 285 " --> pdb=" O ASN G 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS G 295 " --> pdb=" O MET G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU G 311 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS G 313 " --> pdb=" O ARG G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR G 339 " --> pdb=" O GLN G 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA G 341 " --> pdb=" O ASP G 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE G 354 " --> pdb=" O ALA G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR G 376 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY G 386 " --> pdb=" O GLU G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 392 Processing helix chain 'G' and resid 396 through 407 removed outlier: 3.716A pdb=" N VAL G 401 " --> pdb=" O GLN G 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 21 Processing helix chain 'H' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG H 30 " --> pdb=" O PRO H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE H 78 " --> pdb=" O MET H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL H 113 " --> pdb=" O GLY H 109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE H 117 " --> pdb=" O VAL H 113 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET H 118 " --> pdb=" O GLU H 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU H 122 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER H 123 " --> pdb=" O ASN H 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN H 124 " --> pdb=" O TYR H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR H 129 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE H 131 " --> pdb=" O ARG H 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU H 132 " --> pdb=" O VAL H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL H 198 " --> pdb=" O ILE H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA H 285 " --> pdb=" O ASN H 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS H 295 " --> pdb=" O MET H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 313 removed outlier: 3.794A pdb=" N LEU H 311 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS H 313 " --> pdb=" O ARG H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR H 339 " --> pdb=" O GLN H 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL H 340 " --> pdb=" O ALA H 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA H 341 " --> pdb=" O ASP H 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE H 354 " --> pdb=" O ALA H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR H 376 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY H 386 " --> pdb=" O GLU H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 392 Processing helix chain 'H' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL H 401 " --> pdb=" O GLN H 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 21 Processing helix chain 'I' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG I 30 " --> pdb=" O PRO I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN I 67 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE I 78 " --> pdb=" O MET I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE I 117 " --> pdb=" O VAL I 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET I 118 " --> pdb=" O GLU I 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER I 123 " --> pdb=" O ASN I 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN I 124 " --> pdb=" O TYR I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR I 129 " --> pdb=" O SER I 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE I 131 " --> pdb=" O ARG I 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU I 132 " --> pdb=" O VAL I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL I 198 " --> pdb=" O ILE I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA I 285 " --> pdb=" O ASN I 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE I 292 " --> pdb=" O LYS I 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS I 295 " --> pdb=" O MET I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU I 311 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS I 313 " --> pdb=" O ARG I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR I 339 " --> pdb=" O GLN I 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA I 341 " --> pdb=" O ASP I 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE I 354 " --> pdb=" O ALA I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR I 376 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY I 386 " --> pdb=" O GLU I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 392 Processing helix chain 'I' and resid 396 through 407 removed outlier: 3.714A pdb=" N VAL I 401 " --> pdb=" O GLN I 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 21 Processing helix chain 'J' and resid 24 through 36 removed outlier: 3.568A pdb=" N ARG J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN J 67 " --> pdb=" O ALA J 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU J 75 " --> pdb=" O SER J 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE J 78 " --> pdb=" O MET J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL J 113 " --> pdb=" O GLY J 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE J 117 " --> pdb=" O VAL J 113 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET J 118 " --> pdb=" O GLU J 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER J 123 " --> pdb=" O ASN J 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN J 124 " --> pdb=" O TYR J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR J 129 " --> pdb=" O SER J 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE J 131 " --> pdb=" O ARG J 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU J 132 " --> pdb=" O VAL J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL J 198 " --> pdb=" O ILE J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA J 285 " --> pdb=" O ASN J 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE J 292 " --> pdb=" O LYS J 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS J 295 " --> pdb=" O MET J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU J 311 " --> pdb=" O GLN J 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS J 313 " --> pdb=" O ARG J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR J 339 " --> pdb=" O GLN J 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL J 340 " --> pdb=" O ALA J 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA J 341 " --> pdb=" O ASP J 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE J 354 " --> pdb=" O ALA J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR J 376 " --> pdb=" O GLU J 372 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY J 386 " --> pdb=" O GLU J 382 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 392 Processing helix chain 'J' and resid 396 through 407 removed outlier: 3.714A pdb=" N VAL J 401 " --> pdb=" O GLN J 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 21 Processing helix chain 'K' and resid 24 through 36 removed outlier: 3.570A pdb=" N ARG K 30 " --> pdb=" O PRO K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 78 removed outlier: 3.739A pdb=" N ARG K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN K 67 " --> pdb=" O ALA K 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU K 75 " --> pdb=" O SER K 71 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE K 78 " --> pdb=" O MET K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 124 removed outlier: 3.522A pdb=" N VAL K 113 " --> pdb=" O GLY K 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE K 117 " --> pdb=" O VAL K 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET K 118 " --> pdb=" O GLU K 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU K 122 " --> pdb=" O MET K 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER K 123 " --> pdb=" O ASN K 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN K 124 " --> pdb=" O TYR K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR K 129 " --> pdb=" O SER K 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE K 131 " --> pdb=" O ARG K 127 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU K 132 " --> pdb=" O VAL K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL K 198 " --> pdb=" O ILE K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 295 removed outlier: 4.395A pdb=" N ALA K 285 " --> pdb=" O ASN K 281 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE K 292 " --> pdb=" O LYS K 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS K 295 " --> pdb=" O MET K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU K 311 " --> pdb=" O GLN K 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS K 313 " --> pdb=" O ARG K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR K 339 " --> pdb=" O GLN K 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL K 340 " --> pdb=" O ALA K 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA K 341 " --> pdb=" O ASP K 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE K 354 " --> pdb=" O ALA K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR K 376 " --> pdb=" O GLU K 372 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY K 386 " --> pdb=" O GLU K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 392 Processing helix chain 'K' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL K 401 " --> pdb=" O GLN K 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 21 Processing helix chain 'L' and resid 24 through 36 removed outlier: 3.569A pdb=" N ARG L 30 " --> pdb=" O PRO L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 78 removed outlier: 3.740A pdb=" N ARG L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN L 67 " --> pdb=" O ALA L 63 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU L 75 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE L 78 " --> pdb=" O MET L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 124 removed outlier: 3.523A pdb=" N VAL L 113 " --> pdb=" O GLY L 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE L 117 " --> pdb=" O VAL L 113 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N MET L 118 " --> pdb=" O GLU L 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU L 122 " --> pdb=" O MET L 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER L 123 " --> pdb=" O ASN L 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN L 124 " --> pdb=" O TYR L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 138 removed outlier: 4.226A pdb=" N THR L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE L 131 " --> pdb=" O ARG L 127 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU L 132 " --> pdb=" O VAL L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 194 through 199 removed outlier: 3.777A pdb=" N VAL L 198 " --> pdb=" O ILE L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 272 through 295 removed outlier: 4.396A pdb=" N ALA L 285 " --> pdb=" O ASN L 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE L 292 " --> pdb=" O LYS L 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS L 295 " --> pdb=" O MET L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 313 removed outlier: 3.793A pdb=" N LEU L 311 " --> pdb=" O GLN L 307 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS L 313 " --> pdb=" O ARG L 309 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 356 removed outlier: 3.503A pdb=" N THR L 339 " --> pdb=" O GLN L 335 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL L 340 " --> pdb=" O ALA L 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA L 341 " --> pdb=" O ASP L 337 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE L 354 " --> pdb=" O ALA L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 386 removed outlier: 4.070A pdb=" N TYR L 376 " --> pdb=" O GLU L 372 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY L 386 " --> pdb=" O GLU L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 392 Processing helix chain 'L' and resid 396 through 407 removed outlier: 3.715A pdb=" N VAL L 401 " --> pdb=" O GLN L 397 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE A 252 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN A 178 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU A 177 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 211 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN A 178 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU A 177 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 211 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 300 removed outlier: 5.524A pdb=" N GLY A 298 " --> pdb=" O VAL L 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 321 removed outlier: 3.610A pdb=" N VAL B 300 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE B 252 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN B 178 " --> pdb=" O GLN B 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU B 177 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 211 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN B 178 " --> pdb=" O GLN B 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU B 177 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 211 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 319 through 321 removed outlier: 3.634A pdb=" N VAL C 300 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 160 through 161 removed outlier: 3.631A pdb=" N ILE C 252 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN C 178 " --> pdb=" O GLN C 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU C 177 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 211 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN C 178 " --> pdb=" O GLN C 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU C 177 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 211 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 319 through 321 removed outlier: 3.670A pdb=" N VAL D 300 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE D 252 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN D 178 " --> pdb=" O GLN D 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU D 177 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 211 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN D 178 " --> pdb=" O GLN D 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU D 177 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 211 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 319 through 321 removed outlier: 3.642A pdb=" N VAL E 300 " --> pdb=" O VAL D 320 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE E 252 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN E 178 " --> pdb=" O GLN E 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU E 177 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 211 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN E 178 " --> pdb=" O GLN E 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU E 177 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 211 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 319 through 321 removed outlier: 3.584A pdb=" N VAL F 300 " --> pdb=" O VAL E 320 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE F 252 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN F 178 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU F 177 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE F 211 " --> pdb=" O ILE F 185 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN F 178 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU F 177 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE F 211 " --> pdb=" O ILE F 185 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 319 through 321 removed outlier: 3.723A pdb=" N VAL G 300 " --> pdb=" O VAL F 320 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 160 through 161 removed outlier: 3.629A pdb=" N ILE G 252 " --> pdb=" O LEU G 145 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN G 178 " --> pdb=" O GLN G 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU G 177 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 211 " --> pdb=" O ILE G 185 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN G 178 " --> pdb=" O GLN G 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU G 177 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 211 " --> pdb=" O ILE G 185 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 319 through 321 removed outlier: 3.611A pdb=" N VAL H 300 " --> pdb=" O VAL G 320 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 160 through 161 removed outlier: 3.631A pdb=" N ILE H 252 " --> pdb=" O LEU H 145 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN H 178 " --> pdb=" O GLN H 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU H 177 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE H 211 " --> pdb=" O ILE H 185 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN H 178 " --> pdb=" O GLN H 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU H 177 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE H 211 " --> pdb=" O ILE H 185 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 319 through 321 removed outlier: 3.600A pdb=" N VAL I 300 " --> pdb=" O VAL H 320 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE I 252 " --> pdb=" O LEU I 145 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 166 through 170 removed outlier: 3.903A pdb=" N GLN I 178 " --> pdb=" O GLN I 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU I 177 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 211 " --> pdb=" O ILE I 185 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 166 through 170 removed outlier: 3.903A pdb=" N GLN I 178 " --> pdb=" O GLN I 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU I 177 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 211 " --> pdb=" O ILE I 185 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 319 through 321 removed outlier: 3.725A pdb=" N VAL J 300 " --> pdb=" O VAL I 320 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 160 through 161 removed outlier: 3.629A pdb=" N ILE J 252 " --> pdb=" O LEU J 145 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN J 178 " --> pdb=" O GLN J 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU J 177 " --> pdb=" O LEU J 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE J 211 " --> pdb=" O ILE J 185 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 166 through 170 removed outlier: 3.902A pdb=" N GLN J 178 " --> pdb=" O GLN J 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU J 177 " --> pdb=" O LEU J 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE J 211 " --> pdb=" O ILE J 185 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 319 through 321 removed outlier: 3.613A pdb=" N VAL K 300 " --> pdb=" O VAL J 320 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 160 through 161 removed outlier: 3.630A pdb=" N ILE K 252 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 166 through 170 removed outlier: 3.901A pdb=" N GLN K 178 " --> pdb=" O GLN K 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU K 177 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE K 211 " --> pdb=" O ILE K 185 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 166 through 170 removed outlier: 3.901A pdb=" N GLN K 178 " --> pdb=" O GLN K 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU K 177 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE K 211 " --> pdb=" O ILE K 185 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 319 through 321 removed outlier: 3.583A pdb=" N VAL L 300 " --> pdb=" O VAL K 320 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 160 through 161 removed outlier: 3.629A pdb=" N ILE L 252 " --> pdb=" O LEU L 145 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 166 through 170 removed outlier: 3.901A pdb=" N GLN L 178 " --> pdb=" O GLN L 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU L 177 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE L 211 " --> pdb=" O ILE L 185 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 166 through 170 removed outlier: 3.901A pdb=" N GLN L 178 " --> pdb=" O GLN L 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU L 177 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE L 211 " --> pdb=" O ILE L 185 " (cutoff:3.500A) 1595 hydrogen bonds defined for protein. 4641 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: 12.17 Time building geometry restraints manager: 15.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12229 1.34 - 1.46: 6591 1.46 - 1.58: 18632 1.58 - 1.69: 24 1.69 - 1.81: 312 Bond restraints: 37788 Sorted by residual: bond pdb=" C LEU E 417 " pdb=" N PRO E 418 " ideal model delta sigma weight residual 1.328 1.377 -0.049 1.25e-02 6.40e+03 1.52e+01 bond pdb=" C LEU I 417 " pdb=" N PRO I 418 " ideal model delta sigma weight residual 1.328 1.376 -0.048 1.25e-02 6.40e+03 1.50e+01 bond pdb=" C LEU F 417 " pdb=" N PRO F 418 " ideal model delta sigma weight residual 1.328 1.376 -0.048 1.25e-02 6.40e+03 1.49e+01 bond pdb=" C LEU C 417 " pdb=" N PRO C 418 " ideal model delta sigma weight residual 1.328 1.376 -0.048 1.25e-02 6.40e+03 1.47e+01 bond pdb=" C LEU J 417 " pdb=" N PRO J 418 " ideal model delta sigma weight residual 1.328 1.376 -0.048 1.25e-02 6.40e+03 1.47e+01 ... (remaining 37783 not shown) Histogram of bond angle deviations from ideal: 97.43 - 104.75: 780 104.75 - 112.07: 16879 112.07 - 119.38: 14044 119.38 - 126.70: 19127 126.70 - 134.02: 302 Bond angle restraints: 51132 Sorted by residual: angle pdb=" N ILE I 305 " pdb=" CA ILE I 305 " pdb=" C ILE I 305 " ideal model delta sigma weight residual 112.96 106.84 6.12 1.00e+00 1.00e+00 3.75e+01 angle pdb=" N ILE D 305 " pdb=" CA ILE D 305 " pdb=" C ILE D 305 " ideal model delta sigma weight residual 112.96 106.85 6.11 1.00e+00 1.00e+00 3.73e+01 angle pdb=" N ILE H 305 " pdb=" CA ILE H 305 " pdb=" C ILE H 305 " ideal model delta sigma weight residual 112.96 106.86 6.10 1.00e+00 1.00e+00 3.72e+01 angle pdb=" N ILE B 305 " pdb=" CA ILE B 305 " pdb=" C ILE B 305 " ideal model delta sigma weight residual 112.96 106.86 6.10 1.00e+00 1.00e+00 3.72e+01 angle pdb=" N ILE E 305 " pdb=" CA ILE E 305 " pdb=" C ILE E 305 " ideal model delta sigma weight residual 112.96 106.87 6.09 1.00e+00 1.00e+00 3.71e+01 ... (remaining 51127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 19316 17.23 - 34.46: 2657 34.46 - 51.69: 935 51.69 - 68.92: 240 68.92 - 86.15: 96 Dihedral angle restraints: 23244 sinusoidal: 9516 harmonic: 13728 Sorted by residual: dihedral pdb=" CA GLN H 59 " pdb=" C GLN H 59 " pdb=" N ALA H 60 " pdb=" CA ALA H 60 " ideal model delta harmonic sigma weight residual 180.00 -153.75 -26.25 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA GLN A 59 " pdb=" C GLN A 59 " pdb=" N ALA A 60 " pdb=" CA ALA A 60 " ideal model delta harmonic sigma weight residual -180.00 -153.77 -26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA GLN F 59 " pdb=" C GLN F 59 " pdb=" N ALA F 60 " pdb=" CA ALA F 60 " ideal model delta harmonic sigma weight residual -180.00 -153.77 -26.23 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 23241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4242 0.059 - 0.117: 1159 0.117 - 0.176: 325 0.176 - 0.234: 22 0.234 - 0.293: 12 Chirality restraints: 5760 Sorted by residual: chirality pdb=" CB VAL F 237 " pdb=" CA VAL F 237 " pdb=" CG1 VAL F 237 " pdb=" CG2 VAL F 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB VAL B 237 " pdb=" CA VAL B 237 " pdb=" CG1 VAL B 237 " pdb=" CG2 VAL B 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB VAL C 237 " pdb=" CA VAL C 237 " pdb=" CG1 VAL C 237 " pdb=" CG2 VAL C 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 5757 not shown) Planarity restraints: 6660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS I 419 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C LYS I 419 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS I 419 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU I 420 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 419 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C LYS C 419 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS C 419 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU C 420 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 419 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" C LYS D 419 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS D 419 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU D 420 " 0.016 2.00e-02 2.50e+03 ... (remaining 6657 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 12389 2.85 - 3.36: 33862 3.36 - 3.87: 59613 3.87 - 4.39: 63121 4.39 - 4.90: 108188 Nonbonded interactions: 277173 Sorted by model distance: nonbonded pdb=" O GLU B 380 " pdb=" OG1 THR B 384 " model vdw 2.333 2.440 nonbonded pdb=" O GLU G 380 " pdb=" OG1 THR G 384 " model vdw 2.333 2.440 nonbonded pdb=" O GLU F 380 " pdb=" OG1 THR F 384 " model vdw 2.333 2.440 nonbonded pdb=" O GLU H 380 " pdb=" OG1 THR H 384 " model vdw 2.333 2.440 nonbonded pdb=" O GLU I 380 " pdb=" OG1 THR I 384 " model vdw 2.333 2.440 ... (remaining 277168 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.10 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 4.770 Check model and map are aligned: 0.590 Set scattering table: 0.360 Process input model: 89.410 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.240 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 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 : 0.008 0.062 37788 Z= 0.507 Angle : 1.251 13.257 51132 Z= 0.719 Chirality : 0.058 0.293 5760 Planarity : 0.008 0.068 6660 Dihedral : 18.913 86.145 14436 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 8.63 % Allowed : 13.96 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.09), residues: 4632 helix: -3.25 (0.07), residues: 1728 sheet: -1.94 (0.17), residues: 576 loop : -3.47 (0.11), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP L 58 HIS 0.005 0.003 HIS K 216 PHE 0.027 0.002 PHE K 78 TYR 0.015 0.002 TYR C 268 ARG 0.012 0.001 ARG F 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1365 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 1017 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.5900 (t80) cc_final: 0.5537 (t80) REVERT: A 58 TRP cc_start: 0.8133 (t-100) cc_final: 0.6761 (m100) REVERT: A 64 ARG cc_start: 0.7621 (ttp-110) cc_final: 0.7398 (ttp-110) REVERT: A 72 LYS cc_start: 0.7363 (mmtt) cc_final: 0.6925 (mmtm) REVERT: A 116 ILE cc_start: 0.6965 (mm) cc_final: 0.6740 (mm) REVERT: A 124 ASN cc_start: 0.7393 (t0) cc_final: 0.7150 (t0) REVERT: A 132 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6343 (mt-10) REVERT: A 179 MET cc_start: 0.6112 (mtm) cc_final: 0.5789 (mtt) REVERT: A 214 TYR cc_start: 0.7699 (m-80) cc_final: 0.7340 (m-10) REVERT: A 291 MET cc_start: 0.6999 (ttp) cc_final: 0.6767 (ttm) REVERT: A 323 ARG cc_start: 0.7271 (tpp80) cc_final: 0.6892 (mtt-85) REVERT: B 58 TRP cc_start: 0.8102 (t-100) cc_final: 0.6739 (m100) REVERT: B 72 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7276 (mmtp) REVERT: B 80 MET cc_start: 0.7788 (mmt) cc_final: 0.7259 (mmm) REVERT: B 108 GLU cc_start: 0.7445 (mp0) cc_final: 0.6056 (tm-30) REVERT: B 116 ILE cc_start: 0.6460 (mm) cc_final: 0.6249 (mm) REVERT: B 124 ASN cc_start: 0.7448 (t0) cc_final: 0.7146 (t0) REVERT: B 258 ARG cc_start: 0.6847 (tpp80) cc_final: 0.6612 (tpp80) REVERT: B 290 SER cc_start: 0.8802 (t) cc_final: 0.8414 (p) REVERT: B 323 ARG cc_start: 0.7285 (tpp80) cc_final: 0.6934 (mtt-85) REVERT: B 389 TYR cc_start: 0.7767 (t80) cc_final: 0.6998 (t80) REVERT: B 406 LYS cc_start: 0.6275 (OUTLIER) cc_final: 0.6020 (mmtp) REVERT: C 54 TYR cc_start: 0.5748 (t80) cc_final: 0.5468 (t80) REVERT: C 58 TRP cc_start: 0.8178 (t-100) cc_final: 0.6705 (m100) REVERT: C 66 LEU cc_start: 0.7789 (tt) cc_final: 0.7529 (tp) REVERT: C 72 LYS cc_start: 0.7498 (mmtt) cc_final: 0.7026 (mmtm) REVERT: C 80 MET cc_start: 0.7772 (mmt) cc_final: 0.7415 (mmt) REVERT: C 108 GLU cc_start: 0.6628 (mp0) cc_final: 0.4975 (tm-30) REVERT: C 124 ASN cc_start: 0.7528 (t0) cc_final: 0.7235 (t0) REVERT: C 233 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5988 (tp30) REVERT: C 258 ARG cc_start: 0.6980 (tpp80) cc_final: 0.6060 (tpp80) REVERT: C 295 LYS cc_start: 0.8748 (ptmt) cc_final: 0.8364 (mtmm) REVERT: C 307 GLN cc_start: 0.8036 (mp10) cc_final: 0.7431 (mp10) REVERT: C 323 ARG cc_start: 0.7224 (tpp80) cc_final: 0.6925 (mtt-85) REVERT: C 325 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7628 (tm-30) REVERT: C 395 GLU cc_start: 0.6717 (mm-30) cc_final: 0.5965 (mm-30) REVERT: D 39 ILE cc_start: 0.7414 (tp) cc_final: 0.6850 (tt) REVERT: D 54 TYR cc_start: 0.6049 (t80) cc_final: 0.5636 (t80) REVERT: D 58 TRP cc_start: 0.8078 (t-100) cc_final: 0.6810 (m100) REVERT: D 64 ARG cc_start: 0.7560 (ttp-110) cc_final: 0.7139 (ttp-110) REVERT: D 80 MET cc_start: 0.7709 (mmt) cc_final: 0.7495 (mmt) REVERT: D 116 ILE cc_start: 0.6741 (mm) cc_final: 0.6506 (mm) REVERT: D 124 ASN cc_start: 0.7451 (t0) cc_final: 0.6996 (t0) REVERT: D 213 VAL cc_start: 0.7395 (m) cc_final: 0.7135 (m) REVERT: D 214 TYR cc_start: 0.7580 (m-80) cc_final: 0.7231 (m-10) REVERT: D 258 ARG cc_start: 0.6840 (tpp80) cc_final: 0.6588 (tpp80) REVERT: D 262 GLU cc_start: 0.7301 (pt0) cc_final: 0.7047 (pt0) REVERT: D 290 SER cc_start: 0.9011 (t) cc_final: 0.8810 (t) REVERT: D 291 MET cc_start: 0.7091 (ttp) cc_final: 0.6828 (ttm) REVERT: D 323 ARG cc_start: 0.7241 (tpp80) cc_final: 0.6814 (mtt-85) REVERT: E 58 TRP cc_start: 0.8112 (t-100) cc_final: 0.6754 (m100) REVERT: E 72 LYS cc_start: 0.7709 (mmtt) cc_final: 0.7256 (mmtp) REVERT: E 80 MET cc_start: 0.7791 (mmt) cc_final: 0.7251 (mmm) REVERT: E 108 GLU cc_start: 0.7471 (mp0) cc_final: 0.6444 (tm-30) REVERT: E 116 ILE cc_start: 0.6628 (mm) cc_final: 0.6380 (mm) REVERT: E 124 ASN cc_start: 0.7375 (t0) cc_final: 0.7055 (t0) REVERT: E 179 MET cc_start: 0.5779 (mtm) cc_final: 0.5564 (mtt) REVERT: E 230 GLU cc_start: 0.6612 (mp0) cc_final: 0.6207 (mp0) REVERT: E 290 SER cc_start: 0.8814 (t) cc_final: 0.8384 (p) REVERT: E 323 ARG cc_start: 0.7401 (tpp80) cc_final: 0.7106 (mtt-85) REVERT: E 325 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7870 (tm-30) REVERT: F 54 TYR cc_start: 0.5488 (t80) cc_final: 0.5182 (t80) REVERT: F 58 TRP cc_start: 0.8187 (t-100) cc_final: 0.6680 (m100) REVERT: F 66 LEU cc_start: 0.7740 (tt) cc_final: 0.7476 (tp) REVERT: F 72 LYS cc_start: 0.7526 (mmtt) cc_final: 0.7042 (mmtm) REVERT: F 80 MET cc_start: 0.7701 (mmt) cc_final: 0.7311 (mmt) REVERT: F 124 ASN cc_start: 0.7531 (t0) cc_final: 0.7040 (t0) REVERT: F 134 LEU cc_start: 0.7408 (tt) cc_final: 0.7161 (mt) REVERT: F 295 LYS cc_start: 0.8760 (ptmt) cc_final: 0.8372 (mtmm) REVERT: F 307 GLN cc_start: 0.7991 (mp10) cc_final: 0.7327 (mp10) REVERT: F 323 ARG cc_start: 0.7234 (tpp80) cc_final: 0.6908 (mtt-85) REVERT: F 325 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7628 (tm-30) REVERT: F 395 GLU cc_start: 0.6672 (mm-30) cc_final: 0.6046 (mm-30) REVERT: G 39 ILE cc_start: 0.7283 (tp) cc_final: 0.7014 (mm) REVERT: G 54 TYR cc_start: 0.6006 (t80) cc_final: 0.5593 (t80) REVERT: G 58 TRP cc_start: 0.8114 (t-100) cc_final: 0.6744 (m100) REVERT: G 64 ARG cc_start: 0.7568 (ttp-110) cc_final: 0.7367 (ttp-110) REVERT: G 116 ILE cc_start: 0.6832 (mm) cc_final: 0.6611 (mm) REVERT: G 124 ASN cc_start: 0.7400 (t0) cc_final: 0.7157 (t0) REVERT: G 132 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6571 (mt-10) REVERT: G 213 VAL cc_start: 0.7473 (m) cc_final: 0.7237 (m) REVERT: G 214 TYR cc_start: 0.7664 (m-80) cc_final: 0.7291 (m-10) REVERT: G 258 ARG cc_start: 0.6782 (tpp80) cc_final: 0.6484 (tpp80) REVERT: G 262 GLU cc_start: 0.7303 (pt0) cc_final: 0.7055 (pt0) REVERT: G 291 MET cc_start: 0.7010 (ttp) cc_final: 0.6784 (ttm) REVERT: G 323 ARG cc_start: 0.7250 (tpp80) cc_final: 0.6807 (mtt-85) REVERT: H 58 TRP cc_start: 0.8100 (t-100) cc_final: 0.6719 (m100) REVERT: H 72 LYS cc_start: 0.7693 (mmtt) cc_final: 0.7263 (mmtp) REVERT: H 80 MET cc_start: 0.7819 (mmt) cc_final: 0.7311 (mmm) REVERT: H 108 GLU cc_start: 0.7590 (mp0) cc_final: 0.6342 (tm-30) REVERT: H 116 ILE cc_start: 0.6429 (mm) cc_final: 0.6227 (mm) REVERT: H 124 ASN cc_start: 0.7479 (t0) cc_final: 0.7158 (t0) REVERT: H 290 SER cc_start: 0.8821 (t) cc_final: 0.8439 (p) REVERT: H 323 ARG cc_start: 0.7248 (tpp80) cc_final: 0.6904 (mtt-85) REVERT: H 389 TYR cc_start: 0.7757 (t80) cc_final: 0.6967 (t80) REVERT: I 54 TYR cc_start: 0.5977 (t80) cc_final: 0.5630 (t80) REVERT: I 58 TRP cc_start: 0.8188 (t-100) cc_final: 0.6682 (m100) REVERT: I 66 LEU cc_start: 0.7679 (tt) cc_final: 0.7463 (tp) REVERT: I 72 LYS cc_start: 0.7557 (mmtt) cc_final: 0.7101 (mmtm) REVERT: I 80 MET cc_start: 0.7733 (mmt) cc_final: 0.7388 (mmt) REVERT: I 108 GLU cc_start: 0.6797 (mp0) cc_final: 0.5158 (tm-30) REVERT: I 124 ASN cc_start: 0.7587 (t0) cc_final: 0.7141 (t0) REVERT: I 307 GLN cc_start: 0.8021 (mp10) cc_final: 0.7423 (mp10) REVERT: I 323 ARG cc_start: 0.7254 (tpp80) cc_final: 0.6942 (mtt-85) REVERT: I 325 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7613 (tm-30) REVERT: I 395 GLU cc_start: 0.6674 (mm-30) cc_final: 0.5963 (mm-30) REVERT: J 54 TYR cc_start: 0.5991 (t80) cc_final: 0.5649 (t80) REVERT: J 58 TRP cc_start: 0.8114 (t-100) cc_final: 0.6753 (m100) REVERT: J 64 ARG cc_start: 0.7606 (ttp-110) cc_final: 0.7384 (ttp-110) REVERT: J 116 ILE cc_start: 0.6958 (mm) cc_final: 0.6723 (mm) REVERT: J 124 ASN cc_start: 0.7411 (t0) cc_final: 0.7176 (t0) REVERT: J 132 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6280 (mt-10) REVERT: J 179 MET cc_start: 0.6132 (mtm) cc_final: 0.5814 (mtt) REVERT: J 213 VAL cc_start: 0.7462 (m) cc_final: 0.7253 (m) REVERT: J 214 TYR cc_start: 0.7719 (m-80) cc_final: 0.7363 (m-10) REVERT: J 258 ARG cc_start: 0.6789 (tpp80) cc_final: 0.6475 (tpp80) REVERT: J 262 GLU cc_start: 0.7301 (pt0) cc_final: 0.7024 (pt0) REVERT: J 323 ARG cc_start: 0.7268 (tpp80) cc_final: 0.6830 (mtt-85) REVERT: K 58 TRP cc_start: 0.8087 (t-100) cc_final: 0.7447 (m100) REVERT: K 72 LYS cc_start: 0.7725 (mmtt) cc_final: 0.7281 (mmtp) REVERT: K 80 MET cc_start: 0.7852 (mmt) cc_final: 0.7328 (mmm) REVERT: K 108 GLU cc_start: 0.7598 (mp0) cc_final: 0.6169 (tm-30) REVERT: K 124 ASN cc_start: 0.7543 (t0) cc_final: 0.7221 (t0) REVERT: K 290 SER cc_start: 0.8808 (t) cc_final: 0.8438 (p) REVERT: K 323 ARG cc_start: 0.7256 (tpp80) cc_final: 0.6919 (mtt-85) REVERT: K 389 TYR cc_start: 0.7805 (t80) cc_final: 0.6962 (t80) REVERT: K 406 LYS cc_start: 0.6360 (OUTLIER) cc_final: 0.6159 (mmtp) REVERT: L 54 TYR cc_start: 0.6020 (t80) cc_final: 0.5736 (t80) REVERT: L 66 LEU cc_start: 0.7712 (tt) cc_final: 0.7466 (tp) REVERT: L 72 LYS cc_start: 0.7561 (mmtt) cc_final: 0.7128 (mmtm) REVERT: L 80 MET cc_start: 0.7724 (mmt) cc_final: 0.7372 (mmt) REVERT: L 108 GLU cc_start: 0.6700 (mp0) cc_final: 0.5063 (tm-30) REVERT: L 124 ASN cc_start: 0.7576 (t0) cc_final: 0.7322 (t0) REVERT: L 233 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5958 (tp30) REVERT: L 295 LYS cc_start: 0.8789 (ptmt) cc_final: 0.8414 (mtmm) REVERT: L 307 GLN cc_start: 0.8069 (mp10) cc_final: 0.7505 (mp10) REVERT: L 323 ARG cc_start: 0.7253 (tpp80) cc_final: 0.6994 (mtt-85) REVERT: L 325 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7642 (tm-30) REVERT: L 395 GLU cc_start: 0.6674 (mm-30) cc_final: 0.5991 (mm-30) outliers start: 348 outliers final: 138 residues processed: 1269 average time/residue: 0.5246 time to fit residues: 1066.5818 Evaluate side-chains 1005 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 860 time to evaluate : 3.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 395 optimal weight: 1.9990 chunk 354 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 239 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 366 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 chunk 273 optimal weight: 10.0000 chunk 424 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 409 GLN B 175 ASN B 201 GLN B 409 GLN C 175 ASN C 184 GLN C 201 GLN C 409 GLN D 201 GLN D 409 GLN E 175 ASN E 201 GLN E 409 GLN F 175 ASN F 201 GLN ** F 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN G 175 ASN G 201 GLN G 409 GLN H 175 ASN H 201 GLN H 409 GLN I 175 ASN I 201 GLN I 409 GLN J 201 GLN J 409 GLN K 175 ASN K 201 GLN K 409 GLN L 175 ASN L 184 GLN L 201 GLN L 409 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37788 Z= 0.222 Angle : 0.703 8.491 51132 Z= 0.355 Chirality : 0.043 0.144 5760 Planarity : 0.005 0.051 6660 Dihedral : 5.712 25.860 5208 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.02 % Allowed : 3.45 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.11), residues: 4632 helix: -1.41 (0.11), residues: 1824 sheet: -1.47 (0.17), residues: 648 loop : -3.24 (0.11), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP K 83 HIS 0.003 0.001 HIS D 216 PHE 0.014 0.002 PHE D 356 TYR 0.018 0.001 TYR E 268 ARG 0.011 0.001 ARG F 266 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 927 time to evaluate : 4.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.7269 (tp) cc_final: 0.6610 (tt) REVERT: A 54 TYR cc_start: 0.5872 (t80) cc_final: 0.5553 (t80) REVERT: A 64 ARG cc_start: 0.7544 (ttp-110) cc_final: 0.7071 (ttp-110) REVERT: A 108 GLU cc_start: 0.5789 (mp0) cc_final: 0.4809 (mp0) REVERT: A 112 MET cc_start: 0.6191 (mtm) cc_final: 0.5935 (mtm) REVERT: A 214 TYR cc_start: 0.7593 (m-80) cc_final: 0.7288 (m-10) REVERT: A 323 ARG cc_start: 0.7293 (tpp80) cc_final: 0.6799 (mtt-85) REVERT: A 394 GLN cc_start: 0.7451 (mm-40) cc_final: 0.6767 (mm110) REVERT: A 428 THR cc_start: 0.8125 (p) cc_final: 0.7885 (p) REVERT: B 72 LYS cc_start: 0.7552 (mmtt) cc_final: 0.7313 (mmtp) REVERT: B 80 MET cc_start: 0.7775 (mmt) cc_final: 0.7320 (mmm) REVERT: B 108 GLU cc_start: 0.7305 (mp0) cc_final: 0.5924 (tm-30) REVERT: B 112 MET cc_start: 0.5974 (mtt) cc_final: 0.5324 (mtt) REVERT: B 124 ASN cc_start: 0.7483 (t0) cc_final: 0.7037 (t0) REVERT: B 293 SER cc_start: 0.7650 (p) cc_final: 0.7431 (p) REVERT: B 323 ARG cc_start: 0.7313 (tpp80) cc_final: 0.6925 (mtt-85) REVERT: B 330 LEU cc_start: 0.5391 (mt) cc_final: 0.4013 (mp) REVERT: B 428 THR cc_start: 0.7798 (p) cc_final: 0.7526 (p) REVERT: C 27 TYR cc_start: 0.7372 (m-80) cc_final: 0.6562 (m-80) REVERT: C 54 TYR cc_start: 0.5793 (t80) cc_final: 0.5470 (t80) REVERT: C 72 LYS cc_start: 0.7122 (mmtt) cc_final: 0.6808 (mmtm) REVERT: C 80 MET cc_start: 0.7621 (mmt) cc_final: 0.7417 (mmt) REVERT: C 124 ASN cc_start: 0.7561 (t0) cc_final: 0.7175 (t0) REVERT: C 129 THR cc_start: 0.7902 (m) cc_final: 0.7664 (m) REVERT: C 295 LYS cc_start: 0.8703 (ptmt) cc_final: 0.8265 (mtmm) REVERT: C 307 GLN cc_start: 0.7956 (mp10) cc_final: 0.7692 (mt0) REVERT: C 323 ARG cc_start: 0.7246 (tpp80) cc_final: 0.6892 (mtt-85) REVERT: C 394 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7004 (mm-40) REVERT: D 39 ILE cc_start: 0.7283 (tp) cc_final: 0.6822 (tt) REVERT: D 54 TYR cc_start: 0.6034 (t80) cc_final: 0.5527 (t80) REVERT: D 64 ARG cc_start: 0.7473 (ttp-110) cc_final: 0.7016 (ttp-110) REVERT: D 213 VAL cc_start: 0.7499 (m) cc_final: 0.7223 (m) REVERT: D 214 TYR cc_start: 0.7576 (m-80) cc_final: 0.7229 (m-10) REVERT: D 323 ARG cc_start: 0.7212 (tpp80) cc_final: 0.6815 (mtt-85) REVERT: D 330 LEU cc_start: 0.5580 (mt) cc_final: 0.4805 (mp) REVERT: D 394 GLN cc_start: 0.7370 (mm-40) cc_final: 0.6450 (mm-40) REVERT: D 428 THR cc_start: 0.8178 (p) cc_final: 0.7953 (p) REVERT: E 72 LYS cc_start: 0.7598 (mmtt) cc_final: 0.7339 (mmtp) REVERT: E 80 MET cc_start: 0.7715 (mmt) cc_final: 0.7255 (mmm) REVERT: E 108 GLU cc_start: 0.7241 (mp0) cc_final: 0.5895 (tm-30) REVERT: E 124 ASN cc_start: 0.7388 (t0) cc_final: 0.6973 (t0) REVERT: E 323 ARG cc_start: 0.7410 (tpp80) cc_final: 0.7043 (mtt-85) REVERT: E 330 LEU cc_start: 0.5245 (mt) cc_final: 0.4003 (mp) REVERT: E 389 TYR cc_start: 0.7578 (t80) cc_final: 0.7146 (t80) REVERT: E 428 THR cc_start: 0.7832 (p) cc_final: 0.7593 (p) REVERT: F 27 TYR cc_start: 0.7406 (m-80) cc_final: 0.6604 (m-10) REVERT: F 54 TYR cc_start: 0.5389 (t80) cc_final: 0.5132 (t80) REVERT: F 72 LYS cc_start: 0.7296 (mmtt) cc_final: 0.6935 (mmtm) REVERT: F 80 MET cc_start: 0.7687 (mmt) cc_final: 0.7408 (mmt) REVERT: F 134 LEU cc_start: 0.7067 (tt) cc_final: 0.6735 (mp) REVERT: F 295 LYS cc_start: 0.8691 (ptmt) cc_final: 0.8318 (mtmt) REVERT: F 323 ARG cc_start: 0.7217 (tpp80) cc_final: 0.6893 (mtt-85) REVERT: F 394 GLN cc_start: 0.7482 (mm-40) cc_final: 0.6937 (mm-40) REVERT: G 54 TYR cc_start: 0.5920 (t80) cc_final: 0.5575 (t80) REVERT: G 64 ARG cc_start: 0.7524 (ttp-110) cc_final: 0.7068 (ttp-110) REVERT: G 108 GLU cc_start: 0.5955 (mp0) cc_final: 0.4946 (mp0) REVERT: G 112 MET cc_start: 0.6094 (mtm) cc_final: 0.5858 (mtm) REVERT: G 213 VAL cc_start: 0.7537 (m) cc_final: 0.7302 (m) REVERT: G 214 TYR cc_start: 0.7590 (m-80) cc_final: 0.7294 (m-10) REVERT: G 323 ARG cc_start: 0.7257 (tpp80) cc_final: 0.6773 (mtt-85) REVERT: G 394 GLN cc_start: 0.7425 (mm-40) cc_final: 0.6493 (mm-40) REVERT: G 428 THR cc_start: 0.8070 (p) cc_final: 0.7861 (p) REVERT: H 72 LYS cc_start: 0.7532 (mmtt) cc_final: 0.7307 (mmtp) REVERT: H 80 MET cc_start: 0.7748 (mmt) cc_final: 0.7318 (mmm) REVERT: H 108 GLU cc_start: 0.7363 (mp0) cc_final: 0.6158 (tm-30) REVERT: H 116 ILE cc_start: 0.6226 (mm) cc_final: 0.6023 (mm) REVERT: H 124 ASN cc_start: 0.7498 (t0) cc_final: 0.7072 (t0) REVERT: H 257 VAL cc_start: 0.5944 (m) cc_final: 0.5125 (p) REVERT: H 293 SER cc_start: 0.7654 (p) cc_final: 0.7420 (p) REVERT: H 323 ARG cc_start: 0.7289 (tpp80) cc_final: 0.6913 (mtt-85) REVERT: H 428 THR cc_start: 0.7853 (p) cc_final: 0.7593 (p) REVERT: I 27 TYR cc_start: 0.7426 (m-80) cc_final: 0.6606 (m-80) REVERT: I 54 TYR cc_start: 0.5870 (t80) cc_final: 0.5522 (t80) REVERT: I 72 LYS cc_start: 0.7077 (mmtt) cc_final: 0.6863 (mmtm) REVERT: I 132 GLU cc_start: 0.6903 (tt0) cc_final: 0.6656 (tt0) REVERT: I 307 GLN cc_start: 0.7904 (mp10) cc_final: 0.7646 (mt0) REVERT: I 323 ARG cc_start: 0.7249 (tpp80) cc_final: 0.6928 (mtt-85) REVERT: I 394 GLN cc_start: 0.7504 (mm-40) cc_final: 0.6984 (mm-40) REVERT: J 39 ILE cc_start: 0.7299 (tp) cc_final: 0.6811 (tt) REVERT: J 54 TYR cc_start: 0.5894 (t80) cc_final: 0.5600 (t80) REVERT: J 64 ARG cc_start: 0.7549 (ttp-110) cc_final: 0.7044 (ttp-110) REVERT: J 108 GLU cc_start: 0.5826 (mp0) cc_final: 0.4843 (mp0) REVERT: J 112 MET cc_start: 0.6097 (mtm) cc_final: 0.5868 (mtm) REVERT: J 213 VAL cc_start: 0.7543 (m) cc_final: 0.7314 (m) REVERT: J 214 TYR cc_start: 0.7550 (m-80) cc_final: 0.7270 (m-10) REVERT: J 323 ARG cc_start: 0.7283 (tpp80) cc_final: 0.6794 (mtt-85) REVERT: J 394 GLN cc_start: 0.7439 (mm-40) cc_final: 0.6970 (mm-40) REVERT: J 428 THR cc_start: 0.8120 (p) cc_final: 0.7865 (p) REVERT: K 72 LYS cc_start: 0.7558 (mmtt) cc_final: 0.7330 (mmtp) REVERT: K 80 MET cc_start: 0.7804 (mmt) cc_final: 0.7346 (mmm) REVERT: K 108 GLU cc_start: 0.7273 (mp0) cc_final: 0.5912 (tm-30) REVERT: K 112 MET cc_start: 0.5938 (mtt) cc_final: 0.5340 (mtt) REVERT: K 124 ASN cc_start: 0.7502 (t0) cc_final: 0.7068 (t0) REVERT: K 293 SER cc_start: 0.7644 (p) cc_final: 0.7428 (p) REVERT: K 323 ARG cc_start: 0.7293 (tpp80) cc_final: 0.6906 (mtt-85) REVERT: K 330 LEU cc_start: 0.5410 (mt) cc_final: 0.4049 (mp) REVERT: K 428 THR cc_start: 0.7797 (p) cc_final: 0.7523 (p) REVERT: L 27 TYR cc_start: 0.7387 (m-80) cc_final: 0.6687 (m-80) REVERT: L 54 TYR cc_start: 0.5873 (t80) cc_final: 0.5539 (t80) REVERT: L 72 LYS cc_start: 0.7099 (mmtt) cc_final: 0.6816 (mmtm) REVERT: L 124 ASN cc_start: 0.7607 (t0) cc_final: 0.7206 (t0) REVERT: L 129 THR cc_start: 0.7839 (m) cc_final: 0.7600 (m) REVERT: L 258 ARG cc_start: 0.7504 (ttm170) cc_final: 0.7254 (ttm-80) REVERT: L 295 LYS cc_start: 0.8679 (ptmt) cc_final: 0.8262 (mtmm) REVERT: L 323 ARG cc_start: 0.7218 (tpp80) cc_final: 0.6943 (mtt-85) REVERT: L 394 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7107 (mm-40) outliers start: 1 outliers final: 0 residues processed: 927 average time/residue: 0.4822 time to fit residues: 724.5266 Evaluate side-chains 850 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 850 time to evaluate : 3.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 236 optimal weight: 0.0570 chunk 131 optimal weight: 8.9990 chunk 353 optimal weight: 0.5980 chunk 289 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 425 optimal weight: 0.0570 chunk 459 optimal weight: 1.9990 chunk 379 optimal weight: 6.9990 chunk 422 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 341 optimal weight: 2.9990 overall best weight: 1.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 412 GLN B 412 GLN C 281 ASN C 412 GLN D 175 ASN D 412 GLN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 ASN F 412 GLN G 81 GLN G 412 GLN H 412 GLN I 281 ASN I 412 GLN J 412 GLN K 412 GLN ** L 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 ASN L 412 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37788 Z= 0.192 Angle : 0.624 8.079 51132 Z= 0.315 Chirality : 0.042 0.148 5760 Planarity : 0.005 0.040 6660 Dihedral : 5.200 23.296 5208 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.10 % Allowed : 4.44 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.12), residues: 4632 helix: -0.55 (0.12), residues: 1788 sheet: -1.23 (0.18), residues: 636 loop : -2.90 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 83 HIS 0.003 0.001 HIS I 216 PHE 0.018 0.001 PHE E 356 TYR 0.020 0.001 TYR G 268 ARG 0.011 0.001 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 935 time to evaluate : 4.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.5875 (t80) cc_final: 0.5464 (t80) REVERT: A 64 ARG cc_start: 0.7517 (ttp-110) cc_final: 0.7018 (ttp-110) REVERT: A 112 MET cc_start: 0.6180 (mtm) cc_final: 0.5815 (mtm) REVERT: A 214 TYR cc_start: 0.7641 (m-80) cc_final: 0.7273 (m-10) REVERT: A 323 ARG cc_start: 0.7298 (tpp80) cc_final: 0.6850 (mtt-85) REVERT: A 330 LEU cc_start: 0.5509 (mt) cc_final: 0.4898 (mp) REVERT: A 394 GLN cc_start: 0.7429 (mm-40) cc_final: 0.6331 (mm110) REVERT: A 428 THR cc_start: 0.8064 (p) cc_final: 0.7853 (p) REVERT: B 27 TYR cc_start: 0.6931 (m-80) cc_final: 0.6583 (m-10) REVERT: B 80 MET cc_start: 0.7713 (mmt) cc_final: 0.7360 (mmm) REVERT: B 108 GLU cc_start: 0.7305 (mp0) cc_final: 0.5890 (tm-30) REVERT: B 112 MET cc_start: 0.5798 (mtt) cc_final: 0.5507 (mtt) REVERT: B 116 ILE cc_start: 0.6444 (mm) cc_final: 0.6228 (mm) REVERT: B 124 ASN cc_start: 0.7468 (t0) cc_final: 0.7027 (t0) REVERT: B 323 ARG cc_start: 0.7258 (tpp80) cc_final: 0.6960 (mtt-85) REVERT: B 330 LEU cc_start: 0.5354 (mt) cc_final: 0.4784 (mp) REVERT: B 389 TYR cc_start: 0.7687 (t80) cc_final: 0.7234 (t80) REVERT: B 428 THR cc_start: 0.7789 (p) cc_final: 0.7550 (p) REVERT: C 27 TYR cc_start: 0.7323 (m-80) cc_final: 0.6472 (m-80) REVERT: C 54 TYR cc_start: 0.5642 (t80) cc_final: 0.5361 (t80) REVERT: C 80 MET cc_start: 0.7642 (mmt) cc_final: 0.7421 (mmt) REVERT: C 124 ASN cc_start: 0.7368 (t0) cc_final: 0.7166 (t0) REVERT: C 129 THR cc_start: 0.7951 (m) cc_final: 0.7726 (m) REVERT: C 132 GLU cc_start: 0.6922 (tt0) cc_final: 0.6698 (tt0) REVERT: C 295 LYS cc_start: 0.8673 (ptmt) cc_final: 0.8288 (mtmm) REVERT: C 311 LEU cc_start: 0.8104 (tp) cc_final: 0.7719 (tt) REVERT: C 323 ARG cc_start: 0.7222 (tpp80) cc_final: 0.6880 (mtt-85) REVERT: C 394 GLN cc_start: 0.7542 (mm-40) cc_final: 0.6788 (mm-40) REVERT: C 395 GLU cc_start: 0.6710 (mm-30) cc_final: 0.6227 (mm-30) REVERT: D 54 TYR cc_start: 0.5882 (t80) cc_final: 0.5510 (t80) REVERT: D 64 ARG cc_start: 0.7470 (ttp-110) cc_final: 0.7040 (ttp-110) REVERT: D 124 ASN cc_start: 0.7472 (t0) cc_final: 0.7218 (t0) REVERT: D 323 ARG cc_start: 0.7271 (tpp80) cc_final: 0.6858 (mtt-85) REVERT: D 330 LEU cc_start: 0.5525 (mt) cc_final: 0.4973 (mp) REVERT: D 394 GLN cc_start: 0.7119 (mm-40) cc_final: 0.6602 (mm-40) REVERT: E 27 TYR cc_start: 0.6772 (m-80) cc_final: 0.6472 (m-10) REVERT: E 80 MET cc_start: 0.7729 (mmt) cc_final: 0.7304 (mmm) REVERT: E 124 ASN cc_start: 0.7317 (t0) cc_final: 0.6973 (t0) REVERT: E 323 ARG cc_start: 0.7251 (tpp80) cc_final: 0.6974 (mtt-85) REVERT: E 330 LEU cc_start: 0.5190 (mt) cc_final: 0.4622 (mp) REVERT: E 389 TYR cc_start: 0.7606 (t80) cc_final: 0.7220 (t80) REVERT: E 428 THR cc_start: 0.7817 (p) cc_final: 0.7606 (p) REVERT: F 27 TYR cc_start: 0.7413 (m-80) cc_final: 0.6605 (m-10) REVERT: F 54 TYR cc_start: 0.5331 (t80) cc_final: 0.5078 (t80) REVERT: F 80 MET cc_start: 0.7646 (mmt) cc_final: 0.7362 (mmt) REVERT: F 124 ASN cc_start: 0.7369 (t0) cc_final: 0.7017 (t0) REVERT: F 129 THR cc_start: 0.7959 (m) cc_final: 0.7733 (m) REVERT: F 256 MET cc_start: 0.5399 (ppp) cc_final: 0.5136 (ptt) REVERT: F 295 LYS cc_start: 0.8733 (ptmt) cc_final: 0.8283 (mtmm) REVERT: F 323 ARG cc_start: 0.7217 (tpp80) cc_final: 0.6834 (mtt-85) REVERT: F 357 MET cc_start: 0.7679 (tpp) cc_final: 0.7476 (tpp) REVERT: F 395 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6365 (mm-30) REVERT: G 54 TYR cc_start: 0.5917 (t80) cc_final: 0.5460 (t80) REVERT: G 64 ARG cc_start: 0.7487 (ttp-110) cc_final: 0.7009 (ttp-110) REVERT: G 112 MET cc_start: 0.6150 (mtm) cc_final: 0.5809 (mtm) REVERT: G 214 TYR cc_start: 0.7622 (m-80) cc_final: 0.7278 (m-10) REVERT: G 323 ARG cc_start: 0.7272 (tpp80) cc_final: 0.6814 (mtt-85) REVERT: G 330 LEU cc_start: 0.5663 (mt) cc_final: 0.5084 (mp) REVERT: G 394 GLN cc_start: 0.7150 (mm-40) cc_final: 0.6604 (mm-40) REVERT: G 428 THR cc_start: 0.8080 (p) cc_final: 0.7824 (p) REVERT: H 27 TYR cc_start: 0.6934 (m-80) cc_final: 0.6503 (m-10) REVERT: H 80 MET cc_start: 0.7702 (mmt) cc_final: 0.7346 (mmm) REVERT: H 108 GLU cc_start: 0.7301 (mp0) cc_final: 0.5924 (tm-30) REVERT: H 112 MET cc_start: 0.5633 (mtt) cc_final: 0.5345 (mtt) REVERT: H 124 ASN cc_start: 0.7502 (t0) cc_final: 0.7054 (t0) REVERT: H 323 ARG cc_start: 0.7246 (tpp80) cc_final: 0.6958 (mtt-85) REVERT: H 330 LEU cc_start: 0.5293 (mt) cc_final: 0.4731 (mp) REVERT: H 389 TYR cc_start: 0.7640 (t80) cc_final: 0.7194 (t80) REVERT: I 27 TYR cc_start: 0.7292 (m-80) cc_final: 0.6482 (m-80) REVERT: I 54 TYR cc_start: 0.5752 (t80) cc_final: 0.5469 (t80) REVERT: I 72 LYS cc_start: 0.7211 (mmtt) cc_final: 0.6810 (mttt) REVERT: I 116 ILE cc_start: 0.5982 (mm) cc_final: 0.5724 (mm) REVERT: I 132 GLU cc_start: 0.6845 (tt0) cc_final: 0.6634 (tt0) REVERT: I 256 MET cc_start: 0.5460 (ppp) cc_final: 0.5224 (ptt) REVERT: I 294 SER cc_start: 0.8099 (t) cc_final: 0.7846 (m) REVERT: I 307 GLN cc_start: 0.7884 (mp10) cc_final: 0.7668 (mt0) REVERT: I 323 ARG cc_start: 0.7203 (tpp80) cc_final: 0.6798 (mtt-85) REVERT: I 357 MET cc_start: 0.7797 (tpp) cc_final: 0.7348 (tpp) REVERT: I 394 GLN cc_start: 0.7498 (mm-40) cc_final: 0.6855 (mm-40) REVERT: I 395 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6369 (mm-30) REVERT: J 54 TYR cc_start: 0.5926 (t80) cc_final: 0.5488 (t80) REVERT: J 64 ARG cc_start: 0.7493 (ttp-110) cc_final: 0.7003 (ttp-110) REVERT: J 112 MET cc_start: 0.6191 (mtm) cc_final: 0.5835 (mtm) REVERT: J 214 TYR cc_start: 0.7596 (m-80) cc_final: 0.7250 (m-10) REVERT: J 323 ARG cc_start: 0.7299 (tpp80) cc_final: 0.6841 (mtt-85) REVERT: J 330 LEU cc_start: 0.5646 (mt) cc_final: 0.4993 (mp) REVERT: K 80 MET cc_start: 0.7743 (mmt) cc_final: 0.7418 (mmm) REVERT: K 108 GLU cc_start: 0.7242 (mp0) cc_final: 0.5582 (tm-30) REVERT: K 112 MET cc_start: 0.5852 (mtt) cc_final: 0.5407 (mtt) REVERT: K 116 ILE cc_start: 0.6198 (mm) cc_final: 0.5980 (mm) REVERT: K 124 ASN cc_start: 0.7380 (t0) cc_final: 0.6964 (t0) REVERT: K 323 ARG cc_start: 0.7254 (tpp80) cc_final: 0.6960 (mtt-85) REVERT: K 330 LEU cc_start: 0.5402 (mt) cc_final: 0.4804 (mp) REVERT: K 389 TYR cc_start: 0.7604 (t80) cc_final: 0.7181 (t80) REVERT: K 428 THR cc_start: 0.7849 (p) cc_final: 0.7591 (p) REVERT: L 27 TYR cc_start: 0.7310 (m-80) cc_final: 0.6576 (m-80) REVERT: L 54 TYR cc_start: 0.5852 (t80) cc_final: 0.5482 (t80) REVERT: L 116 ILE cc_start: 0.5965 (mm) cc_final: 0.5730 (mm) REVERT: L 124 ASN cc_start: 0.7423 (t0) cc_final: 0.7149 (t0) REVERT: L 256 MET cc_start: 0.5545 (ppp) cc_final: 0.5196 (ptt) REVERT: L 295 LYS cc_start: 0.8682 (ptmt) cc_final: 0.8301 (mtmm) REVERT: L 323 ARG cc_start: 0.7245 (tpp80) cc_final: 0.6873 (mtt-85) REVERT: L 394 GLN cc_start: 0.7611 (mm-40) cc_final: 0.6914 (mm-40) REVERT: L 395 GLU cc_start: 0.6714 (mm-30) cc_final: 0.6240 (mm-30) outliers start: 4 outliers final: 4 residues processed: 939 average time/residue: 0.5165 time to fit residues: 795.7132 Evaluate side-chains 839 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 835 time to evaluate : 3.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 420 optimal weight: 2.9990 chunk 320 optimal weight: 6.9990 chunk 220 optimal weight: 0.0570 chunk 47 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 427 optimal weight: 6.9990 chunk 452 optimal weight: 0.6980 chunk 223 optimal weight: 8.9990 chunk 404 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 124 ASN ** J 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37788 Z= 0.221 Angle : 0.629 8.075 51132 Z= 0.316 Chirality : 0.042 0.156 5760 Planarity : 0.004 0.056 6660 Dihedral : 5.020 22.893 5208 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.12), residues: 4632 helix: -0.12 (0.13), residues: 1788 sheet: -0.96 (0.18), residues: 636 loop : -2.79 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 83 HIS 0.004 0.001 HIS L 216 PHE 0.016 0.002 PHE E 356 TYR 0.023 0.001 TYR K 268 ARG 0.018 0.001 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 914 time to evaluate : 4.028 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: A 27 TYR cc_start: 0.7175 (m-80) cc_final: 0.6917 (m-10) REVERT: A 54 TYR cc_start: 0.5864 (t80) cc_final: 0.5607 (t80) REVERT: A 64 ARG cc_start: 0.7462 (ttp-110) cc_final: 0.7195 (ttp-110) REVERT: A 72 LYS cc_start: 0.7020 (mmtp) cc_final: 0.6818 (mmtp) REVERT: A 112 MET cc_start: 0.6128 (mtm) cc_final: 0.5854 (mtm) REVERT: A 262 GLU cc_start: 0.6842 (pt0) cc_final: 0.6594 (pt0) REVERT: A 323 ARG cc_start: 0.7324 (tpp80) cc_final: 0.6853 (mtt-85) REVERT: A 330 LEU cc_start: 0.5563 (mt) cc_final: 0.4890 (mp) REVERT: A 394 GLN cc_start: 0.7126 (mm-40) cc_final: 0.6662 (mm110) REVERT: A 428 THR cc_start: 0.7980 (p) cc_final: 0.7759 (p) REVERT: B 27 TYR cc_start: 0.6869 (m-80) cc_final: 0.6564 (m-10) REVERT: B 72 LYS cc_start: 0.7266 (mmtp) cc_final: 0.6894 (mttt) REVERT: B 80 MET cc_start: 0.7789 (mmt) cc_final: 0.7381 (mmm) REVERT: B 108 GLU cc_start: 0.7290 (mp0) cc_final: 0.5875 (tm-30) REVERT: B 112 MET cc_start: 0.5900 (mtt) cc_final: 0.5477 (mtt) REVERT: B 116 ILE cc_start: 0.6632 (mm) cc_final: 0.6399 (mm) REVERT: B 124 ASN cc_start: 0.7510 (t0) cc_final: 0.7046 (t0) REVERT: B 323 ARG cc_start: 0.7265 (tpp80) cc_final: 0.6961 (mtt-85) REVERT: B 330 LEU cc_start: 0.5486 (mt) cc_final: 0.4834 (mp) REVERT: B 349 GLU cc_start: 0.6637 (tp30) cc_final: 0.6417 (tp30) REVERT: B 428 THR cc_start: 0.7608 (p) cc_final: 0.7356 (p) REVERT: C 27 TYR cc_start: 0.7322 (m-80) cc_final: 0.6573 (m-80) REVERT: C 80 MET cc_start: 0.7601 (mmt) cc_final: 0.7349 (mmt) REVERT: C 116 ILE cc_start: 0.6330 (mm) cc_final: 0.6093 (mm) REVERT: C 124 ASN cc_start: 0.7440 (t0) cc_final: 0.7154 (t0) REVERT: C 256 MET cc_start: 0.4594 (ptt) cc_final: 0.4325 (ptt) REVERT: C 295 LYS cc_start: 0.8573 (ptmt) cc_final: 0.8250 (mtmm) REVERT: C 323 ARG cc_start: 0.7233 (tpp80) cc_final: 0.6949 (mtt-85) REVERT: C 349 GLU cc_start: 0.6551 (tp30) cc_final: 0.5994 (tp30) REVERT: C 394 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7241 (mm-40) REVERT: C 395 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6517 (mm-30) REVERT: D 54 TYR cc_start: 0.5884 (t80) cc_final: 0.5574 (t80) REVERT: D 64 ARG cc_start: 0.7524 (ttp-110) cc_final: 0.7297 (ttp-110) REVERT: D 72 LYS cc_start: 0.7017 (mmtt) cc_final: 0.6746 (mmtm) REVERT: D 124 ASN cc_start: 0.7570 (t0) cc_final: 0.7034 (t0) REVERT: D 235 MET cc_start: 0.5266 (tpt) cc_final: 0.4825 (mmm) REVERT: D 262 GLU cc_start: 0.6874 (pt0) cc_final: 0.6645 (pt0) REVERT: D 323 ARG cc_start: 0.7309 (tpp80) cc_final: 0.6876 (mtt-85) REVERT: D 330 LEU cc_start: 0.5608 (mt) cc_final: 0.4996 (mp) REVERT: D 356 PHE cc_start: 0.6232 (m-80) cc_final: 0.6026 (m-80) REVERT: D 394 GLN cc_start: 0.7145 (mm-40) cc_final: 0.6538 (mm-40) REVERT: E 27 TYR cc_start: 0.6726 (m-80) cc_final: 0.6462 (m-10) REVERT: E 72 LYS cc_start: 0.7532 (mmtt) cc_final: 0.7178 (mttt) REVERT: E 80 MET cc_start: 0.7737 (mmt) cc_final: 0.7359 (mmm) REVERT: E 108 GLU cc_start: 0.7164 (mp0) cc_final: 0.5608 (tm-30) REVERT: E 112 MET cc_start: 0.5700 (mtt) cc_final: 0.5366 (mtt) REVERT: E 124 ASN cc_start: 0.7272 (t0) cc_final: 0.6920 (t0) REVERT: E 323 ARG cc_start: 0.7395 (tpp80) cc_final: 0.7071 (mtt-85) REVERT: E 330 LEU cc_start: 0.5328 (mt) cc_final: 0.4755 (mp) REVERT: E 394 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7554 (mm110) REVERT: E 428 THR cc_start: 0.7681 (p) cc_final: 0.7448 (p) REVERT: F 27 TYR cc_start: 0.7419 (m-80) cc_final: 0.6555 (m-80) REVERT: F 80 MET cc_start: 0.7688 (mmt) cc_final: 0.7446 (mmt) REVERT: F 124 ASN cc_start: 0.7499 (t0) cc_final: 0.7107 (t0) REVERT: F 295 LYS cc_start: 0.8678 (ptmt) cc_final: 0.8357 (mtmt) REVERT: F 323 ARG cc_start: 0.7212 (tpp80) cc_final: 0.6869 (mtt-85) REVERT: F 349 GLU cc_start: 0.6969 (tt0) cc_final: 0.6762 (tt0) REVERT: F 395 GLU cc_start: 0.6687 (mm-30) cc_final: 0.6484 (mm-30) REVERT: G 54 TYR cc_start: 0.5963 (t80) cc_final: 0.5675 (t80) REVERT: G 64 ARG cc_start: 0.7483 (ttp-110) cc_final: 0.7203 (ttp-110) REVERT: G 112 MET cc_start: 0.6122 (mtm) cc_final: 0.5796 (mtm) REVERT: G 262 GLU cc_start: 0.7019 (pt0) cc_final: 0.6811 (pt0) REVERT: G 323 ARG cc_start: 0.7225 (tpp80) cc_final: 0.6793 (mtt-85) REVERT: G 330 LEU cc_start: 0.5693 (mt) cc_final: 0.5048 (mp) REVERT: H 27 TYR cc_start: 0.6878 (m-80) cc_final: 0.6479 (m-10) REVERT: H 72 LYS cc_start: 0.7221 (mmtp) cc_final: 0.6862 (mttt) REVERT: H 80 MET cc_start: 0.7786 (mmt) cc_final: 0.7432 (mmm) REVERT: H 108 GLU cc_start: 0.7269 (mp0) cc_final: 0.5602 (tm-30) REVERT: H 124 ASN cc_start: 0.7330 (t0) cc_final: 0.6886 (t0) REVERT: H 323 ARG cc_start: 0.7346 (tpp80) cc_final: 0.6975 (mtt-85) REVERT: H 330 LEU cc_start: 0.5663 (mt) cc_final: 0.4998 (mp) REVERT: H 389 TYR cc_start: 0.7538 (t80) cc_final: 0.7175 (t80) REVERT: H 394 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7303 (mm-40) REVERT: H 428 THR cc_start: 0.7699 (p) cc_final: 0.7430 (p) REVERT: I 27 TYR cc_start: 0.7293 (m-80) cc_final: 0.6513 (m-80) REVERT: I 54 TYR cc_start: 0.5556 (t80) cc_final: 0.5298 (t80) REVERT: I 72 LYS cc_start: 0.7100 (mmtt) cc_final: 0.6718 (mttt) REVERT: I 124 ASN cc_start: 0.7603 (t0) cc_final: 0.7203 (t0) REVERT: I 294 SER cc_start: 0.7979 (t) cc_final: 0.7750 (m) REVERT: I 323 ARG cc_start: 0.7189 (tpp80) cc_final: 0.6831 (mtt-85) REVERT: I 349 GLU cc_start: 0.6525 (tp30) cc_final: 0.6039 (tp30) REVERT: I 395 GLU cc_start: 0.6760 (mm-30) cc_final: 0.6390 (mm-30) REVERT: J 54 TYR cc_start: 0.5947 (t80) cc_final: 0.5703 (t80) REVERT: J 64 ARG cc_start: 0.7514 (ttp-110) cc_final: 0.7233 (ttp-110) REVERT: J 72 LYS cc_start: 0.6989 (mmtp) cc_final: 0.6736 (mmtp) REVERT: J 112 MET cc_start: 0.6140 (mtm) cc_final: 0.5853 (mtm) REVERT: J 323 ARG cc_start: 0.7268 (tpp80) cc_final: 0.6827 (mtt-85) REVERT: J 330 LEU cc_start: 0.5644 (mt) cc_final: 0.4929 (mp) REVERT: J 394 GLN cc_start: 0.7141 (mm-40) cc_final: 0.6637 (mm110) REVERT: J 428 THR cc_start: 0.8094 (p) cc_final: 0.7861 (p) REVERT: K 72 LYS cc_start: 0.7206 (mmtp) cc_final: 0.6862 (mttt) REVERT: K 80 MET cc_start: 0.7781 (mmt) cc_final: 0.7419 (mmm) REVERT: K 108 GLU cc_start: 0.7215 (mp0) cc_final: 0.5585 (tm-30) REVERT: K 112 MET cc_start: 0.5914 (mtt) cc_final: 0.5494 (mtt) REVERT: K 116 ILE cc_start: 0.6354 (mm) cc_final: 0.6149 (mm) REVERT: K 124 ASN cc_start: 0.7365 (t0) cc_final: 0.6909 (t0) REVERT: K 323 ARG cc_start: 0.7330 (tpp80) cc_final: 0.6982 (mtt-85) REVERT: K 330 LEU cc_start: 0.5487 (mt) cc_final: 0.4786 (mp) REVERT: K 349 GLU cc_start: 0.6653 (tp30) cc_final: 0.6417 (tp30) REVERT: K 389 TYR cc_start: 0.7569 (t80) cc_final: 0.7143 (t80) REVERT: L 27 TYR cc_start: 0.7283 (m-80) cc_final: 0.6539 (m-80) REVERT: L 54 TYR cc_start: 0.5564 (t80) cc_final: 0.5351 (t80) REVERT: L 124 ASN cc_start: 0.7534 (t0) cc_final: 0.7246 (t0) REVERT: L 323 ARG cc_start: 0.7265 (tpp80) cc_final: 0.6912 (mtt-85) REVERT: L 349 GLU cc_start: 0.6488 (tp30) cc_final: 0.6184 (tp30) REVERT: L 395 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6207 (mm-30) outliers start: 0 outliers final: 0 residues processed: 914 average time/residue: 0.4685 time to fit residues: 698.9018 Evaluate side-chains 839 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 839 time to evaluate : 3.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 376 optimal weight: 0.1980 chunk 256 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 336 optimal weight: 0.0870 chunk 186 optimal weight: 0.8980 chunk 386 optimal weight: 3.9990 chunk 312 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 230 optimal weight: 0.8980 chunk 406 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 136 GLN B 136 GLN B 178 GLN C 307 GLN E 136 GLN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 ASN F 307 GLN G 32 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN H 178 GLN I 281 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 GLN K 178 GLN ** K 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37788 Z= 0.198 Angle : 0.615 11.537 51132 Z= 0.308 Chirality : 0.042 0.170 5760 Planarity : 0.004 0.079 6660 Dihedral : 4.933 23.229 5208 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.05 % Allowed : 2.60 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.12), residues: 4632 helix: 0.22 (0.13), residues: 1788 sheet: -0.91 (0.20), residues: 564 loop : -2.65 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 58 HIS 0.004 0.001 HIS L 216 PHE 0.011 0.001 PHE K 356 TYR 0.028 0.001 TYR G 27 ARG 0.010 0.001 ARG D 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 905 time to evaluate : 4.005 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: A 64 ARG cc_start: 0.7476 (ttp-110) cc_final: 0.7199 (ttp-110) REVERT: A 72 LYS cc_start: 0.7027 (mmtp) cc_final: 0.6774 (mmtm) REVERT: A 112 MET cc_start: 0.6077 (mtm) cc_final: 0.5764 (mtm) REVERT: A 124 ASN cc_start: 0.7116 (t0) cc_final: 0.6819 (t0) REVERT: A 158 MET cc_start: 0.7370 (mmm) cc_final: 0.7013 (mtt) REVERT: A 323 ARG cc_start: 0.7272 (tpp80) cc_final: 0.6874 (mtt-85) REVERT: A 330 LEU cc_start: 0.5580 (mt) cc_final: 0.4888 (mp) REVERT: B 27 TYR cc_start: 0.6611 (m-80) cc_final: 0.6245 (m-10) REVERT: B 72 LYS cc_start: 0.7193 (mmtp) cc_final: 0.6858 (mttt) REVERT: B 80 MET cc_start: 0.7805 (mmt) cc_final: 0.7421 (mmm) REVERT: B 108 GLU cc_start: 0.7223 (mp0) cc_final: 0.5847 (tm-30) REVERT: B 112 MET cc_start: 0.5920 (mtt) cc_final: 0.5567 (mtt) REVERT: B 116 ILE cc_start: 0.6657 (mm) cc_final: 0.6444 (mm) REVERT: B 124 ASN cc_start: 0.7492 (t0) cc_final: 0.7035 (t0) REVERT: B 323 ARG cc_start: 0.7337 (tpp80) cc_final: 0.6994 (mtt-85) REVERT: B 349 GLU cc_start: 0.6796 (tp30) cc_final: 0.6498 (tp30) REVERT: B 428 THR cc_start: 0.7645 (p) cc_final: 0.7266 (p) REVERT: C 27 TYR cc_start: 0.7245 (m-80) cc_final: 0.6500 (m-80) REVERT: C 80 MET cc_start: 0.7593 (mmt) cc_final: 0.7365 (mmt) REVERT: C 124 ASN cc_start: 0.7482 (t0) cc_final: 0.7175 (t0) REVERT: C 255 ARG cc_start: 0.6430 (mpp80) cc_final: 0.5456 (mtm110) REVERT: C 256 MET cc_start: 0.4632 (ptt) cc_final: 0.4402 (ptt) REVERT: C 323 ARG cc_start: 0.7199 (tpp80) cc_final: 0.6944 (mtt-85) REVERT: C 349 GLU cc_start: 0.6583 (tp30) cc_final: 0.5998 (tp30) REVERT: C 394 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7130 (mm-40) REVERT: D 54 TYR cc_start: 0.5896 (t80) cc_final: 0.5613 (t80) REVERT: D 72 LYS cc_start: 0.6857 (mmtt) cc_final: 0.6631 (mmtm) REVERT: D 124 ASN cc_start: 0.7587 (t0) cc_final: 0.7042 (t0) REVERT: D 235 MET cc_start: 0.5249 (tpt) cc_final: 0.4793 (mmm) REVERT: D 289 MET cc_start: 0.7335 (ppp) cc_final: 0.6926 (ttp) REVERT: D 323 ARG cc_start: 0.7266 (tpp80) cc_final: 0.6870 (mtt-85) REVERT: D 330 LEU cc_start: 0.5580 (mt) cc_final: 0.4837 (mp) REVERT: D 394 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6495 (mm-40) REVERT: E 27 TYR cc_start: 0.6653 (m-80) cc_final: 0.6301 (m-10) REVERT: E 72 LYS cc_start: 0.7530 (mmtt) cc_final: 0.7161 (mttt) REVERT: E 80 MET cc_start: 0.7866 (mmt) cc_final: 0.7464 (mmm) REVERT: E 124 ASN cc_start: 0.7268 (t0) cc_final: 0.6909 (t0) REVERT: E 323 ARG cc_start: 0.7390 (tpp80) cc_final: 0.7087 (mtt-85) REVERT: E 330 LEU cc_start: 0.5560 (mt) cc_final: 0.4917 (mp) REVERT: E 349 GLU cc_start: 0.6713 (tp30) cc_final: 0.6363 (tp30) REVERT: F 27 TYR cc_start: 0.7279 (m-80) cc_final: 0.6467 (m-80) REVERT: F 72 LYS cc_start: 0.7051 (mmtm) cc_final: 0.6824 (mttm) REVERT: F 80 MET cc_start: 0.7695 (mmt) cc_final: 0.7481 (mmt) REVERT: F 256 MET cc_start: 0.5660 (ppp) cc_final: 0.5179 (ppp) REVERT: F 262 GLU cc_start: 0.7389 (pt0) cc_final: 0.7041 (pt0) REVERT: F 295 LYS cc_start: 0.8736 (ptmt) cc_final: 0.8292 (mtmm) REVERT: F 323 ARG cc_start: 0.7221 (tpp80) cc_final: 0.6928 (mtt-85) REVERT: F 395 GLU cc_start: 0.6685 (mm-30) cc_final: 0.6479 (mm-30) REVERT: G 54 TYR cc_start: 0.5885 (t80) cc_final: 0.5632 (t80) REVERT: G 64 ARG cc_start: 0.7472 (ttp-110) cc_final: 0.7015 (ttp-110) REVERT: G 72 LYS cc_start: 0.6967 (mmtp) cc_final: 0.6689 (mmtm) REVERT: G 112 MET cc_start: 0.6042 (mtm) cc_final: 0.5723 (mtm) REVERT: G 323 ARG cc_start: 0.7272 (tpp80) cc_final: 0.6787 (mtt-85) REVERT: G 330 LEU cc_start: 0.5490 (mt) cc_final: 0.4924 (mp) REVERT: H 27 TYR cc_start: 0.6806 (m-80) cc_final: 0.6362 (m-10) REVERT: H 72 LYS cc_start: 0.7195 (mmtp) cc_final: 0.6783 (mttt) REVERT: H 74 MET cc_start: 0.7849 (tpp) cc_final: 0.7451 (tpp) REVERT: H 80 MET cc_start: 0.7796 (mmt) cc_final: 0.7399 (mmm) REVERT: H 108 GLU cc_start: 0.7158 (mp0) cc_final: 0.5900 (tm-30) REVERT: H 112 MET cc_start: 0.5815 (mtt) cc_final: 0.5472 (mtt) REVERT: H 124 ASN cc_start: 0.7379 (t0) cc_final: 0.6854 (t0) REVERT: H 323 ARG cc_start: 0.7253 (tpp80) cc_final: 0.6915 (mtt-85) REVERT: H 349 GLU cc_start: 0.6767 (tp30) cc_final: 0.6453 (tp30) REVERT: H 389 TYR cc_start: 0.7514 (t80) cc_final: 0.7204 (t80) REVERT: I 27 TYR cc_start: 0.7137 (m-80) cc_final: 0.6450 (m-80) REVERT: I 124 ASN cc_start: 0.7556 (t0) cc_final: 0.7123 (t0) REVERT: I 294 SER cc_start: 0.8035 (t) cc_final: 0.7750 (m) REVERT: I 323 ARG cc_start: 0.7201 (tpp80) cc_final: 0.6895 (mtt-85) REVERT: I 349 GLU cc_start: 0.6505 (tp30) cc_final: 0.6176 (tp30) REVERT: I 395 GLU cc_start: 0.6714 (mm-30) cc_final: 0.6337 (mm-30) REVERT: J 54 TYR cc_start: 0.5940 (t80) cc_final: 0.5694 (t80) REVERT: J 64 ARG cc_start: 0.7488 (ttp-110) cc_final: 0.7207 (ttp-110) REVERT: J 72 LYS cc_start: 0.7008 (mmtp) cc_final: 0.6735 (mmtm) REVERT: J 112 MET cc_start: 0.6070 (mtm) cc_final: 0.5783 (mtm) REVERT: J 124 ASN cc_start: 0.7153 (t0) cc_final: 0.6952 (t0) REVERT: J 323 ARG cc_start: 0.7303 (tpp80) cc_final: 0.6846 (mtt-85) REVERT: J 330 LEU cc_start: 0.5560 (mt) cc_final: 0.4942 (mp) REVERT: J 394 GLN cc_start: 0.7182 (mm-40) cc_final: 0.6567 (mm110) REVERT: K 72 LYS cc_start: 0.7194 (mmtp) cc_final: 0.6850 (mttt) REVERT: K 108 GLU cc_start: 0.7125 (mp0) cc_final: 0.5536 (tm-30) REVERT: K 112 MET cc_start: 0.5862 (mtt) cc_final: 0.5478 (mtt) REVERT: K 116 ILE cc_start: 0.6500 (mm) cc_final: 0.6278 (mm) REVERT: K 124 ASN cc_start: 0.7392 (t0) cc_final: 0.6951 (t0) REVERT: K 323 ARG cc_start: 0.7356 (tpp80) cc_final: 0.6924 (mtt-85) REVERT: K 349 GLU cc_start: 0.6846 (tp30) cc_final: 0.6584 (tp30) REVERT: K 389 TYR cc_start: 0.7551 (t80) cc_final: 0.7189 (t80) REVERT: L 27 TYR cc_start: 0.7209 (m-80) cc_final: 0.6475 (m-80) REVERT: L 54 TYR cc_start: 0.5564 (t80) cc_final: 0.5284 (t80) REVERT: L 124 ASN cc_start: 0.7528 (t0) cc_final: 0.7246 (t0) REVERT: L 323 ARG cc_start: 0.7170 (tpp80) cc_final: 0.6884 (mtt-85) REVERT: L 349 GLU cc_start: 0.6543 (tp30) cc_final: 0.5977 (tp30) REVERT: L 389 TYR cc_start: 0.7862 (t80) cc_final: 0.7163 (t80) REVERT: L 394 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7418 (mm-40) REVERT: L 395 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6499 (mm-30) outliers start: 2 outliers final: 1 residues processed: 907 average time/residue: 0.4732 time to fit residues: 700.2971 Evaluate side-chains 825 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 824 time to evaluate : 3.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 152 optimal weight: 0.8980 chunk 407 optimal weight: 7.9990 chunk 89 optimal weight: 0.0370 chunk 265 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 452 optimal weight: 0.5980 chunk 375 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 chunk 237 optimal weight: 4.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 178 GLN B 394 GLN D 178 GLN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN G 124 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 307 GLN J 81 GLN K 178 GLN K 394 GLN L 281 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37788 Z= 0.202 Angle : 0.614 8.750 51132 Z= 0.305 Chirality : 0.042 0.173 5760 Planarity : 0.004 0.097 6660 Dihedral : 4.859 22.847 5208 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.12), residues: 4632 helix: 0.50 (0.13), residues: 1764 sheet: -0.51 (0.21), residues: 492 loop : -2.56 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 83 HIS 0.003 0.001 HIS L 216 PHE 0.017 0.001 PHE I 78 TYR 0.025 0.001 TYR A 27 ARG 0.012 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 890 time to evaluate : 4.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 TYR cc_start: 0.6896 (m-80) cc_final: 0.6691 (m-10) REVERT: A 64 ARG cc_start: 0.7415 (ttp-110) cc_final: 0.7171 (ttp-110) REVERT: A 72 LYS cc_start: 0.7030 (mmtp) cc_final: 0.6771 (mmtm) REVERT: A 112 MET cc_start: 0.6054 (mtm) cc_final: 0.5725 (mtm) REVERT: A 124 ASN cc_start: 0.7332 (t0) cc_final: 0.7033 (t0) REVERT: A 323 ARG cc_start: 0.7352 (tpp80) cc_final: 0.6873 (mtt-85) REVERT: A 330 LEU cc_start: 0.5606 (mt) cc_final: 0.4849 (mp) REVERT: B 27 TYR cc_start: 0.6672 (m-80) cc_final: 0.6314 (m-10) REVERT: B 72 LYS cc_start: 0.7233 (mmtp) cc_final: 0.6866 (mttt) REVERT: B 80 MET cc_start: 0.7836 (mmt) cc_final: 0.7446 (mmm) REVERT: B 108 GLU cc_start: 0.7203 (mp0) cc_final: 0.5855 (tm-30) REVERT: B 112 MET cc_start: 0.5929 (mtt) cc_final: 0.5530 (mtt) REVERT: B 116 ILE cc_start: 0.6664 (mm) cc_final: 0.6435 (mm) REVERT: B 323 ARG cc_start: 0.7384 (tpp80) cc_final: 0.6964 (mtt-85) REVERT: B 349 GLU cc_start: 0.6814 (tp30) cc_final: 0.6543 (tp30) REVERT: B 389 TYR cc_start: 0.7625 (t80) cc_final: 0.7155 (t80) REVERT: B 394 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7083 (mm-40) REVERT: B 428 THR cc_start: 0.7517 (p) cc_final: 0.7266 (p) REVERT: C 27 TYR cc_start: 0.7205 (m-80) cc_final: 0.6486 (m-80) REVERT: C 72 LYS cc_start: 0.7147 (mmpt) cc_final: 0.6790 (mttt) REVERT: C 80 MET cc_start: 0.7652 (mmt) cc_final: 0.7401 (mmt) REVERT: C 124 ASN cc_start: 0.7468 (t0) cc_final: 0.7185 (t0) REVERT: C 132 GLU cc_start: 0.6802 (tt0) cc_final: 0.6509 (tt0) REVERT: C 255 ARG cc_start: 0.6597 (mpp80) cc_final: 0.5542 (mtm180) REVERT: C 294 SER cc_start: 0.8135 (t) cc_final: 0.7829 (m) REVERT: C 323 ARG cc_start: 0.7197 (tpp80) cc_final: 0.6864 (mtt-85) REVERT: C 349 GLU cc_start: 0.6554 (tp30) cc_final: 0.5950 (tp30) REVERT: C 357 MET cc_start: 0.7705 (tpt) cc_final: 0.7411 (tpp) REVERT: D 54 TYR cc_start: 0.5812 (t80) cc_final: 0.5522 (t80) REVERT: D 72 LYS cc_start: 0.6889 (mmtt) cc_final: 0.6679 (mmtt) REVERT: D 124 ASN cc_start: 0.7502 (t0) cc_final: 0.7283 (t0) REVERT: D 179 MET cc_start: 0.5669 (mtm) cc_final: 0.5354 (mtp) REVERT: D 235 MET cc_start: 0.5219 (tpt) cc_final: 0.4707 (mmm) REVERT: D 289 MET cc_start: 0.7459 (ppp) cc_final: 0.6899 (ttp) REVERT: D 323 ARG cc_start: 0.7171 (tpp80) cc_final: 0.6853 (mtt-85) REVERT: D 330 LEU cc_start: 0.5536 (mt) cc_final: 0.4799 (mp) REVERT: D 394 GLN cc_start: 0.7164 (mm-40) cc_final: 0.6402 (mm-40) REVERT: E 27 TYR cc_start: 0.6673 (m-80) cc_final: 0.6278 (m-10) REVERT: E 72 LYS cc_start: 0.7587 (mmtt) cc_final: 0.7192 (mttt) REVERT: E 80 MET cc_start: 0.7894 (mmt) cc_final: 0.7418 (mmm) REVERT: E 108 GLU cc_start: 0.7119 (mp0) cc_final: 0.5623 (tm-30) REVERT: E 112 MET cc_start: 0.5637 (mtt) cc_final: 0.5307 (mtt) REVERT: E 323 ARG cc_start: 0.7412 (tpp80) cc_final: 0.7120 (mtt-85) REVERT: E 349 GLU cc_start: 0.6654 (tp30) cc_final: 0.6283 (tp30) REVERT: F 27 TYR cc_start: 0.7244 (m-80) cc_final: 0.6305 (m-80) REVERT: F 80 MET cc_start: 0.7781 (mmt) cc_final: 0.7499 (mmt) REVERT: F 256 MET cc_start: 0.5728 (ppp) cc_final: 0.5132 (ppp) REVERT: F 262 GLU cc_start: 0.7351 (pt0) cc_final: 0.7003 (pt0) REVERT: F 295 LYS cc_start: 0.8664 (ptmt) cc_final: 0.8439 (mtmt) REVERT: F 323 ARG cc_start: 0.7221 (tpp80) cc_final: 0.6876 (mtt-85) REVERT: F 349 GLU cc_start: 0.6498 (tp30) cc_final: 0.5940 (tp30) REVERT: G 54 TYR cc_start: 0.5891 (t80) cc_final: 0.5651 (t80) REVERT: G 64 ARG cc_start: 0.7410 (ttp-110) cc_final: 0.6959 (ttp-110) REVERT: G 72 LYS cc_start: 0.7007 (mmtp) cc_final: 0.6718 (mmtp) REVERT: G 112 MET cc_start: 0.6015 (mtm) cc_final: 0.5669 (mtm) REVERT: G 124 ASN cc_start: 0.7299 (t0) cc_final: 0.6888 (t0) REVERT: G 235 MET cc_start: 0.5170 (tpt) cc_final: 0.4821 (mmm) REVERT: G 323 ARG cc_start: 0.7211 (tpp80) cc_final: 0.6854 (mtt-85) REVERT: G 330 LEU cc_start: 0.5521 (mt) cc_final: 0.4904 (mp) REVERT: H 27 TYR cc_start: 0.6833 (m-80) cc_final: 0.6321 (m-10) REVERT: H 72 LYS cc_start: 0.7267 (mmtp) cc_final: 0.6891 (mttt) REVERT: H 80 MET cc_start: 0.7767 (mmt) cc_final: 0.7397 (mmm) REVERT: H 108 GLU cc_start: 0.7215 (mp0) cc_final: 0.5575 (tm-30) REVERT: H 124 ASN cc_start: 0.7311 (t0) cc_final: 0.6874 (t0) REVERT: H 323 ARG cc_start: 0.7316 (tpp80) cc_final: 0.6986 (mtt-85) REVERT: H 349 GLU cc_start: 0.6772 (tp30) cc_final: 0.6449 (tp30) REVERT: H 370 THR cc_start: 0.7769 (p) cc_final: 0.7554 (p) REVERT: H 389 TYR cc_start: 0.7501 (t80) cc_final: 0.7118 (t80) REVERT: H 394 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6806 (mm-40) REVERT: H 395 GLU cc_start: 0.6632 (mm-30) cc_final: 0.5972 (mm-30) REVERT: I 27 TYR cc_start: 0.7160 (m-80) cc_final: 0.6325 (m-80) REVERT: I 124 ASN cc_start: 0.7565 (t0) cc_final: 0.7141 (t0) REVERT: I 132 GLU cc_start: 0.6749 (tt0) cc_final: 0.6500 (tt0) REVERT: I 294 SER cc_start: 0.8096 (t) cc_final: 0.7816 (m) REVERT: I 307 GLN cc_start: 0.8051 (mp-120) cc_final: 0.7838 (mp10) REVERT: I 323 ARG cc_start: 0.7234 (tpp80) cc_final: 0.6957 (mtt-85) REVERT: I 349 GLU cc_start: 0.6528 (tp30) cc_final: 0.5948 (tp30) REVERT: I 389 TYR cc_start: 0.7817 (t80) cc_final: 0.7511 (t80) REVERT: I 394 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7467 (mm-40) REVERT: I 395 GLU cc_start: 0.6681 (mm-30) cc_final: 0.6295 (mm-30) REVERT: J 64 ARG cc_start: 0.7458 (ttp-110) cc_final: 0.7199 (ttp-110) REVERT: J 72 LYS cc_start: 0.6967 (mmtp) cc_final: 0.6708 (mmtp) REVERT: J 112 MET cc_start: 0.6048 (mtm) cc_final: 0.5725 (mtm) REVERT: J 124 ASN cc_start: 0.7361 (t0) cc_final: 0.7038 (t0) REVERT: J 323 ARG cc_start: 0.7291 (tpp80) cc_final: 0.6805 (mtt-85) REVERT: J 330 LEU cc_start: 0.5475 (mt) cc_final: 0.4779 (mp) REVERT: K 72 LYS cc_start: 0.7290 (mmtp) cc_final: 0.6887 (mttt) REVERT: K 108 GLU cc_start: 0.7160 (mp0) cc_final: 0.5543 (tm-30) REVERT: K 112 MET cc_start: 0.5936 (mtt) cc_final: 0.5476 (mtt) REVERT: K 116 ILE cc_start: 0.6581 (mm) cc_final: 0.6372 (mm) REVERT: K 124 ASN cc_start: 0.7303 (t0) cc_final: 0.6865 (t0) REVERT: K 149 GLU cc_start: 0.7476 (mp0) cc_final: 0.7187 (mp0) REVERT: K 323 ARG cc_start: 0.7319 (tpp80) cc_final: 0.6972 (mtt-85) REVERT: K 349 GLU cc_start: 0.6842 (tp30) cc_final: 0.6557 (tp30) REVERT: K 389 TYR cc_start: 0.7577 (t80) cc_final: 0.7211 (t80) REVERT: K 394 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7066 (mm-40) REVERT: L 27 TYR cc_start: 0.7186 (m-80) cc_final: 0.6481 (m-80) REVERT: L 54 TYR cc_start: 0.5381 (t80) cc_final: 0.5075 (t80) REVERT: L 124 ASN cc_start: 0.7530 (t0) cc_final: 0.7265 (t0) REVERT: L 323 ARG cc_start: 0.7217 (tpp80) cc_final: 0.6921 (mtt-85) REVERT: L 349 GLU cc_start: 0.6545 (tp30) cc_final: 0.5962 (tp30) REVERT: L 394 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7510 (mm-40) REVERT: L 395 GLU cc_start: 0.6678 (mm-30) cc_final: 0.6356 (mm-30) outliers start: 2 outliers final: 0 residues processed: 891 average time/residue: 0.4695 time to fit residues: 690.8307 Evaluate side-chains 830 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 830 time to evaluate : 4.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 436 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 257 optimal weight: 0.7980 chunk 330 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 381 optimal weight: 0.8980 chunk 252 optimal weight: 8.9990 chunk 451 optimal weight: 1.9990 chunk 282 optimal weight: 0.4980 chunk 275 optimal weight: 0.2980 chunk 208 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 124 ASN B 136 GLN B 178 GLN C 394 GLN D 81 GLN D 136 GLN D 178 GLN E 124 ASN E 178 GLN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN G 136 GLN H 136 GLN H 178 GLN I 307 GLN J 136 GLN J 363 GLN K 178 GLN ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37788 Z= 0.184 Angle : 0.611 9.618 51132 Z= 0.303 Chirality : 0.042 0.185 5760 Planarity : 0.004 0.071 6660 Dihedral : 4.784 22.368 5208 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.05 % Allowed : 2.28 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.12), residues: 4632 helix: 0.42 (0.13), residues: 1836 sheet: -0.42 (0.21), residues: 492 loop : -2.53 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 83 HIS 0.004 0.001 HIS C 216 PHE 0.019 0.001 PHE C 78 TYR 0.022 0.001 TYR L 389 ARG 0.009 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 887 time to evaluate : 4.071 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: A 27 TYR cc_start: 0.6477 (m-80) cc_final: 0.6154 (m-10) REVERT: A 72 LYS cc_start: 0.7045 (mmtp) cc_final: 0.6786 (mmtm) REVERT: A 112 MET cc_start: 0.6140 (mtm) cc_final: 0.5764 (mtm) REVERT: A 124 ASN cc_start: 0.7382 (t0) cc_final: 0.7077 (t0) REVERT: A 182 ARG cc_start: 0.5521 (ttp-110) cc_final: 0.4812 (ptp-170) REVERT: A 214 TYR cc_start: 0.7403 (m-80) cc_final: 0.7177 (m-10) REVERT: A 262 GLU cc_start: 0.6731 (pt0) cc_final: 0.6473 (pt0) REVERT: A 323 ARG cc_start: 0.7296 (tpp80) cc_final: 0.6932 (mtt-85) REVERT: A 330 LEU cc_start: 0.5327 (mt) cc_final: 0.4721 (mp) REVERT: B 27 TYR cc_start: 0.6484 (m-80) cc_final: 0.6116 (m-10) REVERT: B 45 LYS cc_start: 0.6039 (ttmt) cc_final: 0.5837 (ttmm) REVERT: B 80 MET cc_start: 0.7820 (mmt) cc_final: 0.7519 (mmm) REVERT: B 108 GLU cc_start: 0.7145 (mp0) cc_final: 0.5808 (tm-30) REVERT: B 112 MET cc_start: 0.5936 (mtt) cc_final: 0.5580 (mtt) REVERT: B 116 ILE cc_start: 0.6748 (mm) cc_final: 0.6531 (mm) REVERT: B 323 ARG cc_start: 0.7330 (tpp80) cc_final: 0.6946 (mtt-85) REVERT: B 349 GLU cc_start: 0.6705 (tp30) cc_final: 0.6491 (tp30) REVERT: B 389 TYR cc_start: 0.7635 (t80) cc_final: 0.7167 (t80) REVERT: B 394 GLN cc_start: 0.7596 (mm-40) cc_final: 0.7239 (mm-40) REVERT: C 27 TYR cc_start: 0.7112 (m-80) cc_final: 0.6473 (m-80) REVERT: C 72 LYS cc_start: 0.7098 (mmpt) cc_final: 0.6749 (mttt) REVERT: C 80 MET cc_start: 0.7606 (mmt) cc_final: 0.7345 (mmt) REVERT: C 132 GLU cc_start: 0.6784 (tt0) cc_final: 0.6497 (tt0) REVERT: C 255 ARG cc_start: 0.6713 (mpp80) cc_final: 0.5694 (mtm110) REVERT: C 323 ARG cc_start: 0.7218 (tpp80) cc_final: 0.6888 (mtt-85) REVERT: C 349 GLU cc_start: 0.6544 (tp30) cc_final: 0.5941 (tp30) REVERT: C 357 MET cc_start: 0.7740 (tpt) cc_final: 0.7469 (tpp) REVERT: C 394 GLN cc_start: 0.6941 (mm110) cc_final: 0.6467 (mm-40) REVERT: D 72 LYS cc_start: 0.6895 (mmtt) cc_final: 0.6616 (mmtt) REVERT: D 124 ASN cc_start: 0.7534 (t0) cc_final: 0.7266 (t0) REVERT: D 235 MET cc_start: 0.5113 (tpt) cc_final: 0.4658 (mmm) REVERT: D 289 MET cc_start: 0.7418 (ppp) cc_final: 0.6889 (ttp) REVERT: D 323 ARG cc_start: 0.7191 (tpp80) cc_final: 0.6865 (mtt-85) REVERT: D 330 LEU cc_start: 0.5493 (mt) cc_final: 0.4844 (mp) REVERT: D 356 PHE cc_start: 0.6154 (m-80) cc_final: 0.5943 (m-80) REVERT: D 370 THR cc_start: 0.7713 (p) cc_final: 0.7292 (p) REVERT: D 394 GLN cc_start: 0.7362 (mm-40) cc_final: 0.6511 (mm-40) REVERT: E 27 TYR cc_start: 0.6539 (m-80) cc_final: 0.6103 (m-10) REVERT: E 72 LYS cc_start: 0.7537 (mmtt) cc_final: 0.7138 (mttt) REVERT: E 80 MET cc_start: 0.7815 (mmt) cc_final: 0.7454 (mmm) REVERT: E 108 GLU cc_start: 0.7079 (mp0) cc_final: 0.5608 (tm-30) REVERT: E 112 MET cc_start: 0.5682 (mtt) cc_final: 0.5256 (mtt) REVERT: E 323 ARG cc_start: 0.7443 (tpp80) cc_final: 0.7107 (mtt-85) REVERT: E 349 GLU cc_start: 0.6594 (tp30) cc_final: 0.6183 (tp30) REVERT: E 394 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7316 (mm-40) REVERT: F 27 TYR cc_start: 0.7172 (m-80) cc_final: 0.6228 (m-80) REVERT: F 80 MET cc_start: 0.7788 (mmt) cc_final: 0.7447 (mmt) REVERT: F 149 GLU cc_start: 0.7341 (mp0) cc_final: 0.7112 (mp0) REVERT: F 256 MET cc_start: 0.5597 (ppp) cc_final: 0.4967 (ppp) REVERT: F 262 GLU cc_start: 0.7366 (pt0) cc_final: 0.6969 (pt0) REVERT: F 307 GLN cc_start: 0.7987 (mp-120) cc_final: 0.7745 (mp10) REVERT: F 323 ARG cc_start: 0.7225 (tpp80) cc_final: 0.6920 (mtt-85) REVERT: F 349 GLU cc_start: 0.6490 (tp30) cc_final: 0.5916 (tp30) REVERT: G 64 ARG cc_start: 0.7380 (ttp-110) cc_final: 0.7094 (ttp-110) REVERT: G 72 LYS cc_start: 0.6910 (mmtp) cc_final: 0.6646 (mmtp) REVERT: G 112 MET cc_start: 0.6092 (mtm) cc_final: 0.5747 (mtm) REVERT: G 235 MET cc_start: 0.5253 (tpt) cc_final: 0.4900 (mmm) REVERT: G 262 GLU cc_start: 0.6970 (pt0) cc_final: 0.6730 (pt0) REVERT: G 323 ARG cc_start: 0.7213 (tpp80) cc_final: 0.6858 (mtt-85) REVERT: G 330 LEU cc_start: 0.5482 (mt) cc_final: 0.4876 (mp) REVERT: H 27 TYR cc_start: 0.6644 (m-80) cc_final: 0.6199 (m-10) REVERT: H 45 LYS cc_start: 0.6024 (ttmt) cc_final: 0.5816 (ttmm) REVERT: H 72 LYS cc_start: 0.7189 (mmtp) cc_final: 0.6786 (mttt) REVERT: H 80 MET cc_start: 0.7749 (mmt) cc_final: 0.7458 (mmm) REVERT: H 108 GLU cc_start: 0.7122 (mp0) cc_final: 0.5531 (tm-30) REVERT: H 124 ASN cc_start: 0.7266 (t0) cc_final: 0.6790 (t0) REVERT: H 290 SER cc_start: 0.8595 (t) cc_final: 0.8319 (p) REVERT: H 323 ARG cc_start: 0.7329 (tpp80) cc_final: 0.6993 (mtt-85) REVERT: H 349 GLU cc_start: 0.6667 (tp30) cc_final: 0.6378 (tp30) REVERT: H 357 MET cc_start: 0.7759 (tpt) cc_final: 0.7423 (tpt) REVERT: H 389 TYR cc_start: 0.7525 (t80) cc_final: 0.7073 (t80) REVERT: H 394 GLN cc_start: 0.7215 (mm-40) cc_final: 0.6794 (mm-40) REVERT: H 395 GLU cc_start: 0.6613 (mm-30) cc_final: 0.5930 (mm-30) REVERT: I 27 TYR cc_start: 0.7055 (m-80) cc_final: 0.6303 (m-80) REVERT: I 124 ASN cc_start: 0.7565 (t0) cc_final: 0.7135 (t0) REVERT: I 132 GLU cc_start: 0.6735 (tt0) cc_final: 0.6465 (tt0) REVERT: I 294 SER cc_start: 0.8117 (t) cc_final: 0.7837 (m) REVERT: I 323 ARG cc_start: 0.7286 (tpp80) cc_final: 0.6934 (mtt-85) REVERT: I 349 GLU cc_start: 0.6532 (tp30) cc_final: 0.5942 (tp30) REVERT: I 359 ASN cc_start: 0.6433 (t0) cc_final: 0.6208 (t0) REVERT: I 394 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7256 (mm-40) REVERT: I 395 GLU cc_start: 0.6601 (mm-30) cc_final: 0.6379 (mm-30) REVERT: J 72 LYS cc_start: 0.7019 (mmtp) cc_final: 0.6728 (mmtp) REVERT: J 112 MET cc_start: 0.6141 (mtm) cc_final: 0.5768 (mtm) REVERT: J 124 ASN cc_start: 0.7363 (t0) cc_final: 0.7047 (t0) REVERT: J 323 ARG cc_start: 0.7253 (tpp80) cc_final: 0.6891 (mtt-85) REVERT: J 330 LEU cc_start: 0.5460 (mt) cc_final: 0.4811 (mp) REVERT: K 27 TYR cc_start: 0.6818 (m-80) cc_final: 0.6339 (m-10) REVERT: K 108 GLU cc_start: 0.7157 (mp0) cc_final: 0.5566 (tm-30) REVERT: K 112 MET cc_start: 0.5983 (mtt) cc_final: 0.5299 (mtt) REVERT: K 116 ILE cc_start: 0.6573 (mm) cc_final: 0.6361 (mm) REVERT: K 124 ASN cc_start: 0.7260 (t0) cc_final: 0.6858 (t0) REVERT: K 149 GLU cc_start: 0.7481 (mp0) cc_final: 0.7240 (mp0) REVERT: K 323 ARG cc_start: 0.7319 (tpp80) cc_final: 0.6977 (mtt-85) REVERT: K 389 TYR cc_start: 0.7534 (t80) cc_final: 0.7196 (t80) REVERT: K 394 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7291 (mm-40) REVERT: L 27 TYR cc_start: 0.6993 (m-80) cc_final: 0.6366 (m-80) REVERT: L 72 LYS cc_start: 0.7084 (mmpt) cc_final: 0.6748 (mttt) REVERT: L 124 ASN cc_start: 0.7574 (t0) cc_final: 0.7169 (t0) REVERT: L 256 MET cc_start: 0.5588 (ppp) cc_final: 0.5070 (ttp) REVERT: L 294 SER cc_start: 0.8093 (t) cc_final: 0.7827 (m) REVERT: L 323 ARG cc_start: 0.7283 (tpp80) cc_final: 0.6908 (mtt-85) REVERT: L 349 GLU cc_start: 0.6545 (tp30) cc_final: 0.5949 (tp30) REVERT: L 357 MET cc_start: 0.7668 (tpt) cc_final: 0.7394 (tpp) REVERT: L 389 TYR cc_start: 0.7488 (t80) cc_final: 0.6958 (t80) REVERT: L 394 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7488 (mm-40) REVERT: L 395 GLU cc_start: 0.6624 (mm-30) cc_final: 0.6278 (mm-30) outliers start: 2 outliers final: 0 residues processed: 887 average time/residue: 0.4643 time to fit residues: 679.6830 Evaluate side-chains 821 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 821 time to evaluate : 4.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 279 optimal weight: 0.5980 chunk 180 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 286 optimal weight: 0.7980 chunk 307 optimal weight: 8.9990 chunk 223 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 354 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN A 307 GLN B 124 ASN B 136 GLN B 178 GLN C 124 ASN C 178 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN D 178 GLN E 124 ASN E 178 GLN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN F 307 GLN G 124 ASN G 178 GLN ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN H 178 GLN I 136 GLN J 363 GLN K 178 GLN L 178 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37788 Z= 0.184 Angle : 0.605 11.388 51132 Z= 0.301 Chirality : 0.042 0.191 5760 Planarity : 0.004 0.054 6660 Dihedral : 4.719 21.887 5208 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.12 % Allowed : 1.39 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.12), residues: 4632 helix: 0.55 (0.13), residues: 1836 sheet: -0.33 (0.21), residues: 492 loop : -2.47 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 83 HIS 0.004 0.001 HIS F 216 PHE 0.027 0.001 PHE H 356 TYR 0.022 0.001 TYR I 389 ARG 0.008 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 888 time to evaluate : 3.757 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: A 27 TYR cc_start: 0.6584 (m-80) cc_final: 0.6233 (m-10) REVERT: A 72 LYS cc_start: 0.6949 (mmtp) cc_final: 0.6689 (mmtm) REVERT: A 112 MET cc_start: 0.6128 (mtm) cc_final: 0.5792 (mtm) REVERT: A 124 ASN cc_start: 0.7409 (t0) cc_final: 0.7097 (t0) REVERT: A 182 ARG cc_start: 0.5575 (ttp-110) cc_final: 0.5203 (ptp-170) REVERT: A 214 TYR cc_start: 0.7427 (m-80) cc_final: 0.7206 (m-10) REVERT: A 262 GLU cc_start: 0.6745 (pt0) cc_final: 0.6486 (pt0) REVERT: A 323 ARG cc_start: 0.7323 (tpp80) cc_final: 0.6949 (mtt-85) REVERT: A 330 LEU cc_start: 0.5387 (mt) cc_final: 0.4809 (mp) REVERT: B 27 TYR cc_start: 0.6620 (m-80) cc_final: 0.6144 (m-10) REVERT: B 45 LYS cc_start: 0.5904 (ttmt) cc_final: 0.5698 (ttmm) REVERT: B 80 MET cc_start: 0.7778 (mmt) cc_final: 0.7512 (mmm) REVERT: B 108 GLU cc_start: 0.7103 (mp0) cc_final: 0.5769 (tm-30) REVERT: B 112 MET cc_start: 0.5987 (mtt) cc_final: 0.5494 (mtt) REVERT: B 323 ARG cc_start: 0.7325 (tpp80) cc_final: 0.6922 (mtt-85) REVERT: B 330 LEU cc_start: 0.5162 (mt) cc_final: 0.4566 (mt) REVERT: B 349 GLU cc_start: 0.6728 (tp30) cc_final: 0.6482 (tp30) REVERT: B 389 TYR cc_start: 0.7642 (t80) cc_final: 0.7135 (t80) REVERT: C 27 TYR cc_start: 0.7150 (m-80) cc_final: 0.6437 (m-80) REVERT: C 72 LYS cc_start: 0.7161 (mmpt) cc_final: 0.6767 (mttt) REVERT: C 80 MET cc_start: 0.7547 (mmt) cc_final: 0.7316 (mmt) REVERT: C 132 GLU cc_start: 0.6717 (tt0) cc_final: 0.6411 (tt0) REVERT: C 149 GLU cc_start: 0.7491 (mp0) cc_final: 0.7069 (mp0) REVERT: C 255 ARG cc_start: 0.6602 (mpp80) cc_final: 0.5609 (mtm110) REVERT: C 323 ARG cc_start: 0.7233 (tpp80) cc_final: 0.6900 (mtt-85) REVERT: C 349 GLU cc_start: 0.6577 (tp30) cc_final: 0.5918 (tp30) REVERT: C 389 TYR cc_start: 0.7413 (t80) cc_final: 0.6899 (t80) REVERT: C 394 GLN cc_start: 0.7009 (mm110) cc_final: 0.6561 (mm-40) REVERT: D 72 LYS cc_start: 0.6894 (mmtt) cc_final: 0.6598 (mmtt) REVERT: D 108 GLU cc_start: 0.5858 (mp0) cc_final: 0.5421 (mp0) REVERT: D 124 ASN cc_start: 0.7592 (t0) cc_final: 0.7336 (t0) REVERT: D 235 MET cc_start: 0.5192 (tpt) cc_final: 0.4674 (mmm) REVERT: D 256 MET cc_start: 0.5666 (ppp) cc_final: 0.4919 (ppp) REVERT: D 257 VAL cc_start: 0.5910 (m) cc_final: 0.4518 (t) REVERT: D 289 MET cc_start: 0.7479 (ppp) cc_final: 0.6975 (ttp) REVERT: D 323 ARG cc_start: 0.7217 (tpp80) cc_final: 0.6900 (mtt-85) REVERT: D 330 LEU cc_start: 0.5551 (mt) cc_final: 0.4786 (mp) REVERT: D 394 GLN cc_start: 0.7364 (mm-40) cc_final: 0.6529 (mm-40) REVERT: E 27 TYR cc_start: 0.6468 (m-80) cc_final: 0.6058 (m-10) REVERT: E 45 LYS cc_start: 0.5953 (ttmt) cc_final: 0.5745 (ttmm) REVERT: E 72 LYS cc_start: 0.7490 (mmtt) cc_final: 0.7081 (mttt) REVERT: E 80 MET cc_start: 0.7794 (mmt) cc_final: 0.7561 (mmm) REVERT: E 108 GLU cc_start: 0.7035 (mp0) cc_final: 0.5661 (tm-30) REVERT: E 112 MET cc_start: 0.5728 (mtt) cc_final: 0.5338 (mtt) REVERT: E 290 SER cc_start: 0.8502 (t) cc_final: 0.8261 (p) REVERT: E 323 ARG cc_start: 0.7447 (tpp80) cc_final: 0.7133 (mtt-85) REVERT: E 330 LEU cc_start: 0.5192 (mt) cc_final: 0.4567 (mp) REVERT: E 349 GLU cc_start: 0.6541 (tp30) cc_final: 0.6099 (tp30) REVERT: E 394 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7287 (mm-40) REVERT: F 27 TYR cc_start: 0.7205 (m-80) cc_final: 0.6295 (m-80) REVERT: F 80 MET cc_start: 0.7723 (mmt) cc_final: 0.7420 (mmt) REVERT: F 256 MET cc_start: 0.5590 (ppp) cc_final: 0.4999 (ppp) REVERT: F 262 GLU cc_start: 0.7373 (pt0) cc_final: 0.6939 (pt0) REVERT: F 323 ARG cc_start: 0.7268 (tpp80) cc_final: 0.6918 (mtt-85) REVERT: F 349 GLU cc_start: 0.6529 (tp30) cc_final: 0.5936 (tp30) REVERT: F 394 GLN cc_start: 0.7428 (mm-40) cc_final: 0.7227 (mm-40) REVERT: G 64 ARG cc_start: 0.7373 (ttp-110) cc_final: 0.7074 (ttp-110) REVERT: G 72 LYS cc_start: 0.6969 (mmtp) cc_final: 0.6679 (mmtp) REVERT: G 112 MET cc_start: 0.6094 (mtm) cc_final: 0.5736 (mtm) REVERT: G 235 MET cc_start: 0.5254 (tpt) cc_final: 0.4873 (mmm) REVERT: G 256 MET cc_start: 0.5713 (ppp) cc_final: 0.5228 (ppp) REVERT: G 323 ARG cc_start: 0.7225 (tpp80) cc_final: 0.6853 (mtt-85) REVERT: G 330 LEU cc_start: 0.5434 (mt) cc_final: 0.4883 (mp) REVERT: H 27 TYR cc_start: 0.6711 (m-80) cc_final: 0.6211 (m-10) REVERT: H 72 LYS cc_start: 0.7222 (mmtp) cc_final: 0.6778 (mttt) REVERT: H 80 MET cc_start: 0.7713 (mmt) cc_final: 0.7399 (mmm) REVERT: H 108 GLU cc_start: 0.7090 (mp0) cc_final: 0.5498 (tm-30) REVERT: H 116 ILE cc_start: 0.6660 (mm) cc_final: 0.6417 (mm) REVERT: H 290 SER cc_start: 0.8622 (t) cc_final: 0.8413 (t) REVERT: H 323 ARG cc_start: 0.7338 (tpp80) cc_final: 0.7025 (mtt-85) REVERT: H 349 GLU cc_start: 0.6694 (tp30) cc_final: 0.6389 (tp30) REVERT: H 357 MET cc_start: 0.7831 (tpt) cc_final: 0.7406 (tpt) REVERT: H 370 THR cc_start: 0.8015 (p) cc_final: 0.7739 (p) REVERT: H 389 TYR cc_start: 0.7487 (t80) cc_final: 0.7034 (t80) REVERT: H 394 GLN cc_start: 0.7192 (mm-40) cc_final: 0.6764 (mm-40) REVERT: H 395 GLU cc_start: 0.6541 (mm-30) cc_final: 0.5921 (mm-30) REVERT: I 27 TYR cc_start: 0.7054 (m-80) cc_final: 0.6319 (m-80) REVERT: I 124 ASN cc_start: 0.7626 (t0) cc_final: 0.7154 (t0) REVERT: I 132 GLU cc_start: 0.6744 (tt0) cc_final: 0.6450 (tt0) REVERT: I 262 GLU cc_start: 0.7311 (pt0) cc_final: 0.7105 (pt0) REVERT: I 323 ARG cc_start: 0.7311 (tpp80) cc_final: 0.6933 (mtt-85) REVERT: I 349 GLU cc_start: 0.6523 (tp30) cc_final: 0.5936 (tp30) REVERT: I 389 TYR cc_start: 0.7367 (t80) cc_final: 0.6824 (t80) REVERT: I 394 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7382 (mm-40) REVERT: I 395 GLU cc_start: 0.6595 (mm-30) cc_final: 0.6327 (mm-30) REVERT: J 72 LYS cc_start: 0.6881 (mmtp) cc_final: 0.6616 (mmtp) REVERT: J 112 MET cc_start: 0.6086 (mtm) cc_final: 0.5743 (mtm) REVERT: J 124 ASN cc_start: 0.7413 (t0) cc_final: 0.7064 (t0) REVERT: J 235 MET cc_start: 0.5324 (tpt) cc_final: 0.5018 (mmm) REVERT: J 323 ARG cc_start: 0.7270 (tpp80) cc_final: 0.6912 (mtt-85) REVERT: J 330 LEU cc_start: 0.5405 (mt) cc_final: 0.4761 (mp) REVERT: K 27 TYR cc_start: 0.6728 (m-80) cc_final: 0.6158 (m-10) REVERT: K 108 GLU cc_start: 0.7135 (mp0) cc_final: 0.5519 (tm-30) REVERT: K 112 MET cc_start: 0.6033 (mtt) cc_final: 0.5326 (mtt) REVERT: K 116 ILE cc_start: 0.6620 (mm) cc_final: 0.6369 (mm) REVERT: K 124 ASN cc_start: 0.7247 (t0) cc_final: 0.6824 (t0) REVERT: K 149 GLU cc_start: 0.7496 (mp0) cc_final: 0.7295 (mp0) REVERT: K 323 ARG cc_start: 0.7419 (tpp80) cc_final: 0.7070 (mtt-85) REVERT: K 330 LEU cc_start: 0.5050 (mt) cc_final: 0.4485 (mp) REVERT: K 349 GLU cc_start: 0.6852 (tp30) cc_final: 0.6506 (tp30) REVERT: K 389 TYR cc_start: 0.7486 (t80) cc_final: 0.7154 (t80) REVERT: K 395 GLU cc_start: 0.6570 (mm-30) cc_final: 0.5958 (mm-30) REVERT: L 27 TYR cc_start: 0.7011 (m-80) cc_final: 0.6231 (m-80) REVERT: L 72 LYS cc_start: 0.7138 (mmpt) cc_final: 0.6727 (mttt) REVERT: L 132 GLU cc_start: 0.6656 (tt0) cc_final: 0.6433 (tt0) REVERT: L 256 MET cc_start: 0.5575 (ppp) cc_final: 0.5090 (ttp) REVERT: L 323 ARG cc_start: 0.7279 (tpp80) cc_final: 0.6904 (mtt-85) REVERT: L 349 GLU cc_start: 0.6557 (tp30) cc_final: 0.5932 (tp30) REVERT: L 389 TYR cc_start: 0.7463 (t80) cc_final: 0.6959 (t80) REVERT: L 394 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7298 (mm-40) REVERT: L 395 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6395 (mm-30) outliers start: 5 outliers final: 1 residues processed: 888 average time/residue: 0.4442 time to fit residues: 652.8863 Evaluate side-chains 830 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 829 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 410 optimal weight: 8.9990 chunk 432 optimal weight: 0.3980 chunk 394 optimal weight: 5.9990 chunk 420 optimal weight: 0.4980 chunk 253 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 330 optimal weight: 7.9990 chunk 128 optimal weight: 0.0670 chunk 379 optimal weight: 1.9990 chunk 397 optimal weight: 30.0000 chunk 418 optimal weight: 0.0170 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN B 124 ASN B 178 GLN C 178 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN D 178 GLN E 124 ASN E 178 GLN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN G 178 GLN ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN H 178 GLN I 136 GLN I 178 GLN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 GLN K 178 GLN L 124 ASN L 178 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37788 Z= 0.169 Angle : 0.595 8.854 51132 Z= 0.294 Chirality : 0.041 0.199 5760 Planarity : 0.004 0.070 6660 Dihedral : 4.620 22.849 5208 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.10 % Allowed : 0.97 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.12), residues: 4632 helix: 0.67 (0.13), residues: 1836 sheet: -0.28 (0.21), residues: 492 loop : -2.38 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 83 HIS 0.004 0.001 HIS F 216 PHE 0.024 0.001 PHE C 78 TYR 0.019 0.001 TYR B 17 ARG 0.019 0.001 ARG C 402 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 887 time to evaluate : 4.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.6945 (mmtp) cc_final: 0.6692 (mmtm) REVERT: A 112 MET cc_start: 0.6153 (mtm) cc_final: 0.5782 (mtm) REVERT: A 124 ASN cc_start: 0.7407 (t0) cc_final: 0.7051 (t0) REVERT: A 182 ARG cc_start: 0.5532 (ttp-110) cc_final: 0.4964 (ptp-170) REVERT: A 214 TYR cc_start: 0.7410 (m-80) cc_final: 0.7179 (m-10) REVERT: A 262 GLU cc_start: 0.6658 (pt0) cc_final: 0.6409 (pt0) REVERT: A 323 ARG cc_start: 0.7270 (tpp80) cc_final: 0.6934 (mtt-85) REVERT: A 330 LEU cc_start: 0.5366 (mt) cc_final: 0.4757 (mp) REVERT: B 27 TYR cc_start: 0.6571 (m-80) cc_final: 0.6040 (m-10) REVERT: B 45 LYS cc_start: 0.5780 (ttmt) cc_final: 0.5574 (ttmm) REVERT: B 80 MET cc_start: 0.7828 (mmt) cc_final: 0.7567 (mmm) REVERT: B 108 GLU cc_start: 0.7078 (mp0) cc_final: 0.5776 (tm-30) REVERT: B 112 MET cc_start: 0.6026 (mtt) cc_final: 0.5520 (mtt) REVERT: B 323 ARG cc_start: 0.7272 (tpp80) cc_final: 0.6853 (mtt-85) REVERT: B 330 LEU cc_start: 0.5090 (mt) cc_final: 0.4575 (mp) REVERT: B 334 LYS cc_start: 0.8373 (ptmt) cc_final: 0.8172 (ptpt) REVERT: B 349 GLU cc_start: 0.6626 (tp30) cc_final: 0.6359 (tp30) REVERT: B 389 TYR cc_start: 0.7578 (t80) cc_final: 0.7052 (t80) REVERT: C 27 TYR cc_start: 0.7015 (m-80) cc_final: 0.6233 (m-80) REVERT: C 80 MET cc_start: 0.7595 (mmt) cc_final: 0.7250 (mmt) REVERT: C 132 GLU cc_start: 0.6714 (tt0) cc_final: 0.6474 (tt0) REVERT: C 149 GLU cc_start: 0.7547 (mp0) cc_final: 0.7265 (mp0) REVERT: C 255 ARG cc_start: 0.6647 (mpp80) cc_final: 0.5655 (mtm110) REVERT: C 323 ARG cc_start: 0.7248 (tpp80) cc_final: 0.6907 (mtt-85) REVERT: C 349 GLU cc_start: 0.6527 (tp30) cc_final: 0.5902 (tp30) REVERT: C 389 TYR cc_start: 0.7362 (t80) cc_final: 0.6975 (t80) REVERT: C 394 GLN cc_start: 0.7025 (mm110) cc_final: 0.6608 (mm-40) REVERT: D 72 LYS cc_start: 0.6904 (mmtt) cc_final: 0.6627 (mmtt) REVERT: D 124 ASN cc_start: 0.7586 (t0) cc_final: 0.7309 (t0) REVERT: D 235 MET cc_start: 0.5126 (tpt) cc_final: 0.4642 (mmm) REVERT: D 256 MET cc_start: 0.5639 (ppp) cc_final: 0.4913 (ppp) REVERT: D 257 VAL cc_start: 0.5825 (m) cc_final: 0.4396 (t) REVERT: D 289 MET cc_start: 0.7451 (ppp) cc_final: 0.6988 (ttp) REVERT: D 323 ARG cc_start: 0.7228 (tpp80) cc_final: 0.6919 (mtt-85) REVERT: D 330 LEU cc_start: 0.5108 (mt) cc_final: 0.4534 (mp) REVERT: D 349 GLU cc_start: 0.6837 (tt0) cc_final: 0.6634 (tt0) REVERT: D 356 PHE cc_start: 0.6093 (m-80) cc_final: 0.5845 (m-80) REVERT: D 394 GLN cc_start: 0.7344 (mm-40) cc_final: 0.6550 (mm-40) REVERT: E 27 TYR cc_start: 0.6334 (m-80) cc_final: 0.5936 (m-10) REVERT: E 72 LYS cc_start: 0.7454 (mmtt) cc_final: 0.6999 (mttt) REVERT: E 80 MET cc_start: 0.7771 (mmt) cc_final: 0.7423 (mmm) REVERT: E 108 GLU cc_start: 0.6975 (mp0) cc_final: 0.5664 (tm-30) REVERT: E 112 MET cc_start: 0.5845 (mtt) cc_final: 0.5354 (mtt) REVERT: E 116 ILE cc_start: 0.6626 (mt) cc_final: 0.6423 (mt) REVERT: E 230 GLU cc_start: 0.6954 (mp0) cc_final: 0.6378 (mp0) REVERT: E 323 ARG cc_start: 0.7450 (tpp80) cc_final: 0.7126 (mtt-85) REVERT: E 330 LEU cc_start: 0.5033 (mt) cc_final: 0.4429 (mp) REVERT: E 334 LYS cc_start: 0.8389 (ptmt) cc_final: 0.8186 (ptpt) REVERT: E 349 GLU cc_start: 0.6525 (tp30) cc_final: 0.6050 (tp30) REVERT: E 394 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7190 (mm-40) REVERT: F 27 TYR cc_start: 0.7079 (m-80) cc_final: 0.6191 (m-80) REVERT: F 80 MET cc_start: 0.7780 (mmt) cc_final: 0.7391 (mmt) REVERT: F 262 GLU cc_start: 0.7328 (pt0) cc_final: 0.6944 (pt0) REVERT: F 295 LYS cc_start: 0.8873 (ptmt) cc_final: 0.8623 (pttt) REVERT: F 323 ARG cc_start: 0.7277 (tpp80) cc_final: 0.6885 (mtt-85) REVERT: F 349 GLU cc_start: 0.6421 (tp30) cc_final: 0.5838 (tp30) REVERT: F 395 GLU cc_start: 0.6496 (mm-30) cc_final: 0.6282 (mm-30) REVERT: G 64 ARG cc_start: 0.7294 (ttp-110) cc_final: 0.6994 (ttp-110) REVERT: G 72 LYS cc_start: 0.6955 (mmtp) cc_final: 0.6664 (mmtp) REVERT: G 112 MET cc_start: 0.5957 (mtm) cc_final: 0.5621 (mtm) REVERT: G 179 MET cc_start: 0.5792 (mtm) cc_final: 0.5500 (mtp) REVERT: G 235 MET cc_start: 0.5299 (tpt) cc_final: 0.4956 (mmm) REVERT: G 323 ARG cc_start: 0.7154 (tpp80) cc_final: 0.6842 (mtt-85) REVERT: G 330 LEU cc_start: 0.5183 (mt) cc_final: 0.4672 (mp) REVERT: H 27 TYR cc_start: 0.6549 (m-80) cc_final: 0.6149 (m-10) REVERT: H 108 GLU cc_start: 0.7041 (mp0) cc_final: 0.5490 (tm-30) REVERT: H 116 ILE cc_start: 0.6633 (mm) cc_final: 0.6415 (mm) REVERT: H 323 ARG cc_start: 0.7353 (tpp80) cc_final: 0.7001 (mtt-85) REVERT: H 330 LEU cc_start: 0.4975 (mt) cc_final: 0.4370 (mt) REVERT: H 334 LYS cc_start: 0.8355 (ptmt) cc_final: 0.8145 (ptpt) REVERT: H 349 GLU cc_start: 0.6682 (tp30) cc_final: 0.6324 (tp30) REVERT: H 370 THR cc_start: 0.7967 (p) cc_final: 0.7715 (p) REVERT: H 394 GLN cc_start: 0.7160 (mm-40) cc_final: 0.6727 (mm-40) REVERT: H 395 GLU cc_start: 0.6601 (mm-30) cc_final: 0.5949 (mm-30) REVERT: I 27 TYR cc_start: 0.6967 (m-80) cc_final: 0.6334 (m-80) REVERT: I 124 ASN cc_start: 0.7621 (t0) cc_final: 0.7316 (t0) REVERT: I 132 GLU cc_start: 0.6665 (tt0) cc_final: 0.6418 (tt0) REVERT: I 323 ARG cc_start: 0.7324 (tpp80) cc_final: 0.6945 (mtt-85) REVERT: I 349 GLU cc_start: 0.6515 (tp30) cc_final: 0.5966 (tp30) REVERT: I 389 TYR cc_start: 0.7311 (t80) cc_final: 0.6916 (t80) REVERT: I 394 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7378 (mm-40) REVERT: I 395 GLU cc_start: 0.6590 (mm-30) cc_final: 0.6318 (mm-30) REVERT: J 72 LYS cc_start: 0.6879 (mmtp) cc_final: 0.6600 (mmtp) REVERT: J 112 MET cc_start: 0.6048 (mtm) cc_final: 0.5756 (mtm) REVERT: J 124 ASN cc_start: 0.7410 (t0) cc_final: 0.7059 (t0) REVERT: J 235 MET cc_start: 0.5271 (tpt) cc_final: 0.4980 (mmm) REVERT: J 323 ARG cc_start: 0.7206 (tpp80) cc_final: 0.6912 (mtt-85) REVERT: J 330 LEU cc_start: 0.5140 (mt) cc_final: 0.4603 (mp) REVERT: K 27 TYR cc_start: 0.6419 (m-80) cc_final: 0.5847 (m-10) REVERT: K 72 LYS cc_start: 0.7204 (mmtp) cc_final: 0.6763 (mttt) REVERT: K 108 GLU cc_start: 0.7110 (mp0) cc_final: 0.5520 (tm-30) REVERT: K 112 MET cc_start: 0.5999 (mtt) cc_final: 0.5268 (mtt) REVERT: K 116 ILE cc_start: 0.6637 (mm) cc_final: 0.6366 (mm) REVERT: K 124 ASN cc_start: 0.7261 (t0) cc_final: 0.6803 (t0) REVERT: K 149 GLU cc_start: 0.7585 (mp0) cc_final: 0.7364 (mp0) REVERT: K 323 ARG cc_start: 0.7425 (tpp80) cc_final: 0.7087 (mtt-85) REVERT: K 330 LEU cc_start: 0.5081 (mt) cc_final: 0.4467 (mp) REVERT: K 349 GLU cc_start: 0.6820 (tp30) cc_final: 0.6455 (tp30) REVERT: L 27 TYR cc_start: 0.6958 (m-80) cc_final: 0.6204 (m-80) REVERT: L 81 GLN cc_start: 0.7723 (mt0) cc_final: 0.7441 (tt0) REVERT: L 256 MET cc_start: 0.5459 (ppp) cc_final: 0.4965 (ttp) REVERT: L 323 ARG cc_start: 0.7290 (tpp80) cc_final: 0.6886 (mtt-85) REVERT: L 349 GLU cc_start: 0.6493 (tp30) cc_final: 0.5898 (tp30) REVERT: L 389 TYR cc_start: 0.7371 (t80) cc_final: 0.6932 (t80) REVERT: L 394 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7652 (mm-40) outliers start: 4 outliers final: 0 residues processed: 887 average time/residue: 0.4710 time to fit residues: 692.2970 Evaluate side-chains 816 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 816 time to evaluate : 5.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 276 optimal weight: 0.0070 chunk 444 optimal weight: 6.9990 chunk 271 optimal weight: 20.0000 chunk 210 optimal weight: 0.4980 chunk 308 optimal weight: 3.9990 chunk 466 optimal weight: 9.9990 chunk 429 optimal weight: 10.0000 chunk 371 optimal weight: 9.9990 chunk 38 optimal weight: 0.0970 chunk 286 optimal weight: 8.9990 chunk 227 optimal weight: 0.8980 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 178 GLN C 178 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN D 335 GLN E 124 ASN E 178 GLN F 124 ASN F 412 GLN G 32 GLN G 124 ASN G 136 GLN G 178 GLN H 124 ASN H 178 GLN I 136 GLN I 178 GLN I 412 GLN ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN K 136 GLN K 178 GLN L 124 ASN L 178 GLN L 412 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37788 Z= 0.190 Angle : 0.610 9.865 51132 Z= 0.302 Chirality : 0.042 0.205 5760 Planarity : 0.004 0.055 6660 Dihedral : 4.637 20.689 5208 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.15 % Allowed : 0.47 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.12), residues: 4632 helix: 0.68 (0.13), residues: 1848 sheet: -0.21 (0.21), residues: 492 loop : -2.36 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 83 HIS 0.003 0.001 HIS F 216 PHE 0.027 0.001 PHE C 78 TYR 0.020 0.001 TYR G 27 ARG 0.008 0.001 ARG D 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 874 time to evaluate : 4.149 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: A 72 LYS cc_start: 0.6971 (mmtp) cc_final: 0.6732 (mmtp) REVERT: A 112 MET cc_start: 0.6124 (mtm) cc_final: 0.5752 (mtm) REVERT: A 124 ASN cc_start: 0.7425 (t0) cc_final: 0.7107 (t0) REVERT: A 182 ARG cc_start: 0.5540 (ttp-110) cc_final: 0.5105 (ptp-170) REVERT: A 214 TYR cc_start: 0.7376 (m-80) cc_final: 0.7172 (m-10) REVERT: A 235 MET cc_start: 0.5310 (tpt) cc_final: 0.5012 (mmm) REVERT: A 262 GLU cc_start: 0.6765 (pt0) cc_final: 0.6513 (pt0) REVERT: A 323 ARG cc_start: 0.7253 (tpp80) cc_final: 0.6928 (mtt-85) REVERT: A 330 LEU cc_start: 0.5309 (mt) cc_final: 0.4698 (mp) REVERT: B 27 TYR cc_start: 0.6608 (m-80) cc_final: 0.6138 (m-10) REVERT: B 45 LYS cc_start: 0.5763 (ttmt) cc_final: 0.5556 (ttmm) REVERT: B 72 LYS cc_start: 0.7209 (mmtp) cc_final: 0.6776 (mttt) REVERT: B 80 MET cc_start: 0.7769 (mmt) cc_final: 0.7445 (mmm) REVERT: B 108 GLU cc_start: 0.7108 (mp0) cc_final: 0.5779 (tm-30) REVERT: B 112 MET cc_start: 0.6025 (mtt) cc_final: 0.5527 (mtt) REVERT: B 323 ARG cc_start: 0.7317 (tpp80) cc_final: 0.6897 (mtt-85) REVERT: B 330 LEU cc_start: 0.5063 (mt) cc_final: 0.4517 (mp) REVERT: B 349 GLU cc_start: 0.6646 (tp30) cc_final: 0.6349 (tp30) REVERT: B 389 TYR cc_start: 0.7433 (t80) cc_final: 0.6939 (t80) REVERT: C 27 TYR cc_start: 0.7126 (m-80) cc_final: 0.6448 (m-80) REVERT: C 80 MET cc_start: 0.7480 (mmt) cc_final: 0.7256 (mmt) REVERT: C 124 ASN cc_start: 0.7463 (t0) cc_final: 0.7234 (t0) REVERT: C 132 GLU cc_start: 0.6744 (tt0) cc_final: 0.6478 (tt0) REVERT: C 255 ARG cc_start: 0.6617 (mpp80) cc_final: 0.6332 (mtm180) REVERT: C 323 ARG cc_start: 0.7244 (tpp80) cc_final: 0.6889 (mtt-85) REVERT: C 349 GLU cc_start: 0.6547 (tp30) cc_final: 0.5929 (tp30) REVERT: C 389 TYR cc_start: 0.7397 (t80) cc_final: 0.6989 (t80) REVERT: C 394 GLN cc_start: 0.6954 (mm110) cc_final: 0.6528 (mm-40) REVERT: D 72 LYS cc_start: 0.6899 (mmtt) cc_final: 0.6630 (mmtt) REVERT: D 124 ASN cc_start: 0.7604 (t0) cc_final: 0.7318 (t0) REVERT: D 235 MET cc_start: 0.5202 (tpt) cc_final: 0.4646 (mmm) REVERT: D 256 MET cc_start: 0.5811 (ppp) cc_final: 0.5067 (ppp) REVERT: D 257 VAL cc_start: 0.5975 (m) cc_final: 0.4634 (t) REVERT: D 289 MET cc_start: 0.7460 (ppp) cc_final: 0.7044 (ttp) REVERT: D 323 ARG cc_start: 0.7243 (tpp80) cc_final: 0.6934 (mtt-85) REVERT: D 330 LEU cc_start: 0.5151 (mt) cc_final: 0.4506 (mp) REVERT: D 356 PHE cc_start: 0.5994 (m-80) cc_final: 0.5758 (m-80) REVERT: E 27 TYR cc_start: 0.6558 (m-80) cc_final: 0.6033 (m-10) REVERT: E 72 LYS cc_start: 0.7466 (mmtt) cc_final: 0.7003 (mttt) REVERT: E 80 MET cc_start: 0.7799 (mmt) cc_final: 0.7523 (mmm) REVERT: E 108 GLU cc_start: 0.7078 (mp0) cc_final: 0.5756 (tm-30) REVERT: E 112 MET cc_start: 0.5802 (mtt) cc_final: 0.5394 (mtt) REVERT: E 230 GLU cc_start: 0.6969 (mp0) cc_final: 0.6417 (mp0) REVERT: E 290 SER cc_start: 0.8532 (t) cc_final: 0.8289 (p) REVERT: E 323 ARG cc_start: 0.7500 (tpp80) cc_final: 0.7141 (mtt-85) REVERT: E 330 LEU cc_start: 0.5050 (mt) cc_final: 0.4403 (mp) REVERT: E 349 GLU cc_start: 0.6536 (tp30) cc_final: 0.6114 (tp30) REVERT: E 357 MET cc_start: 0.7895 (tpt) cc_final: 0.7429 (tpt) REVERT: E 394 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7522 (mm-40) REVERT: F 27 TYR cc_start: 0.7146 (m-80) cc_final: 0.6260 (m-80) REVERT: F 80 MET cc_start: 0.7655 (mmt) cc_final: 0.7376 (mmt) REVERT: F 262 GLU cc_start: 0.7333 (pt0) cc_final: 0.6942 (pt0) REVERT: F 295 LYS cc_start: 0.8860 (ptmt) cc_final: 0.8486 (pttt) REVERT: F 307 GLN cc_start: 0.7986 (mp10) cc_final: 0.7781 (mp10) REVERT: F 323 ARG cc_start: 0.7221 (tpp80) cc_final: 0.6851 (mtt-85) REVERT: F 349 GLU cc_start: 0.6433 (tp30) cc_final: 0.5858 (tp30) REVERT: F 394 GLN cc_start: 0.7173 (mm-40) cc_final: 0.6741 (mm-40) REVERT: G 64 ARG cc_start: 0.7322 (ttp-110) cc_final: 0.6871 (ttp-110) REVERT: G 72 LYS cc_start: 0.6983 (mmtp) cc_final: 0.6692 (mmtp) REVERT: G 112 MET cc_start: 0.5801 (mtm) cc_final: 0.5562 (mtm) REVERT: G 235 MET cc_start: 0.5308 (tpt) cc_final: 0.4876 (mmm) REVERT: G 323 ARG cc_start: 0.7174 (tpp80) cc_final: 0.6870 (mtt-85) REVERT: G 330 LEU cc_start: 0.5174 (mt) cc_final: 0.4604 (mp) REVERT: H 27 TYR cc_start: 0.6657 (m-80) cc_final: 0.6213 (m-10) REVERT: H 108 GLU cc_start: 0.7081 (mp0) cc_final: 0.5483 (tm-30) REVERT: H 323 ARG cc_start: 0.7421 (tpp80) cc_final: 0.7079 (mtt-85) REVERT: H 330 LEU cc_start: 0.5046 (mt) cc_final: 0.4503 (mp) REVERT: H 334 LYS cc_start: 0.8412 (ptmt) cc_final: 0.8194 (ptpt) REVERT: H 349 GLU cc_start: 0.6650 (tp30) cc_final: 0.6329 (tp30) REVERT: H 370 THR cc_start: 0.7928 (p) cc_final: 0.7684 (p) REVERT: H 394 GLN cc_start: 0.7070 (mm-40) cc_final: 0.6695 (mm-40) REVERT: H 395 GLU cc_start: 0.6621 (mm-30) cc_final: 0.5918 (mm-30) REVERT: I 27 TYR cc_start: 0.7003 (m-80) cc_final: 0.6449 (m-80) REVERT: I 124 ASN cc_start: 0.7713 (t0) cc_final: 0.7239 (t0) REVERT: I 132 GLU cc_start: 0.6671 (tt0) cc_final: 0.6404 (tt0) REVERT: I 256 MET cc_start: 0.5423 (ppp) cc_final: 0.4911 (ttp) REVERT: I 323 ARG cc_start: 0.7335 (tpp80) cc_final: 0.6922 (mtt-85) REVERT: I 349 GLU cc_start: 0.6541 (tp30) cc_final: 0.5948 (tp30) REVERT: I 389 TYR cc_start: 0.6892 (t80) cc_final: 0.6304 (t80) REVERT: I 394 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7286 (mm-40) REVERT: I 395 GLU cc_start: 0.6542 (mm-30) cc_final: 0.6219 (mm-30) REVERT: J 72 LYS cc_start: 0.6913 (mmtp) cc_final: 0.6668 (mmtm) REVERT: J 112 MET cc_start: 0.6087 (mtm) cc_final: 0.5689 (mtm) REVERT: J 124 ASN cc_start: 0.7475 (t0) cc_final: 0.7211 (t0) REVERT: J 158 MET cc_start: 0.7843 (mmm) cc_final: 0.5717 (mmm) REVERT: J 235 MET cc_start: 0.5365 (tpt) cc_final: 0.5027 (mmm) REVERT: J 323 ARG cc_start: 0.7236 (tpp80) cc_final: 0.6922 (mtt-85) REVERT: J 330 LEU cc_start: 0.5081 (mt) cc_final: 0.4506 (mp) REVERT: K 27 TYR cc_start: 0.6580 (m-80) cc_final: 0.5992 (m-10) REVERT: K 72 LYS cc_start: 0.7283 (mmtp) cc_final: 0.6848 (mttt) REVERT: K 108 GLU cc_start: 0.7107 (mp0) cc_final: 0.5555 (tm-30) REVERT: K 112 MET cc_start: 0.6028 (mtt) cc_final: 0.5381 (mtt) REVERT: K 116 ILE cc_start: 0.6680 (mm) cc_final: 0.6440 (mm) REVERT: K 124 ASN cc_start: 0.7218 (t0) cc_final: 0.6923 (t0) REVERT: K 158 MET cc_start: 0.7618 (mmm) cc_final: 0.7410 (mpp) REVERT: K 323 ARG cc_start: 0.7454 (tpp80) cc_final: 0.7106 (mtt-85) REVERT: K 330 LEU cc_start: 0.5093 (mt) cc_final: 0.4507 (mp) REVERT: K 349 GLU cc_start: 0.6810 (tp30) cc_final: 0.6441 (tp30) REVERT: K 370 THR cc_start: 0.7757 (p) cc_final: 0.7336 (p) REVERT: K 395 GLU cc_start: 0.6610 (mm-30) cc_final: 0.5917 (mm-30) REVERT: L 27 TYR cc_start: 0.7015 (m-80) cc_final: 0.6351 (m-80) REVERT: L 81 GLN cc_start: 0.7748 (mt0) cc_final: 0.7466 (tt0) REVERT: L 132 GLU cc_start: 0.6674 (tt0) cc_final: 0.6455 (tt0) REVERT: L 262 GLU cc_start: 0.7359 (pt0) cc_final: 0.7149 (pt0) REVERT: L 323 ARG cc_start: 0.7307 (tpp80) cc_final: 0.6884 (mtt-85) REVERT: L 349 GLU cc_start: 0.6511 (tp30) cc_final: 0.5911 (tp30) REVERT: L 394 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7712 (mm-40) outliers start: 6 outliers final: 1 residues processed: 874 average time/residue: 0.4640 time to fit residues: 667.9929 Evaluate side-chains 810 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 809 time to evaluate : 3.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 294 optimal weight: 0.0870 chunk 395 optimal weight: 0.0980 chunk 113 optimal weight: 4.9990 chunk 342 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 371 optimal weight: 8.9990 chunk 155 optimal weight: 0.0020 chunk 381 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.3168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 178 GLN C 178 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN E 124 ASN E 178 GLN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 GLN G 178 GLN H 124 ASN H 178 GLN I 178 GLN ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN L 124 ASN L 178 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.183395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.152049 restraints weight = 51642.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.156400 restraints weight = 32278.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.159409 restraints weight = 22468.968| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3915 r_free = 0.3915 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3904 r_free = 0.3904 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| r_final: 0.3904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 37788 Z= 0.160 Angle : 0.583 8.541 51132 Z= 0.287 Chirality : 0.041 0.210 5760 Planarity : 0.004 0.068 6660 Dihedral : 4.495 22.950 5208 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.10 % Allowed : 0.55 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.12), residues: 4632 helix: 0.93 (0.13), residues: 1836 sheet: -0.10 (0.21), residues: 492 loop : -2.24 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 83 HIS 0.004 0.001 HIS F 216 PHE 0.022 0.001 PHE G 78 TYR 0.016 0.001 TYR H 37 ARG 0.005 0.000 ARG G 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11041.26 seconds wall clock time: 198 minutes 45.27 seconds (11925.27 seconds total)