Starting phenix.real_space_refine on Sat Jan 20 07:40:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhp_32002/01_2024/7vhp_32002.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhp_32002/01_2024/7vhp_32002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhp_32002/01_2024/7vhp_32002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhp_32002/01_2024/7vhp_32002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhp_32002/01_2024/7vhp_32002.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhp_32002/01_2024/7vhp_32002.pdb" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 180 5.16 5 C 41784 2.51 5 N 11892 2.21 5 O 12744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 48": "OE1" <-> "OE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "E TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 304": "OE1" <-> "OE2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 181": "OD1" <-> "OD2" Residue "F TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 300": "OE1" <-> "OE2" Residue "F GLU 304": "OE1" <-> "OE2" Residue "F PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 314": "OE1" <-> "OE2" Residue "G ASP 77": "OD1" <-> "OD2" Residue "G ASP 125": "OD1" <-> "OD2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G GLU 221": "OE1" <-> "OE2" Residue "G GLU 274": "OE1" <-> "OE2" Residue "G PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 269": "NH1" <-> "NH2" Residue "I PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 48": "OE1" <-> "OE2" Residue "e ASP 62": "OD1" <-> "OD2" Residue "W GLU 48": "OE1" <-> "OE2" Residue "W TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 79": "OD1" <-> "OD2" Residue "Y TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 74": "OD1" <-> "OD2" Residue "a GLU 40": "OE1" <-> "OE2" Residue "a ASP 62": "OD1" <-> "OD2" Residue "a GLU 91": "OE1" <-> "OE2" Residue "c GLU 40": "OE1" <-> "OE2" Residue "c GLU 48": "OE1" <-> "OE2" Residue "c TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "g TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 304": "OE1" <-> "OE2" Residue "g PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 181": "OD1" <-> "OD2" Residue "i ARG 209": "NH1" <-> "NH2" Residue "i ARG 213": "NH1" <-> "NH2" Residue "i TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 314": "OE1" <-> "OE2" Residue "k ASP 77": "OD1" <-> "OD2" Residue "k ASP 125": "OD1" <-> "OD2" Residue "k GLU 218": "OE1" <-> "OE2" Residue "k GLU 221": "OE1" <-> "OE2" Residue "k GLU 274": "OE1" <-> "OE2" Residue "k PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 27": "OE1" <-> "OE2" Residue "m PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 263": "OE1" <-> "OE2" Residue "o GLU 265": "OE1" <-> "OE2" Residue "o ARG 266": "NH1" <-> "NH2" Residue "o ARG 269": "NH1" <-> "NH2" Residue "o PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 48": "OE1" <-> "OE2" Residue "s ASP 62": "OD1" <-> "OD2" Residue "X GLU 48": "OE1" <-> "OE2" Residue "X TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 79": "OD1" <-> "OD2" Residue "Z TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 74": "OD1" <-> "OD2" Residue "b GLU 40": "OE1" <-> "OE2" Residue "b ASP 62": "OD1" <-> "OD2" Residue "b GLU 91": "OE1" <-> "OE2" Residue "d GLU 40": "OE1" <-> "OE2" Residue "d GLU 48": "OE1" <-> "OE2" Residue "d TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 91": "OE1" <-> "OE2" Residue "h TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 304": "OE1" <-> "OE2" Residue "h PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 181": "OD1" <-> "OD2" Residue "j GLU 207": "OE1" <-> "OE2" Residue "j ARG 213": "NH1" <-> "NH2" Residue "j ASP 228": "OD1" <-> "OD2" Residue "j TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 314": "OE1" <-> "OE2" Residue "l ASP 77": "OD1" <-> "OD2" Residue "l ASP 125": "OD1" <-> "OD2" Residue "l GLU 218": "OE1" <-> "OE2" Residue "l GLU 221": "OE1" <-> "OE2" Residue "l GLU 274": "OE1" <-> "OE2" Residue "l PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 27": "OE1" <-> "OE2" Residue "n PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 121": "NH1" <-> "NH2" Residue "p ARG 269": "NH1" <-> "NH2" Residue "p PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 48": "OE1" <-> "OE2" Residue "t ASP 62": "OD1" <-> "OD2" Residue "J GLU 48": "OE1" <-> "OE2" Residue "J TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 79": "OD1" <-> "OD2" Residue "K TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 74": "OD1" <-> "OD2" Residue "L GLU 40": "OE1" <-> "OE2" Residue "L ASP 62": "OD1" <-> "OD2" Residue "L GLU 91": "OE1" <-> "OE2" Residue "M GLU 40": "OE1" <-> "OE2" Residue "M GLU 48": "OE1" <-> "OE2" Residue "M TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 91": "OE1" <-> "OE2" Residue "N TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 304": "OE1" <-> "OE2" Residue "N PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 181": "OD1" <-> "OD2" Residue "O ASP 215": "OD1" <-> "OD2" Residue "O TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 314": "OE1" <-> "OE2" Residue "P ASP 77": "OD1" <-> "OD2" Residue "P ASP 125": "OD1" <-> "OD2" Residue "P GLU 218": "OE1" <-> "OE2" Residue "P GLU 221": "OE1" <-> "OE2" Residue "P GLU 274": "OE1" <-> "OE2" Residue "P PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 48": "OE1" <-> "OE2" Residue "T ASP 62": "OD1" <-> "OD2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 66600 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "B" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "C" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "D" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "E" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "F" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "G" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "H" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "I" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "U" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "e" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "f" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "W" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "Y" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "a" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "c" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "g" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "i" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "k" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "m" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "o" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "q" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "s" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "u" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "X" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "Z" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "b" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "d" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "h" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "j" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "l" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "n" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "p" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "r" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "t" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "v" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "J" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "K" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "L" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "M" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "N" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "O" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "P" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "Q" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "R" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2397 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain breaks: 1 Chain: "S" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2121 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain: "T" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "V" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 516 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Time building chain proxies: 26.71, per 1000 atoms: 0.40 Number of scatterers: 66600 At special positions: 0 Unit cell: (225.141, 224.084, 172.291, 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 180 16.00 O 12744 8.00 N 11892 7.00 C 41784 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: 22.20 Conformation dependent library (CDL) restraints added in 9.0 seconds 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15840 Finding SS restraints... Secondary structure from input PDB file: 229 helices and 114 sheets defined 54.8% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.33 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 Processing helix chain 'A' and resid 75 through 84 removed outlier: 4.118A pdb=" N ASP A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 44 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'C' and resid 33 through 43 Processing helix chain 'C' and resid 74 through 84 removed outlier: 3.936A pdb=" N LEU C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 43 Processing helix chain 'D' and resid 75 through 84 removed outlier: 4.102A pdb=" N ASP D 79 " --> pdb=" O PRO D 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 96 Processing helix chain 'E' and resid 169 through 176 removed outlier: 3.554A pdb=" N TYR E 173 " --> pdb=" O ASN E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 199 removed outlier: 3.719A pdb=" N LYS E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR E 199 " --> pdb=" O VAL E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 206 Processing helix chain 'E' and resid 208 through 224 removed outlier: 4.034A pdb=" N ARG E 213 " --> pdb=" O ARG E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 318 removed outlier: 3.816A pdb=" N ALA E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Proline residue: E 277 - end of helix Proline residue: E 313 - end of helix Processing helix chain 'E' and resid 318 through 338 removed outlier: 3.524A pdb=" N THR E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 96 Processing helix chain 'F' and resid 169 through 176 Processing helix chain 'F' and resid 179 through 197 Processing helix chain 'F' and resid 200 through 208 Processing helix chain 'F' and resid 210 through 225 Processing helix chain 'F' and resid 244 through 246 No H-bonds generated for 'chain 'F' and resid 244 through 246' Processing helix chain 'F' and resid 247 through 318 removed outlier: 4.059A pdb=" N ARG F 258 " --> pdb=" O ALA F 254 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU F 259 " --> pdb=" O ILE F 255 " (cutoff:3.500A) Proline residue: F 277 - end of helix Proline residue: F 313 - end of helix removed outlier: 3.750A pdb=" N ALA F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 337 removed outlier: 3.709A pdb=" N THR F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 19 removed outlier: 3.505A pdb=" N ILE G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 107 Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 111 through 133 removed outlier: 3.591A pdb=" N ALA G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP G 125 " --> pdb=" O ARG G 121 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG G 133 " --> pdb=" O SER G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 142 Processing helix chain 'G' and resid 145 through 157 Processing helix chain 'G' and resid 216 through 289 removed outlier: 3.577A pdb=" N LEU G 282 " --> pdb=" O GLU G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 308 removed outlier: 3.532A pdb=" N TYR G 294 " --> pdb=" O ASP G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 326 removed outlier: 4.487A pdb=" N TYR G 325 " --> pdb=" O PHE G 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 19 Processing helix chain 'H' and resid 99 through 107 Processing helix chain 'H' and resid 111 through 134 removed outlier: 4.347A pdb=" N ALA H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 141 Processing helix chain 'H' and resid 146 through 156 Processing helix chain 'H' and resid 218 through 288 removed outlier: 3.737A pdb=" N VAL H 234 " --> pdb=" O GLU H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 307 removed outlier: 3.523A pdb=" N TYR H 294 " --> pdb=" O ASP H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 326 removed outlier: 4.472A pdb=" N TYR H 325 " --> pdb=" O PHE H 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 19 Processing helix chain 'I' and resid 99 through 107 Processing helix chain 'I' and resid 111 through 132 removed outlier: 4.438A pdb=" N ALA I 115 " --> pdb=" O ASP I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 147 removed outlier: 3.599A pdb=" N SER I 143 " --> pdb=" O ILE I 139 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ARG I 144 " --> pdb=" O VAL I 140 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY I 145 " --> pdb=" O THR I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 158 Processing helix chain 'I' and resid 216 through 288 removed outlier: 3.563A pdb=" N VAL I 234 " --> pdb=" O GLU I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 307 Processing helix chain 'I' and resid 321 through 326 removed outlier: 4.553A pdb=" N TYR I 325 " --> pdb=" O PHE I 322 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 96 Processing helix chain 'U' and resid 169 through 176 removed outlier: 3.700A pdb=" N TYR U 173 " --> pdb=" O ASN U 169 " (cutoff:3.500A) Processing helix chain 'U' and resid 179 through 199 removed outlier: 4.013A pdb=" N LYS U 198 " --> pdb=" O GLY U 194 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR U 199 " --> pdb=" O VAL U 195 " (cutoff:3.500A) Processing helix chain 'U' and resid 200 through 228 removed outlier: 7.128A pdb=" N ARG U 209 " --> pdb=" O LEU U 205 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR U 210 " --> pdb=" O THR U 206 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL U 211 " --> pdb=" O GLU U 207 " (cutoff:3.500A) Proline residue: U 226 - end of helix Processing helix chain 'U' and resid 244 through 318 removed outlier: 4.118A pdb=" N ALA U 249 " --> pdb=" O GLU U 245 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ALA U 250 " --> pdb=" O GLU U 246 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN U 262 " --> pdb=" O ARG U 258 " (cutoff:3.500A) Proline residue: U 277 - end of helix Proline residue: U 313 - end of helix removed outlier: 3.558A pdb=" N ALA U 318 " --> pdb=" O GLU U 314 " (cutoff:3.500A) Processing helix chain 'U' and resid 318 through 338 removed outlier: 3.597A pdb=" N THR U 322 " --> pdb=" O ALA U 318 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR U 338 " --> pdb=" O VAL U 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 43 removed outlier: 3.593A pdb=" N PHE e 37 " --> pdb=" O ASP e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 84 removed outlier: 4.453A pdb=" N LEU e 78 " --> pdb=" O ASP e 74 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP e 79 " --> pdb=" O PRO e 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 33 through 43 Processing helix chain 'f' and resid 75 through 84 removed outlier: 4.186A pdb=" N ASP f 79 " --> pdb=" O PRO f 75 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 43 Processing helix chain 'W' and resid 75 through 84 removed outlier: 4.118A pdb=" N ASP W 79 " --> pdb=" O PRO W 75 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 44 Processing helix chain 'Y' and resid 76 through 84 Processing helix chain 'a' and resid 33 through 43 Processing helix chain 'a' and resid 74 through 84 removed outlier: 3.935A pdb=" N LEU a 78 " --> pdb=" O ASP a 74 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 43 Processing helix chain 'c' and resid 75 through 84 removed outlier: 4.101A pdb=" N ASP c 79 " --> pdb=" O PRO c 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 80 through 96 Processing helix chain 'g' and resid 169 through 176 removed outlier: 3.554A pdb=" N TYR g 173 " --> pdb=" O ASN g 169 " (cutoff:3.500A) Processing helix chain 'g' and resid 179 through 199 removed outlier: 3.718A pdb=" N LYS g 198 " --> pdb=" O GLY g 194 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR g 199 " --> pdb=" O VAL g 195 " (cutoff:3.500A) Processing helix chain 'g' and resid 200 through 206 Processing helix chain 'g' and resid 208 through 224 removed outlier: 4.034A pdb=" N ARG g 213 " --> pdb=" O ARG g 209 " (cutoff:3.500A) Processing helix chain 'g' and resid 244 through 318 removed outlier: 3.816A pdb=" N ALA g 250 " --> pdb=" O GLU g 246 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE g 265 " --> pdb=" O GLU g 261 " (cutoff:3.500A) Proline residue: g 277 - end of helix Proline residue: g 313 - end of helix Processing helix chain 'g' and resid 318 through 338 removed outlier: 3.525A pdb=" N THR g 322 " --> pdb=" O ALA g 318 " (cutoff:3.500A) Processing helix chain 'i' and resid 80 through 96 Processing helix chain 'i' and resid 169 through 176 Processing helix chain 'i' and resid 179 through 199 removed outlier: 3.904A pdb=" N TYR i 199 " --> pdb=" O VAL i 195 " (cutoff:3.500A) Processing helix chain 'i' and resid 200 through 228 removed outlier: 5.766A pdb=" N ARG i 209 " --> pdb=" O LEU i 205 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N THR i 210 " --> pdb=" O THR i 206 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN i 217 " --> pdb=" O ARG i 213 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG i 218 " --> pdb=" O SER i 214 " (cutoff:3.500A) Proline residue: i 226 - end of helix Processing helix chain 'i' and resid 244 through 246 No H-bonds generated for 'chain 'i' and resid 244 through 246' Processing helix chain 'i' and resid 247 through 318 removed outlier: 4.058A pdb=" N ARG i 258 " --> pdb=" O ALA i 254 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU i 259 " --> pdb=" O ILE i 255 " (cutoff:3.500A) Proline residue: i 277 - end of helix Proline residue: i 313 - end of helix removed outlier: 3.749A pdb=" N ALA i 318 " --> pdb=" O GLU i 314 " (cutoff:3.500A) Processing helix chain 'i' and resid 318 through 337 removed outlier: 3.709A pdb=" N THR i 322 " --> pdb=" O ALA i 318 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 19 removed outlier: 3.504A pdb=" N ILE k 6 " --> pdb=" O ARG k 2 " (cutoff:3.500A) Processing helix chain 'k' and resid 99 through 107 Processing helix chain 'k' and resid 108 through 110 No H-bonds generated for 'chain 'k' and resid 108 through 110' Processing helix chain 'k' and resid 111 through 133 removed outlier: 3.591A pdb=" N ALA k 115 " --> pdb=" O ASP k 111 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP k 125 " --> pdb=" O ARG k 121 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG k 133 " --> pdb=" O SER k 129 " (cutoff:3.500A) Processing helix chain 'k' and resid 135 through 142 Processing helix chain 'k' and resid 145 through 157 Processing helix chain 'k' and resid 216 through 289 removed outlier: 3.577A pdb=" N LEU k 282 " --> pdb=" O GLU k 278 " (cutoff:3.500A) Processing helix chain 'k' and resid 290 through 308 removed outlier: 3.532A pdb=" N TYR k 294 " --> pdb=" O ASP k 290 " (cutoff:3.500A) Processing helix chain 'm' and resid 2 through 19 Processing helix chain 'm' and resid 99 through 107 Processing helix chain 'm' and resid 111 through 134 removed outlier: 4.348A pdb=" N ALA m 115 " --> pdb=" O ASP m 111 " (cutoff:3.500A) Processing helix chain 'm' and resid 135 through 141 Processing helix chain 'm' and resid 146 through 156 Processing helix chain 'm' and resid 218 through 288 removed outlier: 3.737A pdb=" N VAL m 234 " --> pdb=" O GLU m 230 " (cutoff:3.500A) Processing helix chain 'm' and resid 290 through 307 removed outlier: 3.524A pdb=" N TYR m 294 " --> pdb=" O ASP m 290 " (cutoff:3.500A) Processing helix chain 'm' and resid 321 through 326 removed outlier: 4.472A pdb=" N TYR m 325 " --> pdb=" O PHE m 322 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 19 Processing helix chain 'o' and resid 99 through 107 Processing helix chain 'o' and resid 111 through 132 removed outlier: 4.438A pdb=" N ALA o 115 " --> pdb=" O ASP o 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE o 131 " --> pdb=" O LEU o 127 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY o 132 " --> pdb=" O ARG o 128 " (cutoff:3.500A) Processing helix chain 'o' and resid 135 through 147 removed outlier: 3.599A pdb=" N SER o 143 " --> pdb=" O ILE o 139 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ARG o 144 " --> pdb=" O VAL o 140 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY o 145 " --> pdb=" O THR o 141 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 158 Processing helix chain 'o' and resid 216 through 288 removed outlier: 3.563A pdb=" N VAL o 234 " --> pdb=" O GLU o 230 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA o 264 " --> pdb=" O THR o 260 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLN o 267 " --> pdb=" O GLU o 263 " (cutoff:3.500A) Processing helix chain 'o' and resid 290 through 307 Processing helix chain 'o' and resid 321 through 326 removed outlier: 4.553A pdb=" N TYR o 325 " --> pdb=" O PHE o 322 " (cutoff:3.500A) Processing helix chain 'q' and resid 80 through 96 Processing helix chain 'q' and resid 169 through 176 removed outlier: 3.700A pdb=" N TYR q 173 " --> pdb=" O ASN q 169 " (cutoff:3.500A) Processing helix chain 'q' and resid 179 through 199 removed outlier: 4.013A pdb=" N LYS q 198 " --> pdb=" O GLY q 194 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR q 199 " --> pdb=" O VAL q 195 " (cutoff:3.500A) Processing helix chain 'q' and resid 200 through 228 removed outlier: 7.128A pdb=" N ARG q 209 " --> pdb=" O LEU q 205 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR q 210 " --> pdb=" O THR q 206 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL q 211 " --> pdb=" O GLU q 207 " (cutoff:3.500A) Proline residue: q 226 - end of helix Processing helix chain 'q' and resid 244 through 318 removed outlier: 4.118A pdb=" N ALA q 249 " --> pdb=" O GLU q 245 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA q 250 " --> pdb=" O GLU q 246 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN q 262 " --> pdb=" O ARG q 258 " (cutoff:3.500A) Proline residue: q 277 - end of helix Proline residue: q 313 - end of helix removed outlier: 3.558A pdb=" N ALA q 318 " --> pdb=" O GLU q 314 " (cutoff:3.500A) Processing helix chain 'q' and resid 318 through 338 removed outlier: 3.598A pdb=" N THR q 322 " --> pdb=" O ALA q 318 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR q 338 " --> pdb=" O VAL q 334 " (cutoff:3.500A) Processing helix chain 's' and resid 33 through 43 removed outlier: 3.594A pdb=" N PHE s 37 " --> pdb=" O ASP s 33 " (cutoff:3.500A) Processing helix chain 's' and resid 74 through 84 removed outlier: 4.453A pdb=" N LEU s 78 " --> pdb=" O ASP s 74 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP s 79 " --> pdb=" O PRO s 75 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 43 Processing helix chain 'u' and resid 75 through 84 removed outlier: 4.186A pdb=" N ASP u 79 " --> pdb=" O PRO u 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 43 Processing helix chain 'X' and resid 75 through 84 removed outlier: 4.117A pdb=" N ASP X 79 " --> pdb=" O PRO X 75 " (cutoff:3.500A) Processing helix chain 'Z' and resid 33 through 44 Processing helix chain 'Z' and resid 76 through 84 Processing helix chain 'b' and resid 33 through 43 Processing helix chain 'b' and resid 74 through 84 removed outlier: 3.936A pdb=" N LEU b 78 " --> pdb=" O ASP b 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 33 through 43 Processing helix chain 'd' and resid 75 through 84 removed outlier: 4.102A pdb=" N ASP d 79 " --> pdb=" O PRO d 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 80 through 96 Processing helix chain 'h' and resid 169 through 176 removed outlier: 3.554A pdb=" N TYR h 173 " --> pdb=" O ASN h 169 " (cutoff:3.500A) Processing helix chain 'h' and resid 179 through 199 removed outlier: 3.718A pdb=" N LYS h 198 " --> pdb=" O GLY h 194 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR h 199 " --> pdb=" O VAL h 195 " (cutoff:3.500A) Processing helix chain 'h' and resid 200 through 206 Processing helix chain 'h' and resid 208 through 224 removed outlier: 4.034A pdb=" N ARG h 213 " --> pdb=" O ARG h 209 " (cutoff:3.500A) Processing helix chain 'h' and resid 244 through 318 removed outlier: 3.816A pdb=" N ALA h 250 " --> pdb=" O GLU h 246 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE h 265 " --> pdb=" O GLU h 261 " (cutoff:3.500A) Proline residue: h 277 - end of helix Proline residue: h 313 - end of helix Processing helix chain 'h' and resid 318 through 338 removed outlier: 3.524A pdb=" N THR h 322 " --> pdb=" O ALA h 318 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 96 Processing helix chain 'j' and resid 169 through 176 Processing helix chain 'j' and resid 179 through 197 Processing helix chain 'j' and resid 200 through 224 removed outlier: 5.475A pdb=" N ARG j 209 " --> pdb=" O LEU j 205 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR j 210 " --> pdb=" O THR j 206 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL j 211 " --> pdb=" O GLU j 207 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER j 214 " --> pdb=" O THR j 210 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU j 221 " --> pdb=" O GLN j 217 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU j 222 " --> pdb=" O ARG j 218 " (cutoff:3.500A) Processing helix chain 'j' and resid 244 through 246 No H-bonds generated for 'chain 'j' and resid 244 through 246' Processing helix chain 'j' and resid 247 through 318 removed outlier: 4.059A pdb=" N ARG j 258 " --> pdb=" O ALA j 254 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU j 259 " --> pdb=" O ILE j 255 " (cutoff:3.500A) Proline residue: j 277 - end of helix removed outlier: 3.508A pdb=" N LYS j 310 " --> pdb=" O ALA j 306 " (cutoff:3.500A) Proline residue: j 313 - end of helix removed outlier: 3.750A pdb=" N ALA j 318 " --> pdb=" O GLU j 314 " (cutoff:3.500A) Processing helix chain 'j' and resid 318 through 337 removed outlier: 3.709A pdb=" N THR j 322 " --> pdb=" O ALA j 318 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 19 removed outlier: 3.504A pdb=" N ILE l 6 " --> pdb=" O ARG l 2 " (cutoff:3.500A) Processing helix chain 'l' and resid 99 through 107 Processing helix chain 'l' and resid 108 through 110 No H-bonds generated for 'chain 'l' and resid 108 through 110' Processing helix chain 'l' and resid 111 through 133 removed outlier: 3.591A pdb=" N ALA l 115 " --> pdb=" O ASP l 111 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP l 125 " --> pdb=" O ARG l 121 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG l 133 " --> pdb=" O SER l 129 " (cutoff:3.500A) Processing helix chain 'l' and resid 135 through 142 Processing helix chain 'l' and resid 145 through 157 Processing helix chain 'l' and resid 216 through 289 removed outlier: 3.577A pdb=" N LEU l 282 " --> pdb=" O GLU l 278 " (cutoff:3.500A) Processing helix chain 'l' and resid 290 through 308 removed outlier: 3.532A pdb=" N TYR l 294 " --> pdb=" O ASP l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 320 through 326 removed outlier: 4.517A pdb=" N TYR l 325 " --> pdb=" O PHE l 322 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 19 Processing helix chain 'n' and resid 99 through 107 Processing helix chain 'n' and resid 111 through 134 removed outlier: 4.348A pdb=" N ALA n 115 " --> pdb=" O ASP n 111 " (cutoff:3.500A) Processing helix chain 'n' and resid 135 through 141 Processing helix chain 'n' and resid 146 through 156 Processing helix chain 'n' and resid 218 through 288 removed outlier: 3.737A pdb=" N VAL n 234 " --> pdb=" O GLU n 230 " (cutoff:3.500A) Processing helix chain 'n' and resid 290 through 307 removed outlier: 3.524A pdb=" N TYR n 294 " --> pdb=" O ASP n 290 " (cutoff:3.500A) Processing helix chain 'n' and resid 321 through 326 removed outlier: 4.472A pdb=" N TYR n 325 " --> pdb=" O PHE n 322 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 19 Processing helix chain 'p' and resid 99 through 107 Processing helix chain 'p' and resid 111 through 132 removed outlier: 4.121A pdb=" N ALA p 115 " --> pdb=" O ASP p 111 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) Processing helix chain 'p' and resid 135 through 147 removed outlier: 3.599A pdb=" N SER p 143 " --> pdb=" O ILE p 139 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ARG p 144 " --> pdb=" O VAL p 140 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY p 145 " --> pdb=" O THR p 141 " (cutoff:3.500A) Processing helix chain 'p' and resid 147 through 158 Processing helix chain 'p' and resid 216 through 288 removed outlier: 3.563A pdb=" N VAL p 234 " --> pdb=" O GLU p 230 " (cutoff:3.500A) Processing helix chain 'p' and resid 290 through 307 Processing helix chain 'p' and resid 321 through 326 removed outlier: 4.553A pdb=" N TYR p 325 " --> pdb=" O PHE p 322 " (cutoff:3.500A) Processing helix chain 'r' and resid 80 through 96 Processing helix chain 'r' and resid 169 through 176 removed outlier: 3.699A pdb=" N TYR r 173 " --> pdb=" O ASN r 169 " (cutoff:3.500A) Processing helix chain 'r' and resid 179 through 199 removed outlier: 4.013A pdb=" N LYS r 198 " --> pdb=" O GLY r 194 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR r 199 " --> pdb=" O VAL r 195 " (cutoff:3.500A) Processing helix chain 'r' and resid 200 through 228 removed outlier: 7.128A pdb=" N ARG r 209 " --> pdb=" O LEU r 205 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR r 210 " --> pdb=" O THR r 206 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL r 211 " --> pdb=" O GLU r 207 " (cutoff:3.500A) Proline residue: r 226 - end of helix Processing helix chain 'r' and resid 244 through 318 removed outlier: 4.118A pdb=" N ALA r 249 " --> pdb=" O GLU r 245 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA r 250 " --> pdb=" O GLU r 246 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN r 262 " --> pdb=" O ARG r 258 " (cutoff:3.500A) Proline residue: r 277 - end of helix Proline residue: r 313 - end of helix removed outlier: 3.558A pdb=" N ALA r 318 " --> pdb=" O GLU r 314 " (cutoff:3.500A) Processing helix chain 'r' and resid 318 through 338 removed outlier: 3.597A pdb=" N THR r 322 " --> pdb=" O ALA r 318 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR r 338 " --> pdb=" O VAL r 334 " (cutoff:3.500A) Processing helix chain 't' and resid 33 through 43 removed outlier: 3.594A pdb=" N PHE t 37 " --> pdb=" O ASP t 33 " (cutoff:3.500A) Processing helix chain 't' and resid 74 through 84 removed outlier: 4.454A pdb=" N LEU t 78 " --> pdb=" O ASP t 74 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP t 79 " --> pdb=" O PRO t 75 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 43 Processing helix chain 'v' and resid 75 through 84 removed outlier: 4.185A pdb=" N ASP v 79 " --> pdb=" O PRO v 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 43 Processing helix chain 'J' and resid 75 through 84 removed outlier: 4.118A pdb=" N ASP J 79 " --> pdb=" O PRO J 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 44 Processing helix chain 'K' and resid 76 through 84 Processing helix chain 'L' and resid 33 through 43 Processing helix chain 'L' and resid 74 through 84 removed outlier: 3.936A pdb=" N LEU L 78 " --> pdb=" O ASP L 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 43 Processing helix chain 'M' and resid 75 through 84 removed outlier: 4.102A pdb=" N ASP M 79 " --> pdb=" O PRO M 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 96 Processing helix chain 'N' and resid 169 through 176 removed outlier: 3.554A pdb=" N TYR N 173 " --> pdb=" O ASN N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 199 removed outlier: 3.718A pdb=" N LYS N 198 " --> pdb=" O GLY N 194 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR N 199 " --> pdb=" O VAL N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 206 Processing helix chain 'N' and resid 208 through 224 removed outlier: 4.035A pdb=" N ARG N 213 " --> pdb=" O ARG N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 244 through 318 removed outlier: 3.816A pdb=" N ALA N 250 " --> pdb=" O GLU N 246 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE N 265 " --> pdb=" O GLU N 261 " (cutoff:3.500A) Proline residue: N 277 - end of helix Proline residue: N 313 - end of helix Processing helix chain 'N' and resid 318 through 338 removed outlier: 3.524A pdb=" N THR N 322 " --> pdb=" O ALA N 318 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 96 Processing helix chain 'O' and resid 169 through 176 Processing helix chain 'O' and resid 179 through 197 Processing helix chain 'O' and resid 200 through 208 Processing helix chain 'O' and resid 210 through 225 removed outlier: 3.572A pdb=" N THR O 216 " --> pdb=" O ILE O 212 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU O 222 " --> pdb=" O ARG O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 244 through 246 No H-bonds generated for 'chain 'O' and resid 244 through 246' Processing helix chain 'O' and resid 247 through 318 removed outlier: 4.058A pdb=" N ARG O 258 " --> pdb=" O ALA O 254 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU O 259 " --> pdb=" O ILE O 255 " (cutoff:3.500A) Proline residue: O 277 - end of helix Proline residue: O 313 - end of helix removed outlier: 3.751A pdb=" N ALA O 318 " --> pdb=" O GLU O 314 " (cutoff:3.500A) Processing helix chain 'O' and resid 318 through 337 removed outlier: 3.709A pdb=" N THR O 322 " --> pdb=" O ALA O 318 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 19 removed outlier: 3.504A pdb=" N ILE P 6 " --> pdb=" O ARG P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 107 Processing helix chain 'P' and resid 108 through 110 No H-bonds generated for 'chain 'P' and resid 108 through 110' Processing helix chain 'P' and resid 111 through 133 removed outlier: 3.591A pdb=" N ALA P 115 " --> pdb=" O ASP P 111 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP P 125 " --> pdb=" O ARG P 121 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG P 133 " --> pdb=" O SER P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 135 through 142 Processing helix chain 'P' and resid 145 through 157 Processing helix chain 'P' and resid 216 through 289 removed outlier: 3.577A pdb=" N LEU P 282 " --> pdb=" O GLU P 278 " (cutoff:3.500A) Processing helix chain 'P' and resid 290 through 308 removed outlier: 3.533A pdb=" N TYR P 294 " --> pdb=" O ASP P 290 " (cutoff:3.500A) Processing helix chain 'P' and resid 320 through 325 removed outlier: 4.414A pdb=" N TYR P 325 " --> pdb=" O PHE P 322 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 19 Processing helix chain 'Q' and resid 99 through 107 Processing helix chain 'Q' and resid 111 through 134 removed outlier: 4.348A pdb=" N ALA Q 115 " --> pdb=" O ASP Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 135 through 141 Processing helix chain 'Q' and resid 146 through 156 Processing helix chain 'Q' and resid 218 through 288 removed outlier: 3.737A pdb=" N VAL Q 234 " --> pdb=" O GLU Q 230 " (cutoff:3.500A) Processing helix chain 'Q' and resid 290 through 307 removed outlier: 3.523A pdb=" N TYR Q 294 " --> pdb=" O ASP Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 321 through 326 removed outlier: 4.472A pdb=" N TYR Q 325 " --> pdb=" O PHE Q 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 19 Processing helix chain 'R' and resid 99 through 107 Processing helix chain 'R' and resid 111 through 132 removed outlier: 4.438A pdb=" N ALA R 115 " --> pdb=" O ASP R 111 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY R 132 " --> pdb=" O ARG R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 147 removed outlier: 3.598A pdb=" N SER R 143 " --> pdb=" O ILE R 139 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ARG R 144 " --> pdb=" O VAL R 140 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY R 145 " --> pdb=" O THR R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 158 Processing helix chain 'R' and resid 216 through 288 removed outlier: 3.563A pdb=" N VAL R 234 " --> pdb=" O GLU R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 307 Processing helix chain 'R' and resid 321 through 326 removed outlier: 4.553A pdb=" N TYR R 325 " --> pdb=" O PHE R 322 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 96 Processing helix chain 'S' and resid 169 through 176 removed outlier: 3.700A pdb=" N TYR S 173 " --> pdb=" O ASN S 169 " (cutoff:3.500A) Processing helix chain 'S' and resid 179 through 199 removed outlier: 4.012A pdb=" N LYS S 198 " --> pdb=" O GLY S 194 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR S 199 " --> pdb=" O VAL S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 200 through 228 removed outlier: 7.128A pdb=" N ARG S 209 " --> pdb=" O LEU S 205 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR S 210 " --> pdb=" O THR S 206 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL S 211 " --> pdb=" O GLU S 207 " (cutoff:3.500A) Proline residue: S 226 - end of helix Processing helix chain 'S' and resid 244 through 318 removed outlier: 4.118A pdb=" N ALA S 249 " --> pdb=" O GLU S 245 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA S 250 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN S 262 " --> pdb=" O ARG S 258 " (cutoff:3.500A) Proline residue: S 277 - end of helix Proline residue: S 313 - end of helix removed outlier: 3.558A pdb=" N ALA S 318 " --> pdb=" O GLU S 314 " (cutoff:3.500A) Processing helix chain 'S' and resid 318 through 338 removed outlier: 3.597A pdb=" N THR S 322 " --> pdb=" O ALA S 318 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR S 338 " --> pdb=" O VAL S 334 " (cutoff:3.500A) Processing helix chain 'T' and resid 33 through 43 removed outlier: 3.593A pdb=" N PHE T 37 " --> pdb=" O ASP T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 84 removed outlier: 4.453A pdb=" N LEU T 78 " --> pdb=" O ASP T 74 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP T 79 " --> pdb=" O PRO T 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 43 Processing helix chain 'V' and resid 75 through 84 removed outlier: 4.187A pdb=" N ASP V 79 " --> pdb=" O PRO V 75 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.380A pdb=" N TYR A 69 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG A 47 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL A 89 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA A 49 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 65 through 69 removed outlier: 3.776A pdb=" N GLU B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG B 47 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL B 89 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA B 49 " --> pdb=" O VAL B 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 65 through 69 removed outlier: 6.509A pdb=" N ARG C 47 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL C 89 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA C 49 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 65 through 69 removed outlier: 6.445A pdb=" N ARG D 47 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL D 89 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA D 49 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'E' and resid 113 through 118 removed outlier: 4.943A pdb=" N PHE E 114 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG E 110 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU E 131 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 141 through 150 removed outlier: 6.751A pdb=" N GLU E 160 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG E 166 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU E 233 " --> pdb=" O ARG E 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 339 through 341 removed outlier: 5.801A pdb=" N ARG F 339 " --> pdb=" O MET G 314 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS E 340 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL G 315 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU E 342 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG E 339 " --> pdb=" O MET H 314 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N MET H 316 " --> pdb=" O ARG E 339 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL E 341 " --> pdb=" O MET H 316 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP I 312 " --> pdb=" O ARG U 339 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL U 341 " --> pdb=" O ASP I 312 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N MET I 314 " --> pdb=" O VAL U 341 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG O 339 " --> pdb=" O MET P 314 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS N 340 " --> pdb=" O VAL P 313 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL P 315 " --> pdb=" O LYS N 340 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU N 342 " --> pdb=" O VAL P 315 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG N 339 " --> pdb=" O MET Q 314 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N MET Q 316 " --> pdb=" O ARG N 339 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL N 341 " --> pdb=" O MET Q 316 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N MET R 314 " --> pdb=" O VAL S 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AB1, first strand: chain 'F' and resid 113 through 118 removed outlier: 5.042A pdb=" N PHE F 114 " --> pdb=" O ARG F 110 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG F 110 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS F 116 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 141 through 150 removed outlier: 6.662A pdb=" N ARG F 158 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA F 240 " --> pdb=" O ARG F 158 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLU F 160 " --> pdb=" O PHE F 238 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N PHE F 238 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN F 162 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL F 236 " --> pdb=" O ASN F 162 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN F 164 " --> pdb=" O LEU F 234 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 20 through 22 Processing sheet with id=AB4, first strand: chain 'G' and resid 27 through 33 Processing sheet with id=AB5, first strand: chain 'G' and resid 39 through 40 Processing sheet with id=AB6, first strand: chain 'G' and resid 70 through 80 removed outlier: 4.059A pdb=" N SER G 91 " --> pdb=" O ASN G 74 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA G 76 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL G 89 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG G 78 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU G 87 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE G 88 " --> pdb=" O ILE G 213 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE G 213 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP G 90 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP G 207 " --> pdb=" O LYS G 94 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG G 96 " --> pdb=" O VAL G 205 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL G 205 " --> pdb=" O ARG G 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 21 through 22 Processing sheet with id=AB8, first strand: chain 'H' and resid 47 through 48 Processing sheet with id=AB9, first strand: chain 'H' and resid 39 through 40 removed outlier: 3.638A pdb=" N LYS H 44 " --> pdb=" O ASP H 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 70 through 80 removed outlier: 3.959A pdb=" N ALA H 76 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL H 89 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG H 78 " --> pdb=" O LEU H 87 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU H 87 " --> pdb=" O ARG H 78 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE H 88 " --> pdb=" O GLN H 212 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN H 212 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP H 90 " --> pdb=" O ILE H 210 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE H 210 " --> pdb=" O ASP H 90 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR H 92 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL H 208 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS H 94 " --> pdb=" O VAL H 206 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 20 through 21 Processing sheet with id=AC3, first strand: chain 'I' and resid 27 through 28 Processing sheet with id=AC4, first strand: chain 'I' and resid 32 through 33 Processing sheet with id=AC5, first strand: chain 'I' and resid 70 through 74 removed outlier: 3.631A pdb=" N SER I 91 " --> pdb=" O ASN I 74 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 70 through 74 removed outlier: 3.631A pdb=" N SER I 91 " --> pdb=" O ASN I 74 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR I 92 " --> pdb=" O ILE I 210 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE I 210 " --> pdb=" O TYR I 92 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LYS I 94 " --> pdb=" O VAL I 208 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL I 208 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG I 96 " --> pdb=" O VAL I 206 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL I 206 " --> pdb=" O ARG I 96 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 97 through 100 Processing sheet with id=AC8, first strand: chain 'U' and resid 116 through 118 Processing sheet with id=AC9, first strand: chain 'U' and resid 141 through 150 removed outlier: 6.651A pdb=" N GLU U 160 " --> pdb=" O GLN U 239 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG U 166 " --> pdb=" O LEU U 233 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU U 233 " --> pdb=" O ARG U 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'e' and resid 65 through 69 removed outlier: 6.192A pdb=" N ARG e 47 " --> pdb=" O LYS e 87 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL e 89 " --> pdb=" O ARG e 47 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA e 49 " --> pdb=" O VAL e 89 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 65 through 69 removed outlier: 6.488A pdb=" N ARG f 47 " --> pdb=" O LYS f 87 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL f 89 " --> pdb=" O ARG f 47 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA f 49 " --> pdb=" O VAL f 89 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'W' and resid 31 through 32 removed outlier: 4.380A pdb=" N TYR W 69 " --> pdb=" O VAL W 32 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU W 48 " --> pdb=" O THR W 59 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG W 47 " --> pdb=" O LYS W 87 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL W 89 " --> pdb=" O ARG W 47 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA W 49 " --> pdb=" O VAL W 89 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Y' and resid 65 through 69 removed outlier: 3.776A pdb=" N GLU Y 48 " --> pdb=" O THR Y 59 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ARG Y 47 " --> pdb=" O LYS Y 87 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL Y 89 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA Y 49 " --> pdb=" O VAL Y 89 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'a' and resid 65 through 69 removed outlier: 6.509A pdb=" N ARG a 47 " --> pdb=" O LYS a 87 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL a 89 " --> pdb=" O ARG a 47 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA a 49 " --> pdb=" O VAL a 89 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'c' and resid 65 through 69 removed outlier: 6.445A pdb=" N ARG c 47 " --> pdb=" O LYS c 87 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL c 89 " --> pdb=" O ARG c 47 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA c 49 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'g' and resid 97 through 98 Processing sheet with id=AD8, first strand: chain 'g' and resid 113 through 118 removed outlier: 4.943A pdb=" N PHE g 114 " --> pdb=" O ARG g 110 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG g 110 " --> pdb=" O PHE g 114 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU g 131 " --> pdb=" O THR g 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'g' and resid 141 through 150 removed outlier: 6.752A pdb=" N GLU g 160 " --> pdb=" O GLN g 239 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG g 166 " --> pdb=" O LEU g 233 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU g 233 " --> pdb=" O ARG g 166 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'o' and resid 313 through 316 removed outlier: 6.387A pdb=" N MET o 314 " --> pdb=" O VAL q 341 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG g 339 " --> pdb=" O MET m 314 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N MET m 316 " --> pdb=" O ARG g 339 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL g 341 " --> pdb=" O MET m 316 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS g 340 " --> pdb=" O VAL k 313 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL k 315 " --> pdb=" O LYS g 340 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU g 342 " --> pdb=" O VAL k 315 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ARG i 339 " --> pdb=" O MET k 314 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS i 340 " --> pdb=" O VAL p 313 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL p 315 " --> pdb=" O LYS i 340 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP p 312 " --> pdb=" O ARG r 339 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL r 341 " --> pdb=" O ASP p 312 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N MET p 314 " --> pdb=" O VAL r 341 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG h 339 " --> pdb=" O MET n 314 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N MET n 316 " --> pdb=" O ARG h 339 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL h 341 " --> pdb=" O MET n 316 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS h 340 " --> pdb=" O VAL l 313 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL l 315 " --> pdb=" O LYS h 340 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU h 342 " --> pdb=" O VAL l 315 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ARG j 339 " --> pdb=" O MET l 314 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'i' and resid 97 through 98 Processing sheet with id=AE3, first strand: chain 'i' and resid 113 through 118 removed outlier: 5.042A pdb=" N PHE i 114 " --> pdb=" O ARG i 110 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG i 110 " --> pdb=" O PHE i 114 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS i 116 " --> pdb=" O VAL i 108 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'i' and resid 141 through 150 removed outlier: 3.810A pdb=" N ALA i 240 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN i 162 " --> pdb=" O PHE i 238 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N PHE i 238 " --> pdb=" O ASN i 162 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLN i 164 " --> pdb=" O VAL i 236 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL i 236 " --> pdb=" O GLN i 164 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ARG i 166 " --> pdb=" O LEU i 234 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU i 234 " --> pdb=" O ARG i 166 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'k' and resid 20 through 22 Processing sheet with id=AE6, first strand: chain 'k' and resid 27 through 33 Processing sheet with id=AE7, first strand: chain 'k' and resid 39 through 40 Processing sheet with id=AE8, first strand: chain 'k' and resid 70 through 80 removed outlier: 4.058A pdb=" N SER k 91 " --> pdb=" O ASN k 74 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA k 76 " --> pdb=" O VAL k 89 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL k 89 " --> pdb=" O ALA k 76 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG k 78 " --> pdb=" O LEU k 87 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU k 87 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE k 88 " --> pdb=" O ILE k 213 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE k 213 " --> pdb=" O ILE k 88 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP k 90 " --> pdb=" O LYS k 211 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP k 207 " --> pdb=" O LYS k 94 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG k 96 " --> pdb=" O VAL k 205 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL k 205 " --> pdb=" O ARG k 96 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'm' and resid 21 through 22 Processing sheet with id=AF1, first strand: chain 'm' and resid 47 through 48 Processing sheet with id=AF2, first strand: chain 'm' and resid 39 through 40 removed outlier: 3.637A pdb=" N LYS m 44 " --> pdb=" O ASP m 40 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'm' and resid 70 through 80 removed outlier: 3.959A pdb=" N ALA m 76 " --> pdb=" O VAL m 89 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL m 89 " --> pdb=" O ALA m 76 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG m 78 " --> pdb=" O LEU m 87 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU m 87 " --> pdb=" O ARG m 78 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE m 88 " --> pdb=" O GLN m 212 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN m 212 " --> pdb=" O ILE m 88 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP m 90 " --> pdb=" O ILE m 210 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE m 210 " --> pdb=" O ASP m 90 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR m 92 " --> pdb=" O VAL m 208 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL m 208 " --> pdb=" O TYR m 92 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS m 94 " --> pdb=" O VAL m 206 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'o' and resid 20 through 21 Processing sheet with id=AF5, first strand: chain 'o' and resid 27 through 28 Processing sheet with id=AF6, first strand: chain 'o' and resid 32 through 33 Processing sheet with id=AF7, first strand: chain 'o' and resid 70 through 74 removed outlier: 3.632A pdb=" N SER o 91 " --> pdb=" O ASN o 74 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'o' and resid 70 through 74 removed outlier: 3.632A pdb=" N SER o 91 " --> pdb=" O ASN o 74 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR o 92 " --> pdb=" O ILE o 210 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE o 210 " --> pdb=" O TYR o 92 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LYS o 94 " --> pdb=" O VAL o 208 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL o 208 " --> pdb=" O LYS o 94 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG o 96 " --> pdb=" O VAL o 206 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL o 206 " --> pdb=" O ARG o 96 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'q' and resid 97 through 100 Processing sheet with id=AG1, first strand: chain 'q' and resid 116 through 118 Processing sheet with id=AG2, first strand: chain 'q' and resid 141 through 150 removed outlier: 6.651A pdb=" N GLU q 160 " --> pdb=" O GLN q 239 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG q 166 " --> pdb=" O LEU q 233 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU q 233 " --> pdb=" O ARG q 166 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 's' and resid 65 through 69 removed outlier: 6.192A pdb=" N ARG s 47 " --> pdb=" O LYS s 87 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL s 89 " --> pdb=" O ARG s 47 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA s 49 " --> pdb=" O VAL s 89 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'u' and resid 65 through 69 removed outlier: 6.487A pdb=" N ARG u 47 " --> pdb=" O LYS u 87 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL u 89 " --> pdb=" O ARG u 47 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA u 49 " --> pdb=" O VAL u 89 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 31 through 32 removed outlier: 4.380A pdb=" N TYR X 69 " --> pdb=" O VAL X 32 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU X 48 " --> pdb=" O THR X 59 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG X 47 " --> pdb=" O LYS X 87 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL X 89 " --> pdb=" O ARG X 47 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA X 49 " --> pdb=" O VAL X 89 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Z' and resid 65 through 69 removed outlier: 3.776A pdb=" N GLU Z 48 " --> pdb=" O THR Z 59 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ARG Z 47 " --> pdb=" O LYS Z 87 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL Z 89 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA Z 49 " --> pdb=" O VAL Z 89 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'b' and resid 65 through 69 removed outlier: 6.508A pdb=" N ARG b 47 " --> pdb=" O LYS b 87 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL b 89 " --> pdb=" O ARG b 47 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA b 49 " --> pdb=" O VAL b 89 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'd' and resid 65 through 69 removed outlier: 6.445A pdb=" N ARG d 47 " --> pdb=" O LYS d 87 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL d 89 " --> pdb=" O ARG d 47 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA d 49 " --> pdb=" O VAL d 89 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'h' and resid 97 through 98 Processing sheet with id=AH1, first strand: chain 'h' and resid 113 through 118 removed outlier: 4.943A pdb=" N PHE h 114 " --> pdb=" O ARG h 110 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG h 110 " --> pdb=" O PHE h 114 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU h 131 " --> pdb=" O THR h 109 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'h' and resid 141 through 150 removed outlier: 6.751A pdb=" N GLU h 160 " --> pdb=" O GLN h 239 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG h 166 " --> pdb=" O LEU h 233 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU h 233 " --> pdb=" O ARG h 166 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'j' and resid 97 through 98 Processing sheet with id=AH4, first strand: chain 'j' and resid 113 through 118 removed outlier: 5.042A pdb=" N PHE j 114 " --> pdb=" O ARG j 110 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG j 110 " --> pdb=" O PHE j 114 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS j 116 " --> pdb=" O VAL j 108 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'j' and resid 141 through 150 removed outlier: 6.662A pdb=" N ARG j 158 " --> pdb=" O ALA j 240 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA j 240 " --> pdb=" O ARG j 158 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLU j 160 " --> pdb=" O PHE j 238 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N PHE j 238 " --> pdb=" O GLU j 160 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN j 162 " --> pdb=" O VAL j 236 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL j 236 " --> pdb=" O ASN j 162 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN j 164 " --> pdb=" O LEU j 234 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'l' and resid 20 through 22 Processing sheet with id=AH7, first strand: chain 'l' and resid 27 through 33 Processing sheet with id=AH8, first strand: chain 'l' and resid 39 through 40 Processing sheet with id=AH9, first strand: chain 'l' and resid 70 through 80 removed outlier: 4.059A pdb=" N SER l 91 " --> pdb=" O ASN l 74 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA l 76 " --> pdb=" O VAL l 89 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL l 89 " --> pdb=" O ALA l 76 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG l 78 " --> pdb=" O LEU l 87 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU l 87 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE l 88 " --> pdb=" O ILE l 213 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE l 213 " --> pdb=" O ILE l 88 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP l 90 " --> pdb=" O LYS l 211 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP l 207 " --> pdb=" O LYS l 94 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG l 96 " --> pdb=" O VAL l 205 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL l 205 " --> pdb=" O ARG l 96 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'n' and resid 21 through 22 Processing sheet with id=AI2, first strand: chain 'n' and resid 47 through 48 Processing sheet with id=AI3, first strand: chain 'n' and resid 39 through 40 removed outlier: 3.637A pdb=" N LYS n 44 " --> pdb=" O ASP n 40 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'n' and resid 70 through 80 removed outlier: 3.958A pdb=" N ALA n 76 " --> pdb=" O VAL n 89 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL n 89 " --> pdb=" O ALA n 76 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG n 78 " --> pdb=" O LEU n 87 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU n 87 " --> pdb=" O ARG n 78 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE n 88 " --> pdb=" O GLN n 212 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN n 212 " --> pdb=" O ILE n 88 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP n 90 " --> pdb=" O ILE n 210 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE n 210 " --> pdb=" O ASP n 90 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR n 92 " --> pdb=" O VAL n 208 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL n 208 " --> pdb=" O TYR n 92 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LYS n 94 " --> pdb=" O VAL n 206 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'p' and resid 20 through 21 Processing sheet with id=AI6, first strand: chain 'p' and resid 27 through 28 Processing sheet with id=AI7, first strand: chain 'p' and resid 32 through 33 Processing sheet with id=AI8, first strand: chain 'p' and resid 70 through 74 removed outlier: 3.631A pdb=" N SER p 91 " --> pdb=" O ASN p 74 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'p' and resid 70 through 74 removed outlier: 3.631A pdb=" N SER p 91 " --> pdb=" O ASN p 74 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR p 92 " --> pdb=" O ILE p 210 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE p 210 " --> pdb=" O TYR p 92 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LYS p 94 " --> pdb=" O VAL p 208 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL p 208 " --> pdb=" O LYS p 94 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG p 96 " --> pdb=" O VAL p 206 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL p 206 " --> pdb=" O ARG p 96 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'r' and resid 97 through 100 Processing sheet with id=AJ2, first strand: chain 'r' and resid 116 through 118 Processing sheet with id=AJ3, first strand: chain 'r' and resid 141 through 150 removed outlier: 6.651A pdb=" N GLU r 160 " --> pdb=" O GLN r 239 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG r 166 " --> pdb=" O LEU r 233 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU r 233 " --> pdb=" O ARG r 166 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 't' and resid 65 through 69 removed outlier: 6.192A pdb=" N ARG t 47 " --> pdb=" O LYS t 87 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL t 89 " --> pdb=" O ARG t 47 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA t 49 " --> pdb=" O VAL t 89 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'v' and resid 65 through 69 removed outlier: 6.488A pdb=" N ARG v 47 " --> pdb=" O LYS v 87 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL v 89 " --> pdb=" O ARG v 47 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA v 49 " --> pdb=" O VAL v 89 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'J' and resid 31 through 32 removed outlier: 4.380A pdb=" N TYR J 69 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU J 48 " --> pdb=" O THR J 59 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG J 47 " --> pdb=" O LYS J 87 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL J 89 " --> pdb=" O ARG J 47 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA J 49 " --> pdb=" O VAL J 89 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'K' and resid 65 through 69 removed outlier: 3.776A pdb=" N GLU K 48 " --> pdb=" O THR K 59 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ARG K 47 " --> pdb=" O LYS K 87 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL K 89 " --> pdb=" O ARG K 47 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA K 49 " --> pdb=" O VAL K 89 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'L' and resid 65 through 69 removed outlier: 6.509A pdb=" N ARG L 47 " --> pdb=" O LYS L 87 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL L 89 " --> pdb=" O ARG L 47 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA L 49 " --> pdb=" O VAL L 89 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'M' and resid 65 through 69 removed outlier: 6.444A pdb=" N ARG M 47 " --> pdb=" O LYS M 87 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL M 89 " --> pdb=" O ARG M 47 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA M 49 " --> pdb=" O VAL M 89 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'N' and resid 97 through 98 Processing sheet with id=AK2, first strand: chain 'N' and resid 113 through 118 removed outlier: 4.943A pdb=" N PHE N 114 " --> pdb=" O ARG N 110 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG N 110 " --> pdb=" O PHE N 114 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU N 131 " --> pdb=" O THR N 109 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'N' and resid 141 through 150 removed outlier: 6.751A pdb=" N GLU N 160 " --> pdb=" O GLN N 239 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG N 166 " --> pdb=" O LEU N 233 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU N 233 " --> pdb=" O ARG N 166 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'O' and resid 97 through 98 Processing sheet with id=AK5, first strand: chain 'O' and resid 113 through 118 removed outlier: 5.042A pdb=" N PHE O 114 " --> pdb=" O ARG O 110 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG O 110 " --> pdb=" O PHE O 114 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS O 116 " --> pdb=" O VAL O 108 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'O' and resid 141 through 150 removed outlier: 6.662A pdb=" N ARG O 158 " --> pdb=" O ALA O 240 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA O 240 " --> pdb=" O ARG O 158 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N GLU O 160 " --> pdb=" O PHE O 238 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N PHE O 238 " --> pdb=" O GLU O 160 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN O 162 " --> pdb=" O VAL O 236 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL O 236 " --> pdb=" O ASN O 162 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN O 164 " --> pdb=" O LEU O 234 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'P' and resid 20 through 22 Processing sheet with id=AK8, first strand: chain 'P' and resid 27 through 33 Processing sheet with id=AK9, first strand: chain 'P' and resid 39 through 40 Processing sheet with id=AL1, first strand: chain 'P' and resid 70 through 80 removed outlier: 4.059A pdb=" N SER P 91 " --> pdb=" O ASN P 74 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA P 76 " --> pdb=" O VAL P 89 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL P 89 " --> pdb=" O ALA P 76 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG P 78 " --> pdb=" O LEU P 87 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU P 87 " --> pdb=" O ARG P 78 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE P 88 " --> pdb=" O ILE P 213 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE P 213 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP P 90 " --> pdb=" O LYS P 211 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP P 207 " --> pdb=" O LYS P 94 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG P 96 " --> pdb=" O VAL P 205 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL P 205 " --> pdb=" O ARG P 96 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'Q' and resid 21 through 22 Processing sheet with id=AL3, first strand: chain 'Q' and resid 47 through 48 Processing sheet with id=AL4, first strand: chain 'Q' and resid 39 through 40 removed outlier: 3.637A pdb=" N LYS Q 44 " --> pdb=" O ASP Q 40 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'Q' and resid 70 through 80 removed outlier: 3.959A pdb=" N ALA Q 76 " --> pdb=" O VAL Q 89 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL Q 89 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG Q 78 " --> pdb=" O LEU Q 87 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU Q 87 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE Q 88 " --> pdb=" O GLN Q 212 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN Q 212 " --> pdb=" O ILE Q 88 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASP Q 90 " --> pdb=" O ILE Q 210 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE Q 210 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR Q 92 " --> pdb=" O VAL Q 208 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL Q 208 " --> pdb=" O TYR Q 92 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS Q 94 " --> pdb=" O VAL Q 206 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'R' and resid 20 through 21 Processing sheet with id=AL7, first strand: chain 'R' and resid 27 through 28 Processing sheet with id=AL8, first strand: chain 'R' and resid 32 through 33 Processing sheet with id=AL9, first strand: chain 'R' and resid 70 through 74 removed outlier: 3.631A pdb=" N SER R 91 " --> pdb=" O ASN R 74 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'R' and resid 70 through 74 removed outlier: 3.631A pdb=" N SER R 91 " --> pdb=" O ASN R 74 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR R 92 " --> pdb=" O ILE R 210 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE R 210 " --> pdb=" O TYR R 92 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LYS R 94 " --> pdb=" O VAL R 208 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL R 208 " --> pdb=" O LYS R 94 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG R 96 " --> pdb=" O VAL R 206 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL R 206 " --> pdb=" O ARG R 96 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'S' and resid 97 through 100 Processing sheet with id=AM3, first strand: chain 'S' and resid 116 through 118 Processing sheet with id=AM4, first strand: chain 'S' and resid 141 through 150 removed outlier: 6.651A pdb=" N GLU S 160 " --> pdb=" O GLN S 239 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG S 166 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU S 233 " --> pdb=" O ARG S 166 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'T' and resid 65 through 69 removed outlier: 6.192A pdb=" N ARG T 47 " --> pdb=" O LYS T 87 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL T 89 " --> pdb=" O ARG T 47 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA T 49 " --> pdb=" O VAL T 89 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'V' and resid 65 through 69 removed outlier: 6.488A pdb=" N ARG V 47 " --> pdb=" O LYS V 87 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL V 89 " --> pdb=" O ARG V 47 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA V 49 " --> pdb=" O VAL V 89 " (cutoff:3.500A) 4158 hydrogen bonds defined for protein. 12114 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: 27.68 Time building geometry restraints manager: 24.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 12369 1.32 - 1.45: 15764 1.45 - 1.57: 39067 1.57 - 1.69: 0 1.69 - 1.81: 360 Bond restraints: 67560 Sorted by residual: bond pdb=" C ILE F 212 " pdb=" O ILE F 212 " ideal model delta sigma weight residual 1.237 1.202 0.034 1.13e-02 7.83e+03 9.25e+00 bond pdb=" C ARG F 213 " pdb=" O ARG F 213 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.19e-02 7.06e+03 8.15e+00 bond pdb=" CA ILE F 212 " pdb=" C ILE F 212 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.22e-02 6.72e+03 5.36e+00 bond pdb=" C SER F 214 " pdb=" O SER F 214 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.19e-02 7.06e+03 4.99e+00 bond pdb=" C ASP F 215 " pdb=" O ASP F 215 " ideal model delta sigma weight residual 1.237 1.211 0.025 1.17e-02 7.31e+03 4.67e+00 ... (remaining 67555 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.04: 1046 105.04 - 112.27: 33965 112.27 - 119.50: 22298 119.50 - 126.72: 33472 126.72 - 133.95: 431 Bond angle restraints: 91212 Sorted by residual: angle pdb=" N ILE O 212 " pdb=" CA ILE O 212 " pdb=" C ILE O 212 " ideal model delta sigma weight residual 110.53 117.22 -6.69 9.40e-01 1.13e+00 5.07e+01 angle pdb=" N ILE p 112 " pdb=" CA ILE p 112 " pdb=" C ILE p 112 " ideal model delta sigma weight residual 110.62 117.64 -7.02 1.02e+00 9.61e-01 4.74e+01 angle pdb=" N ALA o 264 " pdb=" CA ALA o 264 " pdb=" C ALA o 264 " ideal model delta sigma weight residual 110.80 98.99 11.81 2.13e+00 2.20e-01 3.07e+01 angle pdb=" N ILE i 224 " pdb=" CA ILE i 224 " pdb=" C ILE i 224 " ideal model delta sigma weight residual 110.72 116.21 -5.49 1.01e+00 9.80e-01 2.95e+01 angle pdb=" N ILE I 131 " pdb=" CA ILE I 131 " pdb=" C ILE I 131 " ideal model delta sigma weight residual 110.72 115.86 -5.14 1.01e+00 9.80e-01 2.59e+01 ... (remaining 91207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 37488 17.00 - 34.00: 3716 34.00 - 51.00: 609 51.00 - 68.00: 67 68.00 - 85.00: 60 Dihedral angle restraints: 41940 sinusoidal: 17532 harmonic: 24408 Sorted by residual: dihedral pdb=" CA GLY q 208 " pdb=" C GLY q 208 " pdb=" N ARG q 209 " pdb=" CA ARG q 209 " ideal model delta harmonic sigma weight residual -180.00 -156.39 -23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLY U 208 " pdb=" C GLY U 208 " pdb=" N ARG U 209 " pdb=" CA ARG U 209 " ideal model delta harmonic sigma weight residual -180.00 -156.40 -23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLY S 208 " pdb=" C GLY S 208 " pdb=" N ARG S 209 " pdb=" CA ARG S 209 " ideal model delta harmonic sigma weight residual -180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 41937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 8608 0.059 - 0.117: 1539 0.117 - 0.176: 192 0.176 - 0.235: 16 0.235 - 0.293: 1 Chirality restraints: 10356 Sorted by residual: chirality pdb=" CA ALA o 264 " pdb=" N ALA o 264 " pdb=" C ALA o 264 " pdb=" CB ALA o 264 " both_signs ideal model delta sigma weight residual False 2.48 2.78 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ILE j 298 " pdb=" N ILE j 298 " pdb=" C ILE j 298 " pdb=" CB ILE j 298 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ASP j 228 " pdb=" N ASP j 228 " pdb=" C ASP j 228 " pdb=" CB ASP j 228 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 10353 not shown) Planarity restraints: 11940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY O 208 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C GLY O 208 " 0.063 2.00e-02 2.50e+03 pdb=" O GLY O 208 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG O 209 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN o 194 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.18e+00 pdb=" N PRO o 195 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO o 195 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO o 195 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 194 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO I 195 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO I 195 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO I 195 " 0.041 5.00e-02 4.00e+02 ... (remaining 11937 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 43 1.90 - 2.65: 991 2.65 - 3.40: 94775 3.40 - 4.15: 152189 4.15 - 4.90: 281621 Nonbonded interactions: 529619 Sorted by model distance: nonbonded pdb=" O GLU p 263 " pdb=" CD GLN p 267 " model vdw 1.149 3.270 nonbonded pdb=" OE2 GLU i 221 " pdb=" NH1 ARG i 225 " model vdw 1.151 2.520 nonbonded pdb=" CG2 VAL j 195 " pdb=" OD2 ASP j 215 " model vdw 1.301 3.460 nonbonded pdb=" CE1 TYR j 227 " pdb=" CD LYS l 94 " model vdw 1.301 3.740 nonbonded pdb=" OE1 GLU i 221 " pdb=" NH2 ARG i 225 " model vdw 1.309 2.520 ... (remaining 529614 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 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'N' selection = chain 'O' selection = chain 'S' selection = chain 'U' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 0.070 Extract box with map and model: 14.870 Check model and map are aligned: 0.760 Set scattering table: 0.460 Process input model: 143.370 Find NCS groups from input model: 4.310 Set up NCS constraints: 0.780 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:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 67560 Z= 0.200 Angle : 0.632 11.808 91212 Z= 0.375 Chirality : 0.045 0.293 10356 Planarity : 0.004 0.076 11940 Dihedral : 13.465 85.002 26100 Min Nonbonded Distance : 1.149 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.84 % Rotamer: Outliers : 0.32 % Allowed : 0.55 % Favored : 99.13 % 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: 1.82 (0.09), residues: 8184 helix: 2.46 (0.08), residues: 4148 sheet: 0.93 (0.15), residues: 1368 loop : -0.71 (0.12), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP U 92 HIS 0.002 0.001 HIS Q 53 PHE 0.023 0.001 PHE G 287 TYR 0.020 0.001 TYR Q 17 ARG 0.011 0.000 ARG M 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1940 residues out of total 7224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1917 time to evaluate : 7.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 ASN cc_start: 0.4997 (m-40) cc_final: 0.4672 (m-40) REVERT: B 70 ILE cc_start: 0.7879 (mt) cc_final: 0.7436 (pt) REVERT: B 78 LEU cc_start: 0.6665 (pp) cc_final: 0.6422 (tt) REVERT: D 91 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6569 (mt-10) REVERT: E 242 ARG cc_start: 0.7265 (mmm-85) cc_final: 0.6795 (ptp-110) REVERT: E 252 ASP cc_start: 0.7306 (m-30) cc_final: 0.6000 (m-30) REVERT: E 345 ASP cc_start: 0.6389 (m-30) cc_final: 0.5980 (m-30) REVERT: F 131 GLU cc_start: 0.6628 (tp30) cc_final: 0.6397 (mp0) REVERT: F 158 ARG cc_start: 0.7151 (mmm-85) cc_final: 0.6858 (tpp80) REVERT: F 214 SER cc_start: 0.7548 (t) cc_final: 0.7216 (p) REVERT: F 344 ASN cc_start: 0.8178 (t0) cc_final: 0.7830 (t0) REVERT: H 319 ASP cc_start: 0.8146 (t70) cc_final: 0.7930 (t0) REVERT: I 18 MET cc_start: 0.6600 (tpt) cc_final: 0.6365 (mmp) REVERT: I 84 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7584 (mptt) REVERT: I 125 ASP cc_start: 0.7814 (t0) cc_final: 0.7362 (m-30) REVERT: I 232 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7821 (mm-30) REVERT: I 316 MET cc_start: 0.7340 (mtm) cc_final: 0.7135 (mtp) REVERT: U 148 VAL cc_start: 0.8408 (t) cc_final: 0.8153 (m) REVERT: U 162 ASN cc_start: 0.7860 (m-40) cc_final: 0.7453 (m-40) REVERT: U 164 GLN cc_start: 0.8239 (mt0) cc_final: 0.7916 (mt0) REVERT: e 31 LYS cc_start: 0.7172 (tppt) cc_final: 0.6864 (tptt) REVERT: e 43 ASN cc_start: 0.7474 (t0) cc_final: 0.7156 (m-40) REVERT: e 76 LYS cc_start: 0.5960 (mmmt) cc_final: 0.5693 (ptmt) REVERT: f 76 LYS cc_start: 0.8455 (mmmt) cc_final: 0.7685 (ptmm) REVERT: f 77 LEU cc_start: 0.8005 (tt) cc_final: 0.7598 (tt) REVERT: W 76 LYS cc_start: 0.4857 (ptmt) cc_final: 0.4549 (mtpt) REVERT: Y 57 ASN cc_start: 0.5566 (m-40) cc_final: 0.4662 (m-40) REVERT: Y 69 TYR cc_start: 0.6086 (m-80) cc_final: 0.5882 (m-80) REVERT: Y 70 ILE cc_start: 0.7303 (mt) cc_final: 0.6899 (pt) REVERT: a 40 GLU cc_start: 0.5082 (tt0) cc_final: 0.4711 (tt0) REVERT: c 34 TYR cc_start: 0.5267 (t80) cc_final: 0.4987 (t80) REVERT: c 65 ARG cc_start: 0.6486 (mtp-110) cc_final: 0.6153 (ptm-80) REVERT: c 70 ILE cc_start: 0.5886 (mp) cc_final: 0.5278 (mp) REVERT: i 132 VAL cc_start: 0.6650 (p) cc_final: 0.6444 (p) REVERT: i 146 SER cc_start: 0.6845 (t) cc_final: 0.6600 (p) REVERT: i 162 ASN cc_start: 0.8631 (m-40) cc_final: 0.8362 (m-40) REVERT: i 237 ASN cc_start: 0.7799 (p0) cc_final: 0.7122 (p0) REVERT: k 18 MET cc_start: 0.5515 (mmp) cc_final: 0.5281 (mtt) REVERT: k 74 ASN cc_start: 0.7598 (m110) cc_final: 0.7298 (m110) REVERT: k 265 GLU cc_start: 0.8009 (tp30) cc_final: 0.7765 (tp30) REVERT: k 314 MET cc_start: 0.8273 (ttt) cc_final: 0.7838 (ttm) REVERT: m 120 LYS cc_start: 0.8229 (ttmm) cc_final: 0.7978 (mttt) REVERT: m 198 MET cc_start: 0.7348 (mmt) cc_final: 0.6971 (mmt) REVERT: m 319 ASP cc_start: 0.8330 (t70) cc_final: 0.8084 (t0) REVERT: q 100 ILE cc_start: 0.7504 (mt) cc_final: 0.7133 (tt) REVERT: q 153 ASP cc_start: 0.7896 (m-30) cc_final: 0.7649 (p0) REVERT: q 210 THR cc_start: 0.7227 (p) cc_final: 0.6868 (p) REVERT: q 248 LYS cc_start: 0.7728 (ttmt) cc_final: 0.7196 (ttmm) REVERT: q 267 GLU cc_start: 0.7799 (tp30) cc_final: 0.7583 (tp30) REVERT: s 38 LEU cc_start: 0.8125 (mt) cc_final: 0.7885 (tt) REVERT: s 47 ARG cc_start: 0.7156 (ttm170) cc_final: 0.6826 (ttp-170) REVERT: s 79 ASP cc_start: 0.6790 (m-30) cc_final: 0.6495 (t70) REVERT: u 50 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7594 (mtp85) REVERT: u 76 LYS cc_start: 0.8291 (mmmt) cc_final: 0.7510 (ptmt) REVERT: u 80 ASN cc_start: 0.8145 (t0) cc_final: 0.7857 (t0) REVERT: X 76 LYS cc_start: 0.4770 (ptmt) cc_final: 0.4426 (tptt) REVERT: Z 57 ASN cc_start: 0.5614 (m-40) cc_final: 0.4464 (m110) REVERT: Z 70 ILE cc_start: 0.7505 (mt) cc_final: 0.7218 (pt) REVERT: h 274 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7857 (tt0) REVERT: j 162 ASN cc_start: 0.8469 (m-40) cc_final: 0.7842 (m110) REVERT: j 344 ASN cc_start: 0.8479 (t0) cc_final: 0.8250 (t0) REVERT: l 74 ASN cc_start: 0.7554 (m110) cc_final: 0.7128 (m110) REVERT: l 212 GLN cc_start: 0.7476 (pt0) cc_final: 0.7268 (pm20) REVERT: l 314 MET cc_start: 0.8522 (ttt) cc_final: 0.8156 (ttm) REVERT: l 321 ASP cc_start: 0.7531 (m-30) cc_final: 0.7231 (p0) REVERT: n 198 MET cc_start: 0.7335 (mmt) cc_final: 0.7025 (tpp) REVERT: n 227 MET cc_start: 0.8387 (mtm) cc_final: 0.8163 (mtp) REVERT: n 316 MET cc_start: 0.7998 (mtm) cc_final: 0.7463 (mtm) REVERT: n 319 ASP cc_start: 0.8285 (t70) cc_final: 0.7943 (t0) REVERT: p 125 ASP cc_start: 0.7523 (t0) cc_final: 0.7208 (m-30) REVERT: p 314 MET cc_start: 0.8088 (ttm) cc_final: 0.7582 (mtp) REVERT: r 149 MET cc_start: 0.6860 (mmm) cc_final: 0.6050 (mpp) REVERT: r 153 ASP cc_start: 0.7912 (m-30) cc_final: 0.7618 (p0) REVERT: r 161 MET cc_start: 0.7749 (mmt) cc_final: 0.7483 (mmm) REVERT: r 186 GLN cc_start: 0.7805 (mt0) cc_final: 0.7603 (mm-40) REVERT: r 210 THR cc_start: 0.6957 (p) cc_final: 0.6726 (p) REVERT: r 238 PHE cc_start: 0.8249 (t80) cc_final: 0.7792 (t80) REVERT: r 248 LYS cc_start: 0.7505 (ttmt) cc_final: 0.6782 (ttmm) REVERT: r 331 MET cc_start: 0.7396 (mmm) cc_final: 0.7142 (mmm) REVERT: t 56 ILE cc_start: 0.8773 (mt) cc_final: 0.8571 (mp) REVERT: v 76 LYS cc_start: 0.8651 (mmmt) cc_final: 0.8045 (ptmt) REVERT: J 34 TYR cc_start: 0.5304 (t80) cc_final: 0.5034 (t80) REVERT: J 76 LYS cc_start: 0.5415 (ptmt) cc_final: 0.5126 (ptmm) REVERT: K 39 GLN cc_start: 0.7101 (tp40) cc_final: 0.6861 (tp40) REVERT: K 62 ASP cc_start: 0.6284 (p0) cc_final: 0.6005 (p0) REVERT: K 70 ILE cc_start: 0.7272 (mt) cc_final: 0.6687 (pt) REVERT: L 40 GLU cc_start: 0.5737 (tt0) cc_final: 0.5453 (tt0) REVERT: M 70 ILE cc_start: 0.6100 (mp) cc_final: 0.5896 (mp) REVERT: M 87 LYS cc_start: 0.6989 (ttmm) cc_final: 0.6364 (tppt) REVERT: N 198 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8280 (pttt) REVERT: O 160 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7261 (mt-10) REVERT: P 240 SER cc_start: 0.7937 (t) cc_final: 0.7719 (m) REVERT: P 310 ASN cc_start: 0.6645 (t0) cc_final: 0.6179 (t0) REVERT: Q 70 GLN cc_start: 0.8150 (mt0) cc_final: 0.7903 (mt0) REVERT: Q 214 ASN cc_start: 0.8232 (m-40) cc_final: 0.7932 (t0) REVERT: R 18 MET cc_start: 0.6125 (tpt) cc_final: 0.5823 (mmp) REVERT: R 96 ARG cc_start: 0.7743 (ttp-110) cc_final: 0.7416 (ttp-170) REVERT: S 161 MET cc_start: 0.7997 (mmt) cc_final: 0.7743 (mmm) REVERT: S 248 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7533 (ttmm) REVERT: T 47 ARG cc_start: 0.7598 (ttm170) cc_final: 0.7085 (ttp-170) REVERT: T 48 GLU cc_start: 0.7663 (tt0) cc_final: 0.7355 (mp0) REVERT: T 79 ASP cc_start: 0.6886 (m-30) cc_final: 0.6273 (t70) REVERT: V 76 LYS cc_start: 0.8588 (mmmt) cc_final: 0.7821 (ptmm) REVERT: V 77 LEU cc_start: 0.8100 (tt) cc_final: 0.7827 (tt) REVERT: V 80 ASN cc_start: 0.8539 (t0) cc_final: 0.8276 (t0) outliers start: 23 outliers final: 6 residues processed: 1932 average time/residue: 0.6878 time to fit residues: 2164.9072 Evaluate side-chains 948 residues out of total 7224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 942 time to evaluate : 6.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain i residue 195 VAL Chi-restraints excluded: chain j residue 213 ARG Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 223 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 678 optimal weight: 1.9990 chunk 609 optimal weight: 10.0000 chunk 338 optimal weight: 8.9990 chunk 208 optimal weight: 3.9990 chunk 411 optimal weight: 9.9990 chunk 325 optimal weight: 5.9990 chunk 630 optimal weight: 8.9990 chunk 243 optimal weight: 2.9990 chunk 383 optimal weight: 0.9990 chunk 469 optimal weight: 7.9990 chunk 730 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN F 116 HIS F 155 ASN G 310 ASN I 70 GLN U 239 GLN e 64 ASN W 52 ASN a 42 ASN g 260 ASN k 70 GLN m 75 GLN o 114 GLN o 310 ASN q 217 GLN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 337 ASN p 114 GLN p 156 ASN p 310 ASN t 64 ASN v 39 GLN J 52 ASN K 39 GLN L 42 ASN Q 196 ASN ** V 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 67560 Z= 0.310 Angle : 0.608 7.206 91212 Z= 0.329 Chirality : 0.046 0.201 10356 Planarity : 0.005 0.049 11940 Dihedral : 4.364 38.467 9334 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.15 % Favored : 96.84 % Rotamer: Outliers : 1.91 % Allowed : 11.03 % Favored : 87.06 % 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: 1.69 (0.09), residues: 8184 helix: 2.28 (0.08), residues: 4296 sheet: 0.80 (0.14), residues: 1504 loop : -0.86 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP U 92 HIS 0.007 0.001 HIS F 116 PHE 0.029 0.002 PHE k 287 TYR 0.023 0.002 TYR I 224 ARG 0.006 0.001 ARG n 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 7224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1024 time to evaluate : 6.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.5185 (t80) cc_final: 0.4797 (t80) REVERT: A 77 LEU cc_start: 0.6665 (pp) cc_final: 0.6412 (mt) REVERT: B 43 ASN cc_start: 0.7002 (t0) cc_final: 0.6498 (t0) REVERT: B 54 ARG cc_start: 0.4179 (mtp-110) cc_final: 0.3894 (ttm-80) REVERT: D 89 VAL cc_start: 0.5652 (t) cc_final: 0.5324 (p) REVERT: E 242 ARG cc_start: 0.7462 (mmm-85) cc_final: 0.6902 (ptp-110) REVERT: F 131 GLU cc_start: 0.6685 (tp30) cc_final: 0.6325 (mp0) REVERT: G 326 MET cc_start: 0.8495 (mmt) cc_final: 0.8238 (mtt) REVERT: H 198 MET cc_start: 0.7308 (mtp) cc_final: 0.6969 (tpp) REVERT: H 311 GLN cc_start: 0.6871 (mp-120) cc_final: 0.6653 (mp10) REVERT: I 63 LYS cc_start: 0.6282 (pptt) cc_final: 0.5991 (ptmm) REVERT: I 84 LYS cc_start: 0.7893 (mtmt) cc_final: 0.7605 (mppt) REVERT: I 117 VAL cc_start: 0.7717 (t) cc_final: 0.7504 (m) REVERT: I 125 ASP cc_start: 0.8199 (t0) cc_final: 0.7676 (m-30) REVERT: U 148 VAL cc_start: 0.8629 (t) cc_final: 0.8269 (m) REVERT: U 149 MET cc_start: 0.6975 (mmt) cc_final: 0.6760 (mtt) REVERT: U 162 ASN cc_start: 0.8024 (m-40) cc_final: 0.7476 (m-40) REVERT: U 169 ASN cc_start: 0.6971 (p0) cc_final: 0.6757 (p0) REVERT: U 238 PHE cc_start: 0.7954 (t80) cc_final: 0.7621 (t80) REVERT: U 239 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7939 (mt0) REVERT: e 42 ASN cc_start: 0.8074 (t0) cc_final: 0.7726 (t0) REVERT: e 76 LYS cc_start: 0.6091 (mmmt) cc_final: 0.5805 (pttp) REVERT: f 76 LYS cc_start: 0.8436 (mmmt) cc_final: 0.7601 (ptmm) REVERT: Y 30 ARG cc_start: 0.4800 (ttt90) cc_final: 0.4493 (ttt-90) REVERT: Y 43 ASN cc_start: 0.7576 (t0) cc_final: 0.6991 (t0) REVERT: Y 45 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7128 (mp10) REVERT: Y 69 TYR cc_start: 0.6349 (m-80) cc_final: 0.6048 (m-80) REVERT: Y 70 ILE cc_start: 0.7010 (mt) cc_final: 0.6729 (pt) REVERT: Y 87 LYS cc_start: 0.6666 (OUTLIER) cc_final: 0.6279 (mtpt) REVERT: c 34 TYR cc_start: 0.5428 (t80) cc_final: 0.4990 (t80) REVERT: c 46 VAL cc_start: 0.6691 (p) cc_final: 0.6301 (m) REVERT: c 59 THR cc_start: 0.6442 (m) cc_final: 0.5663 (p) REVERT: c 70 ILE cc_start: 0.5659 (mp) cc_final: 0.5144 (mp) REVERT: c 84 LYS cc_start: 0.6191 (mmtt) cc_final: 0.5975 (tttt) REVERT: g 331 MET cc_start: 0.8321 (mmm) cc_final: 0.8014 (mmm) REVERT: i 229 MET cc_start: 0.7438 (mtm) cc_final: 0.7153 (ttm) REVERT: i 287 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8411 (mt) REVERT: k 265 GLU cc_start: 0.8090 (tp30) cc_final: 0.7491 (tp30) REVERT: k 314 MET cc_start: 0.8463 (ttt) cc_final: 0.8129 (ttm) REVERT: m 72 MET cc_start: 0.8492 (ptm) cc_final: 0.8281 (ptm) REVERT: m 120 LYS cc_start: 0.8293 (ttmm) cc_final: 0.7985 (mttm) REVERT: m 319 ASP cc_start: 0.8386 (t70) cc_final: 0.8184 (t0) REVERT: q 100 ILE cc_start: 0.7392 (mt) cc_final: 0.7180 (tt) REVERT: q 238 PHE cc_start: 0.8283 (t80) cc_final: 0.8034 (t80) REVERT: q 239 GLN cc_start: 0.8573 (tt0) cc_final: 0.8048 (mt0) REVERT: q 267 GLU cc_start: 0.7702 (tp30) cc_final: 0.7396 (tp30) REVERT: s 47 ARG cc_start: 0.7347 (ttm170) cc_final: 0.7071 (ttp-170) REVERT: s 76 LYS cc_start: 0.5756 (ptmt) cc_final: 0.5034 (tmtt) REVERT: s 79 ASP cc_start: 0.7027 (m-30) cc_final: 0.6500 (t70) REVERT: u 76 LYS cc_start: 0.8422 (mmmt) cc_final: 0.7640 (ptmt) REVERT: X 55 GLU cc_start: 0.4836 (tm-30) cc_final: 0.4596 (tp30) REVERT: X 76 LYS cc_start: 0.4922 (ptmt) cc_final: 0.4525 (tptt) REVERT: Z 43 ASN cc_start: 0.7754 (t0) cc_final: 0.7206 (t0) REVERT: b 70 ILE cc_start: 0.4524 (mp) cc_final: 0.4240 (mm) REVERT: d 34 TYR cc_start: 0.5807 (t80) cc_final: 0.5219 (t80) REVERT: d 47 ARG cc_start: 0.6291 (tmm-80) cc_final: 0.6010 (tmm160) REVERT: d 70 ILE cc_start: 0.5758 (mp) cc_final: 0.5153 (mm) REVERT: d 89 VAL cc_start: 0.5966 (t) cc_final: 0.5720 (p) REVERT: l 18 MET cc_start: 0.6727 (tpp) cc_final: 0.5212 (mtt) REVERT: l 135 ASP cc_start: 0.7179 (m-30) cc_final: 0.6936 (m-30) REVERT: l 237 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7249 (ttm170) REVERT: l 241 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7602 (tm-30) REVERT: l 314 MET cc_start: 0.8551 (ttt) cc_final: 0.8186 (ttm) REVERT: n 316 MET cc_start: 0.8172 (mtm) cc_final: 0.7589 (mtm) REVERT: n 319 ASP cc_start: 0.8341 (t70) cc_final: 0.8063 (t0) REVERT: p 84 LYS cc_start: 0.8060 (mtmt) cc_final: 0.7563 (mppt) REVERT: p 121 ARG cc_start: 0.7393 (ttm110) cc_final: 0.7040 (ttm110) REVERT: p 146 ARG cc_start: 0.7763 (mmm-85) cc_final: 0.7469 (mtp85) REVERT: r 160 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7537 (mt-10) REVERT: r 161 MET cc_start: 0.7994 (mmt) cc_final: 0.7627 (mmm) REVERT: r 331 MET cc_start: 0.7949 (mmm) cc_final: 0.7604 (mmm) REVERT: v 76 LYS cc_start: 0.8728 (mmmt) cc_final: 0.7983 (ptmt) REVERT: J 76 LYS cc_start: 0.5594 (ptmt) cc_final: 0.5264 (ptmm) REVERT: K 43 ASN cc_start: 0.7465 (t0) cc_final: 0.7031 (t0) REVERT: K 55 GLU cc_start: 0.5053 (tp30) cc_final: 0.4773 (tp30) REVERT: K 70 ILE cc_start: 0.7161 (mt) cc_final: 0.6922 (pt) REVERT: L 82 LEU cc_start: 0.6047 (mt) cc_final: 0.5809 (mp) REVERT: M 34 TYR cc_start: 0.6229 (t80) cc_final: 0.5606 (t80) REVERT: M 70 ILE cc_start: 0.6218 (mp) cc_final: 0.5867 (mp) REVERT: M 89 VAL cc_start: 0.6163 (t) cc_final: 0.5914 (p) REVERT: N 331 MET cc_start: 0.8409 (mmm) cc_final: 0.8092 (mmm) REVERT: P 240 SER cc_start: 0.8042 (t) cc_final: 0.7785 (m) REVERT: P 310 ASN cc_start: 0.6602 (t0) cc_final: 0.6357 (t0) REVERT: Q 70 GLN cc_start: 0.8397 (mt0) cc_final: 0.8061 (mt0) REVERT: Q 120 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7824 (mttm) REVERT: R 18 MET cc_start: 0.5917 (tpt) cc_final: 0.5582 (tpp) REVERT: R 21 PHE cc_start: 0.5510 (t80) cc_final: 0.5242 (t80) REVERT: R 84 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8062 (mttp) REVERT: R 96 ARG cc_start: 0.7667 (ttp-110) cc_final: 0.7313 (ttp-170) REVERT: R 129 SER cc_start: 0.8258 (t) cc_final: 0.7965 (m) REVERT: R 290 ASP cc_start: 0.7912 (t0) cc_final: 0.7571 (t0) REVERT: S 160 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7264 (mp0) REVERT: T 40 GLU cc_start: 0.7892 (tt0) cc_final: 0.7558 (tt0) REVERT: T 79 ASP cc_start: 0.7178 (m-30) cc_final: 0.6621 (t70) REVERT: V 52 ASN cc_start: 0.6163 (p0) cc_final: 0.5609 (p0) REVERT: V 64 ASN cc_start: 0.7822 (m110) cc_final: 0.7579 (m-40) REVERT: V 65 ARG cc_start: 0.8047 (ptp90) cc_final: 0.7713 (ptp90) REVERT: V 76 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8021 (ptmm) REVERT: V 80 ASN cc_start: 0.8375 (t0) cc_final: 0.8170 (t0) outliers start: 138 outliers final: 85 residues processed: 1106 average time/residue: 0.6399 time to fit residues: 1191.9022 Evaluate side-chains 924 residues out of total 7224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 834 time to evaluate : 6.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 190 SER Chi-restraints excluded: chain U residue 239 GLN Chi-restraints excluded: chain U residue 287 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 54 ARG Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain c residue 88 VAL Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain g residue 149 MET Chi-restraints excluded: chain g residue 338 THR Chi-restraints excluded: chain g residue 343 VAL Chi-restraints excluded: chain i residue 181 ASP Chi-restraints excluded: chain i residue 184 LEU Chi-restraints excluded: chain i residue 220 LEU Chi-restraints excluded: chain i residue 287 LEU Chi-restraints excluded: chain k residue 240 SER Chi-restraints excluded: chain m residue 85 LYS Chi-restraints excluded: chain o residue 236 ARG Chi-restraints excluded: chain o residue 285 ASP Chi-restraints excluded: chain q residue 143 LEU Chi-restraints excluded: chain q residue 196 ILE Chi-restraints excluded: chain q residue 217 GLN Chi-restraints excluded: chain s residue 31 LYS Chi-restraints excluded: chain u residue 33 ASP Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain u residue 72 VAL Chi-restraints excluded: chain u residue 77 LEU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 68 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 332 GLU Chi-restraints excluded: chain j residue 176 SER Chi-restraints excluded: chain j residue 181 ASP Chi-restraints excluded: chain l residue 27 GLU Chi-restraints excluded: chain l residue 30 ILE Chi-restraints excluded: chain l residue 237 ARG Chi-restraints excluded: chain p residue 118 LEU Chi-restraints excluded: chain p residue 310 ASN Chi-restraints excluded: chain r residue 100 ILE Chi-restraints excluded: chain r residue 143 LEU Chi-restraints excluded: chain r residue 201 MET Chi-restraints excluded: chain r residue 237 ASN Chi-restraints excluded: chain t residue 62 ASP Chi-restraints excluded: chain v residue 62 ASP Chi-restraints excluded: chain v residue 77 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 201 MET Chi-restraints excluded: chain N residue 332 GLU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 181 ASP Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain P residue 14 VAL Chi-restraints excluded: chain P residue 237 ARG Chi-restraints excluded: chain P residue 321 ASP Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 314 MET Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain T residue 57 ASN Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain V residue 33 ASP Chi-restraints excluded: chain V residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 405 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 chunk 607 optimal weight: 8.9990 chunk 497 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 731 optimal weight: 2.9990 chunk 790 optimal weight: 3.9990 chunk 651 optimal weight: 0.9990 chunk 725 optimal weight: 0.9980 chunk 249 optimal weight: 0.9980 chunk 586 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 239 GLN F 186 GLN G 310 ASN I 114 GLN U 239 GLN e 64 ASN e 85 ASN Y 39 GLN a 42 ASN i 162 ASN i 239 GLN q 217 GLN s 42 ASN ** b 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 74 ASN n 196 ASN t 64 ASN v 39 GLN L 42 ASN M 42 ASN M 57 ASN ** P 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 GLN R 310 ASN ** V 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 67560 Z= 0.255 Angle : 0.553 9.029 91212 Z= 0.300 Chirality : 0.044 0.169 10356 Planarity : 0.004 0.041 11940 Dihedral : 4.264 24.356 9325 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.19 % Favored : 96.80 % Rotamer: Outliers : 2.52 % Allowed : 13.88 % Favored : 83.60 % 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: 1.63 (0.09), residues: 8184 helix: 2.23 (0.08), residues: 4308 sheet: 0.71 (0.13), residues: 1512 loop : -0.83 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP U 92 HIS 0.004 0.001 HIS G 238 PHE 0.029 0.002 PHE U 238 TYR 0.019 0.002 TYR A 69 ARG 0.007 0.001 ARG S 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 7224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 916 time to evaluate : 6.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.5505 (t80) cc_final: 0.5095 (t80) REVERT: A 77 LEU cc_start: 0.6508 (pp) cc_final: 0.6238 (mt) REVERT: B 43 ASN cc_start: 0.6989 (t0) cc_final: 0.6502 (t0) REVERT: D 89 VAL cc_start: 0.5919 (t) cc_final: 0.5578 (p) REVERT: E 242 ARG cc_start: 0.7545 (mmm-85) cc_final: 0.7015 (ptp-110) REVERT: F 131 GLU cc_start: 0.6558 (tp30) cc_final: 0.6181 (mp0) REVERT: F 149 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7409 (mpp) REVERT: F 160 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7077 (mt-10) REVERT: H 36 LYS cc_start: 0.6595 (tttt) cc_final: 0.6346 (pttt) REVERT: H 198 MET cc_start: 0.7399 (mtp) cc_final: 0.6935 (tpp) REVERT: H 311 GLN cc_start: 0.6900 (mp-120) cc_final: 0.6598 (mp10) REVERT: I 27 GLU cc_start: 0.6684 (pm20) cc_final: 0.6461 (pm20) REVERT: I 84 LYS cc_start: 0.7936 (mtmt) cc_final: 0.7656 (mppt) REVERT: I 117 VAL cc_start: 0.7712 (t) cc_final: 0.7492 (m) REVERT: U 169 ASN cc_start: 0.7048 (p0) cc_final: 0.6837 (p0) REVERT: U 305 VAL cc_start: 0.8662 (OUTLIER) cc_final: 0.8454 (t) REVERT: e 38 LEU cc_start: 0.8079 (tp) cc_final: 0.7730 (tt) REVERT: f 76 LYS cc_start: 0.8389 (mmmt) cc_final: 0.7476 (ptmm) REVERT: Y 43 ASN cc_start: 0.7251 (t0) cc_final: 0.6633 (t0) REVERT: Y 45 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6967 (mp10) REVERT: Y 69 TYR cc_start: 0.6399 (m-80) cc_final: 0.6109 (m-10) REVERT: Y 70 ILE cc_start: 0.7038 (mt) cc_final: 0.6654 (pt) REVERT: Y 87 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6274 (ttmt) REVERT: c 46 VAL cc_start: 0.6800 (p) cc_final: 0.6314 (m) REVERT: c 59 THR cc_start: 0.6118 (m) cc_final: 0.5398 (p) REVERT: c 70 ILE cc_start: 0.5769 (mp) cc_final: 0.5083 (mp) REVERT: c 84 LYS cc_start: 0.6269 (mmtt) cc_final: 0.6017 (tttt) REVERT: c 91 GLU cc_start: 0.6076 (mm-30) cc_final: 0.5838 (mt-10) REVERT: g 117 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7995 (mt) REVERT: g 149 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.8008 (mtm) REVERT: g 331 MET cc_start: 0.8295 (mmm) cc_final: 0.7972 (mmm) REVERT: k 241 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7629 (tm-30) REVERT: k 314 MET cc_start: 0.8395 (ttt) cc_final: 0.8093 (ttm) REVERT: m 120 LYS cc_start: 0.8335 (ttmm) cc_final: 0.8040 (mttm) REVERT: q 100 ILE cc_start: 0.7399 (mt) cc_final: 0.7114 (tt) REVERT: q 217 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6666 (mm-40) REVERT: q 238 PHE cc_start: 0.8303 (t80) cc_final: 0.8038 (t80) REVERT: q 267 GLU cc_start: 0.7693 (tp30) cc_final: 0.7380 (tp30) REVERT: s 76 LYS cc_start: 0.5730 (ptmt) cc_final: 0.5129 (tmtt) REVERT: s 79 ASP cc_start: 0.7198 (m-30) cc_final: 0.6426 (t70) REVERT: u 76 LYS cc_start: 0.8513 (mmmt) cc_final: 0.7742 (ptmt) REVERT: X 58 VAL cc_start: 0.5764 (t) cc_final: 0.5486 (t) REVERT: X 76 LYS cc_start: 0.4822 (ptmt) cc_final: 0.4332 (tptt) REVERT: Z 43 ASN cc_start: 0.7903 (t0) cc_final: 0.7098 (t0) REVERT: b 82 LEU cc_start: 0.6661 (mp) cc_final: 0.6442 (mp) REVERT: d 34 TYR cc_start: 0.5804 (t80) cc_final: 0.5538 (t80) REVERT: d 47 ARG cc_start: 0.6428 (tmm-80) cc_final: 0.6186 (tmm-80) REVERT: d 52 ASN cc_start: 0.5958 (t0) cc_final: 0.5717 (m-40) REVERT: d 70 ILE cc_start: 0.5893 (mp) cc_final: 0.5613 (mm) REVERT: d 89 VAL cc_start: 0.5918 (t) cc_final: 0.5672 (p) REVERT: d 91 GLU cc_start: 0.6748 (mm-30) cc_final: 0.5855 (mt-10) REVERT: l 135 ASP cc_start: 0.7069 (m-30) cc_final: 0.6826 (m-30) REVERT: l 237 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7256 (ttm170) REVERT: l 241 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7616 (tm-30) REVERT: l 314 MET cc_start: 0.8559 (ttt) cc_final: 0.8193 (ttm) REVERT: n 319 ASP cc_start: 0.8314 (t70) cc_final: 0.8090 (t0) REVERT: p 84 LYS cc_start: 0.7828 (mtmt) cc_final: 0.7394 (mppt) REVERT: p 314 MET cc_start: 0.8290 (ttm) cc_final: 0.7509 (mtp) REVERT: r 161 MET cc_start: 0.7836 (mmt) cc_final: 0.7569 (mmm) REVERT: v 76 LYS cc_start: 0.8781 (mmmt) cc_final: 0.7957 (ptmt) REVERT: J 66 TYR cc_start: 0.3033 (p90) cc_final: 0.2803 (p90) REVERT: J 76 LYS cc_start: 0.5408 (ptmt) cc_final: 0.5085 (ptmm) REVERT: K 43 ASN cc_start: 0.7612 (t0) cc_final: 0.7025 (t0) REVERT: K 70 ILE cc_start: 0.7059 (mt) cc_final: 0.6704 (pt) REVERT: L 81 LEU cc_start: 0.7198 (mp) cc_final: 0.6793 (tt) REVERT: L 82 LEU cc_start: 0.6228 (mt) cc_final: 0.6026 (mp) REVERT: M 34 TYR cc_start: 0.6180 (t80) cc_final: 0.5824 (t80) REVERT: M 70 ILE cc_start: 0.6225 (mp) cc_final: 0.6006 (mp) REVERT: M 89 VAL cc_start: 0.6048 (t) cc_final: 0.5801 (p) REVERT: N 149 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7555 (mmm) REVERT: O 232 THR cc_start: 0.7459 (OUTLIER) cc_final: 0.7174 (p) REVERT: P 212 GLN cc_start: 0.8032 (pt0) cc_final: 0.7412 (pp30) REVERT: P 240 SER cc_start: 0.8038 (t) cc_final: 0.7765 (m) REVERT: P 241 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7586 (tm-30) REVERT: Q 70 GLN cc_start: 0.8393 (mt0) cc_final: 0.7975 (mt0) REVERT: Q 120 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7843 (mttm) REVERT: R 18 MET cc_start: 0.5961 (tpt) cc_final: 0.5615 (tpp) REVERT: R 84 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8038 (mttp) REVERT: R 129 SER cc_start: 0.8193 (t) cc_final: 0.7962 (m) REVERT: R 290 ASP cc_start: 0.7926 (t0) cc_final: 0.7664 (t70) REVERT: S 124 TRP cc_start: 0.6140 (t60) cc_final: 0.5922 (t60) REVERT: S 149 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6913 (mtp) REVERT: T 79 ASP cc_start: 0.7219 (m-30) cc_final: 0.6653 (t70) REVERT: V 64 ASN cc_start: 0.7800 (m110) cc_final: 0.7527 (m-40) REVERT: V 76 LYS cc_start: 0.8880 (mmmt) cc_final: 0.7904 (ptmm) outliers start: 182 outliers final: 116 residues processed: 1029 average time/residue: 0.6227 time to fit residues: 1091.1349 Evaluate side-chains 932 residues out of total 7224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 805 time to evaluate : 6.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 332 GLU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 190 SER Chi-restraints excluded: chain U residue 210 THR Chi-restraints excluded: chain U residue 305 VAL Chi-restraints excluded: chain e residue 39 GLN Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain f residue 33 ASP Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 54 ARG Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain c residue 88 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain g residue 149 MET Chi-restraints excluded: chain g residue 343 VAL Chi-restraints excluded: chain i residue 114 PHE Chi-restraints excluded: chain i residue 162 ASN Chi-restraints excluded: chain i residue 184 LEU Chi-restraints excluded: chain i residue 220 LEU Chi-restraints excluded: chain i residue 224 ILE Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 135 ASP Chi-restraints excluded: chain k residue 240 SER Chi-restraints excluded: chain m residue 85 LYS Chi-restraints excluded: chain o residue 131 ILE Chi-restraints excluded: chain o residue 204 GLU Chi-restraints excluded: chain o residue 236 ARG Chi-restraints excluded: chain o residue 285 ASP Chi-restraints excluded: chain q residue 143 LEU Chi-restraints excluded: chain q residue 196 ILE Chi-restraints excluded: chain q residue 217 GLN Chi-restraints excluded: chain s residue 31 LYS Chi-restraints excluded: chain u residue 33 ASP Chi-restraints excluded: chain u residue 68 THR Chi-restraints excluded: chain u residue 72 VAL Chi-restraints excluded: chain u residue 77 LEU Chi-restraints excluded: chain X residue 80 ASN Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain b residue 56 ILE Chi-restraints excluded: chain d residue 68 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 231 ILE Chi-restraints excluded: chain h residue 332 GLU Chi-restraints excluded: chain j residue 176 SER Chi-restraints excluded: chain j residue 181 ASP Chi-restraints excluded: chain j residue 184 LEU Chi-restraints excluded: chain j residue 223 THR Chi-restraints excluded: chain j residue 233 LEU Chi-restraints excluded: chain j residue 253 ASP Chi-restraints excluded: chain l residue 27 GLU Chi-restraints excluded: chain l residue 237 ARG Chi-restraints excluded: chain l residue 240 SER Chi-restraints excluded: chain n residue 87 LEU Chi-restraints excluded: chain p residue 86 ASP Chi-restraints excluded: chain p residue 201 LEU Chi-restraints excluded: chain r residue 100 ILE Chi-restraints excluded: chain r residue 143 LEU Chi-restraints excluded: chain r residue 201 MET Chi-restraints excluded: chain r residue 210 THR Chi-restraints excluded: chain r residue 237 ASN Chi-restraints excluded: chain t residue 62 ASP Chi-restraints excluded: chain v residue 33 ASP Chi-restraints excluded: chain v residue 77 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 149 MET Chi-restraints excluded: chain N residue 201 MET Chi-restraints excluded: chain N residue 332 GLU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain O residue 181 ASP Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 272 THR Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 237 ARG Chi-restraints excluded: chain P residue 321 ASP Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 314 MET Chi-restraints excluded: chain R residue 86 ASP Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 310 ASN Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 149 MET Chi-restraints excluded: chain S residue 288 GLU Chi-restraints excluded: chain S residue 310 LYS Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain V residue 33 ASP Chi-restraints excluded: chain V residue 77 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 722 optimal weight: 0.3980 chunk 549 optimal weight: 0.0570 chunk 379 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 349 optimal weight: 0.9980 chunk 491 optimal weight: 0.0980 chunk 734 optimal weight: 0.6980 chunk 777 optimal weight: 0.8980 chunk 383 optimal weight: 0.9990 chunk 695 optimal weight: 0.6980 chunk 209 optimal weight: 5.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 214 ASN f 42 ASN a 42 ASN g 260 ASN k 310 ASN o 310 ASN ** j 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 310 ASN p 114 GLN p 310 ASN t 64 ASN v 39 GLN L 42 ASN ** P 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 310 ASN ** T 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 ASN V 43 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 67560 Z= 0.144 Angle : 0.503 13.177 91212 Z= 0.269 Chirality : 0.042 0.174 10356 Planarity : 0.003 0.043 11940 Dihedral : 4.028 24.388 9325 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.94 % Favored : 97.04 % Rotamer: Outliers : 1.98 % Allowed : 15.68 % Favored : 82.34 % 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: 1.91 (0.09), residues: 8184 helix: 2.48 (0.08), residues: 4328 sheet: 0.73 (0.13), residues: 1524 loop : -0.73 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 92 HIS 0.002 0.001 HIS U 116 PHE 0.027 0.001 PHE r 238 TYR 0.026 0.001 TYR c 34 ARG 0.006 0.000 ARG p 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 7224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 890 time to evaluate : 6.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.5471 (t80) cc_final: 0.5177 (t80) REVERT: A 77 LEU cc_start: 0.6564 (pp) cc_final: 0.6278 (mt) REVERT: B 43 ASN cc_start: 0.7200 (t0) cc_final: 0.6716 (t0) REVERT: B 47 ARG cc_start: 0.7014 (mtm110) cc_final: 0.6436 (mtm180) REVERT: B 48 GLU cc_start: 0.4951 (pp20) cc_final: 0.4640 (tm-30) REVERT: D 41 VAL cc_start: 0.7726 (t) cc_final: 0.7469 (p) REVERT: D 81 LEU cc_start: 0.7678 (tt) cc_final: 0.7408 (mt) REVERT: D 89 VAL cc_start: 0.5897 (t) cc_final: 0.5639 (p) REVERT: E 242 ARG cc_start: 0.7488 (mmm-85) cc_final: 0.7008 (ptp-110) REVERT: F 104 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6081 (pm20) REVERT: F 131 GLU cc_start: 0.6684 (tp30) cc_final: 0.6305 (mp0) REVERT: F 149 MET cc_start: 0.7715 (mmm) cc_final: 0.7346 (mpp) REVERT: F 160 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6972 (mt-10) REVERT: H 66 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7375 (p0) REVERT: H 198 MET cc_start: 0.7347 (mtp) cc_final: 0.7023 (tpp) REVERT: H 311 GLN cc_start: 0.6867 (mp-120) cc_final: 0.6599 (mp10) REVERT: I 84 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7628 (mppt) REVERT: U 149 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6783 (mtp) REVERT: e 38 LEU cc_start: 0.8092 (tp) cc_final: 0.7735 (tt) REVERT: e 76 LYS cc_start: 0.6664 (pttt) cc_final: 0.6085 (tptp) REVERT: f 76 LYS cc_start: 0.8380 (mmmt) cc_final: 0.7420 (ptmm) REVERT: Y 43 ASN cc_start: 0.7288 (t0) cc_final: 0.6635 (t0) REVERT: Y 45 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6947 (mp10) REVERT: Y 54 ARG cc_start: 0.5068 (OUTLIER) cc_final: 0.4457 (ttm110) REVERT: Y 69 TYR cc_start: 0.6382 (m-80) cc_final: 0.6122 (m-10) REVERT: Y 70 ILE cc_start: 0.6998 (mt) cc_final: 0.6413 (pt) REVERT: Y 87 LYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6408 (ttmt) REVERT: a 82 LEU cc_start: 0.5634 (tp) cc_final: 0.5396 (mp) REVERT: c 59 THR cc_start: 0.6236 (m) cc_final: 0.5593 (p) REVERT: c 91 GLU cc_start: 0.6168 (mm-30) cc_final: 0.5841 (mt-10) REVERT: g 331 MET cc_start: 0.8235 (mmm) cc_final: 0.7947 (mmm) REVERT: i 161 MET cc_start: 0.7734 (tpt) cc_final: 0.7511 (tpt) REVERT: k 314 MET cc_start: 0.8420 (ttt) cc_final: 0.8097 (ttm) REVERT: m 120 LYS cc_start: 0.8251 (ttmm) cc_final: 0.8025 (mttm) REVERT: o 72 MET cc_start: 0.6954 (ptm) cc_final: 0.6552 (ptm) REVERT: q 149 MET cc_start: 0.6929 (mtp) cc_final: 0.6474 (mtp) REVERT: q 238 PHE cc_start: 0.8257 (t80) cc_final: 0.8012 (t80) REVERT: q 267 GLU cc_start: 0.7687 (tp30) cc_final: 0.7473 (tp30) REVERT: s 76 LYS cc_start: 0.5766 (ptmt) cc_final: 0.5099 (tmtt) REVERT: s 79 ASP cc_start: 0.7256 (m-30) cc_final: 0.6492 (t70) REVERT: u 76 LYS cc_start: 0.8567 (mmmt) cc_final: 0.7806 (ptmt) REVERT: u 80 ASN cc_start: 0.7870 (t0) cc_final: 0.7665 (t0) REVERT: Z 43 ASN cc_start: 0.7684 (t0) cc_final: 0.6848 (t0) REVERT: b 70 ILE cc_start: 0.4295 (mp) cc_final: 0.3671 (mm) REVERT: d 34 TYR cc_start: 0.5951 (t80) cc_final: 0.5666 (t80) REVERT: d 52 ASN cc_start: 0.5893 (t0) cc_final: 0.5607 (m-40) REVERT: d 59 THR cc_start: 0.5898 (m) cc_final: 0.5333 (p) REVERT: d 70 ILE cc_start: 0.5881 (mp) cc_final: 0.5607 (mm) REVERT: d 89 VAL cc_start: 0.5832 (t) cc_final: 0.5598 (p) REVERT: d 91 GLU cc_start: 0.6645 (mm-30) cc_final: 0.5807 (mt-10) REVERT: h 149 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7388 (mmm) REVERT: j 160 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6884 (mp0) REVERT: l 135 ASP cc_start: 0.7017 (m-30) cc_final: 0.6771 (m-30) REVERT: l 237 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7343 (ttm170) REVERT: l 241 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7626 (tm-30) REVERT: l 314 MET cc_start: 0.8518 (ttt) cc_final: 0.8225 (ttm) REVERT: n 319 ASP cc_start: 0.8316 (t70) cc_final: 0.8061 (t0) REVERT: p 84 LYS cc_start: 0.7910 (mtmt) cc_final: 0.7494 (mppt) REVERT: p 146 ARG cc_start: 0.7848 (mmm-85) cc_final: 0.7336 (mtp85) REVERT: p 314 MET cc_start: 0.8298 (ttm) cc_final: 0.7541 (mtp) REVERT: t 85 ASN cc_start: 0.7529 (t0) cc_final: 0.7303 (t0) REVERT: v 50 ARG cc_start: 0.7973 (mtp-110) cc_final: 0.7739 (mtp-110) REVERT: v 76 LYS cc_start: 0.8789 (mmmt) cc_final: 0.7859 (ptmt) REVERT: J 37 PHE cc_start: 0.6372 (t80) cc_final: 0.6138 (t80) REVERT: J 76 LYS cc_start: 0.5271 (ptmt) cc_final: 0.4914 (ptmm) REVERT: K 43 ASN cc_start: 0.7616 (t0) cc_final: 0.6992 (t0) REVERT: K 70 ILE cc_start: 0.6913 (mt) cc_final: 0.6686 (pt) REVERT: L 81 LEU cc_start: 0.7144 (mp) cc_final: 0.6741 (tt) REVERT: M 34 TYR cc_start: 0.5987 (t80) cc_final: 0.5703 (t80) REVERT: N 128 PHE cc_start: 0.7852 (m-10) cc_final: 0.7648 (m-10) REVERT: O 142 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: P 212 GLN cc_start: 0.8032 (pt0) cc_final: 0.7588 (pp30) REVERT: P 240 SER cc_start: 0.8037 (t) cc_final: 0.7799 (m) REVERT: P 241 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7476 (tm-30) REVERT: P 310 ASN cc_start: 0.6050 (OUTLIER) cc_final: 0.5573 (t0) REVERT: Q 70 GLN cc_start: 0.8229 (mt0) cc_final: 0.7809 (mp10) REVERT: Q 120 LYS cc_start: 0.8073 (ttmm) cc_final: 0.7858 (mttm) REVERT: R 18 MET cc_start: 0.5957 (tpt) cc_final: 0.5589 (tpp) REVERT: R 84 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8063 (mppt) REVERT: R 290 ASP cc_start: 0.7747 (t0) cc_final: 0.7448 (t0) REVERT: S 124 TRP cc_start: 0.6163 (t60) cc_final: 0.5904 (t60) REVERT: T 79 ASP cc_start: 0.7339 (m-30) cc_final: 0.6728 (t70) REVERT: V 55 GLU cc_start: 0.7195 (tt0) cc_final: 0.6808 (tt0) REVERT: V 76 LYS cc_start: 0.8906 (mmmt) cc_final: 0.7937 (ptmm) outliers start: 143 outliers final: 77 residues processed: 970 average time/residue: 0.6081 time to fit residues: 1004.9043 Evaluate side-chains 889 residues out of total 7224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 802 time to evaluate : 6.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain H residue 66 ASP Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 149 MET Chi-restraints excluded: chain e residue 39 GLN Chi-restraints excluded: chain f residue 33 ASP Chi-restraints excluded: chain Y residue 32 VAL Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 54 ARG Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain i residue 114 PHE Chi-restraints excluded: chain i residue 181 ASP Chi-restraints excluded: chain i residue 184 LEU Chi-restraints excluded: chain i residue 196 ILE Chi-restraints excluded: chain i residue 220 LEU Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 135 ASP Chi-restraints excluded: chain k residue 240 SER Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain o residue 131 ILE Chi-restraints excluded: chain s residue 31 LYS Chi-restraints excluded: chain u residue 33 ASP Chi-restraints excluded: chain u residue 62 ASP Chi-restraints excluded: chain u residue 72 VAL Chi-restraints excluded: chain u residue 77 LEU Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain d residue 68 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain h residue 149 MET Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 332 GLU Chi-restraints excluded: chain j residue 181 ASP Chi-restraints excluded: chain j residue 184 LEU Chi-restraints excluded: chain j residue 189 ASP Chi-restraints excluded: chain j residue 233 LEU Chi-restraints excluded: chain j residue 253 ASP Chi-restraints excluded: chain l residue 27 GLU Chi-restraints excluded: chain l residue 237 ARG Chi-restraints excluded: chain l residue 240 SER Chi-restraints excluded: chain n residue 58 PHE Chi-restraints excluded: chain n residue 87 LEU Chi-restraints excluded: chain p residue 201 LEU Chi-restraints excluded: chain r residue 100 ILE Chi-restraints excluded: chain r residue 237 ASN Chi-restraints excluded: chain t residue 39 GLN Chi-restraints excluded: chain t residue 62 ASP Chi-restraints excluded: chain v residue 33 ASP Chi-restraints excluded: chain v residue 62 ASP Chi-restraints excluded: chain v residue 77 LEU Chi-restraints excluded: chain v residue 91 GLU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 332 GLU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 181 ASP Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 310 ASN Chi-restraints excluded: chain P residue 321 ASP Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 314 MET Chi-restraints excluded: chain R residue 98 SER Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain V residue 33 ASP Chi-restraints excluded: chain V residue 52 ASN Chi-restraints excluded: chain V residue 77 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 647 optimal weight: 3.9990 chunk 441 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 578 optimal weight: 0.9990 chunk 320 optimal weight: 1.9990 chunk 663 optimal weight: 0.0970 chunk 537 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 396 optimal weight: 6.9990 chunk 697 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN a 42 ASN k 310 ASN o 267 GLN q 217 GLN u 39 GLN b 45 GLN j 186 GLN ** j 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 310 ASN p 114 GLN t 64 ASN v 39 GLN v 42 ASN L 42 ASN P 74 ASN R 310 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 67560 Z= 0.193 Angle : 0.509 14.733 91212 Z= 0.273 Chirality : 0.043 0.174 10356 Planarity : 0.003 0.042 11940 Dihedral : 4.004 23.353 9325 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.18 % Favored : 96.81 % Rotamer: Outliers : 2.70 % Allowed : 15.79 % Favored : 81.51 % 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: 1.90 (0.09), residues: 8184 helix: 2.48 (0.08), residues: 4332 sheet: 0.70 (0.13), residues: 1536 loop : -0.74 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 92 HIS 0.004 0.001 HIS O 116 PHE 0.026 0.001 PHE U 238 TYR 0.020 0.001 TYR J 66 ARG 0.006 0.000 ARG R 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16368 Ramachandran restraints generated. 8184 Oldfield, 0 Emsley, 8184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 7224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 838 time to evaluate : 6.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.6557 (pp) cc_final: 0.6256 (mt) REVERT: B 43 ASN cc_start: 0.6894 (t0) cc_final: 0.6403 (t0) REVERT: D 41 VAL cc_start: 0.7674 (t) cc_final: 0.7419 (p) REVERT: D 70 ILE cc_start: 0.5806 (mm) cc_final: 0.5301 (mm) REVERT: D 81 LEU cc_start: 0.7644 (tt) cc_final: 0.7433 (mt) REVERT: D 89 VAL cc_start: 0.5998 (t) cc_final: 0.5719 (p) REVERT: E 131 GLU cc_start: 0.7022 (tp30) cc_final: 0.6690 (tp30) REVERT: E 242 ARG cc_start: 0.7527 (mmm-85) cc_final: 0.7037 (ptp-110) REVERT: F 104 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6053 (pm20) REVERT: F 131 GLU cc_start: 0.6699 (tp30) cc_final: 0.6260 (mp0) REVERT: F 160 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6978 (mt-10) REVERT: F 215 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6352 (m-30) REVERT: F 343 VAL cc_start: 0.9633 (m) cc_final: 0.9308 (t) REVERT: G 241 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7551 (tm-30) REVERT: H 66 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7400 (p0) REVERT: H 198 MET cc_start: 0.7381 (mtp) cc_final: 0.6915 (tpp) REVERT: H 311 GLN cc_start: 0.6848 (mp-120) cc_final: 0.6580 (mp10) REVERT: I 84 LYS cc_start: 0.7986 (mtmt) cc_final: 0.7610 (mppt) REVERT: U 149 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6779 (mtp) REVERT: U 151 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8779 (p) REVERT: e 38 LEU cc_start: 0.8163 (tp) cc_final: 0.7817 (tt) REVERT: e 76 LYS cc_start: 0.6752 (pttt) cc_final: 0.6049 (tptp) REVERT: f 76 LYS cc_start: 0.8460 (mmmt) cc_final: 0.7395 (ptmm) R------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain H residue 66 ASP Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 149 MET Chi-restraints excluded: chain U residue 151 THR Chi-restraints excluded: chain U residue 190 SER Chi-restraints excluded: chain U residue 210 THR Chi-restraints excluded: chain e residue 39 GLN Chi-restraints excluded: chain f residue 33 ASP Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain Y residue 54 ARG Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain g residue 167 VAL Chi-restraints excluded: chain g residue 237 ASN Chi-restraints excluded: chain g residue 343 VAL Chi-restraints excluded: chain i residue 114 PHE Chi-restraints excluded: chain i residue 181 ASP Chi-restraints excluded: chain i residue 184 LEU Chi-restraints excluded: chain i residue 196 ILE Chi-restraints excluded: chain i residue 220 LEU Chi-restraints excluded: chain i residue 253 ASP Chi-restraints excluded: chain i residue 275 VAL Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 240 SER Chi-restraints excluded: chain m residue 66 ASP Chi-restraints excluded: chain m residue 74 ASN Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain o residue 131 ILE Chi-restraints excluded: chain o residue 204 GLU Chi-restraints excluded: chain o residue 267 GLN Chi-restraints excluded: chain q residue 100 ILE Chi-restraints excluded: chain q residue 217 GLN Chi-restraints excluded: chain s residue 36 THR Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain u residue 33 ASP Chi-restraints excluded: chain u residue 62 ASP Chi-restraints excluded: chain u residue 72 VAL Chi-restraints excluded: chain u residue 77 LEU Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Z residue 32 VAL Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain b residue 56 ILE Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain d residue 68 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain h residue 149 MET Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 332 GLU Chi-restraints excluded: chain j residue 176 SER Chi-restraints excluded: chain j residue 181 ASP Chi-restraints excluded: chain j residue 184 LEU Chi-restraints excluded: chain j residue 189 ASP Chi-restraints excluded: chain j residue 223 THR Chi-restraints excluded: chain j residue 233 LEU Chi-restraints excluded: chain j residue 236 VAL Chi-restraints excluded: chain j residue 253 ASP Chi-restraints excluded: chain l residue 27 GLU Chi-restraints excluded: chain l residue 237 ARG Chi-restraints excluded: chain l residue 240 SER Chi-restraints excluded: chain n residue 58 PHE Chi-restraints excluded: chain n residue 87 LEU Chi-restraints excluded: chain n residue 314 MET Chi-restraints excluded: chain p residue 86 ASP Chi-restraints excluded: chain p residue 201 LEU Chi-restraints excluded: chain p residue 285 ASP Chi-restraints excluded: chain r residue 100 ILE Chi-restraints excluded: chain r residue 201 MET Chi-restraints excluded: chain r residue 237 ASN Chi-restraints excluded: chain v residue 33 ASP Chi-restraints excluded: chain v residue 62 ASP Chi-restraints excluded: chain v residue 77 LEU Chi-restraints excluded: chain v residue 91 GLU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 237 ASN Chi-restraints excluded: chain N residue 332 GLU Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain O residue 181 ASP Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 316 MET Chi-restraints excluded: chain P residue 321 ASP Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 64 MET Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 314 MET Chi-restraints excluded: chain R residue 86 ASP Chi-restraints excluded: chain R residue 98 SER Chi-restraints excluded: chain R residue 285 ASP Chi-restraints excluded: chain R residue 310 ASN Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 288 GLU Chi-restraints excluded: chain T residue 31 LYS Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain V residue 52 ASN Chi-restraints excluded: chain V residue 77 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 261 optimal weight: 7.9990 chunk 699 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 456 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 777 optimal weight: 7.9990 chunk 645 optimal weight: 2.9990 chunk 360 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 257 optimal weight: 6.9990 chunk 408 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: