Starting phenix.real_space_refine on Sat Mar 23 17:44:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tre_10560/03_2024/6tre_10560.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tre_10560/03_2024/6tre_10560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tre_10560/03_2024/6tre_10560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tre_10560/03_2024/6tre_10560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tre_10560/03_2024/6tre_10560.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tre_10560/03_2024/6tre_10560.pdb" } resolution = 3.3 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= 0.002 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 96 5.16 5 C 23232 2.51 5 N 7136 2.21 5 O 7712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 244": "NH1" <-> "NH2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "A PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 381": "OD1" <-> "OD2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 381": "OD1" <-> "OD2" Residue "C GLU 383": "OE1" <-> "OE2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ASP 407": "OD1" <-> "OD2" Residue "C PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 381": "OD1" <-> "OD2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ASP 407": "OD1" <-> "OD2" Residue "D PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 381": "OD1" <-> "OD2" Residue "E GLU 383": "OE1" <-> "OE2" Residue "E ARG 384": "NH1" <-> "NH2" Residue "E ASP 407": "OD1" <-> "OD2" Residue "E PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 381": "OD1" <-> "OD2" Residue "F GLU 383": "OE1" <-> "OE2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F ASP 407": "OD1" <-> "OD2" Residue "F PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 381": "OD1" <-> "OD2" Residue "G GLU 383": "OE1" <-> "OE2" Residue "G ARG 384": "NH1" <-> "NH2" Residue "G ASP 407": "OD1" <-> "OD2" Residue "G PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 244": "NH1" <-> "NH2" Residue "H TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 381": "OD1" <-> "OD2" Residue "H GLU 383": "OE1" <-> "OE2" Residue "H ARG 384": "NH1" <-> "NH2" Residue "H ASP 407": "OD1" <-> "OD2" Residue "H PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 244": "NH1" <-> "NH2" Residue "I TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 381": "OD1" <-> "OD2" Residue "I GLU 383": "OE1" <-> "OE2" Residue "I ARG 384": "NH1" <-> "NH2" Residue "I ASP 407": "OD1" <-> "OD2" Residue "I PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 244": "NH1" <-> "NH2" Residue "J TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 381": "OD1" <-> "OD2" Residue "J GLU 383": "OE1" <-> "OE2" Residue "J ARG 384": "NH1" <-> "NH2" Residue "J ASP 407": "OD1" <-> "OD2" Residue "J PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 244": "NH1" <-> "NH2" Residue "K TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 381": "OD1" <-> "OD2" Residue "K GLU 383": "OE1" <-> "OE2" Residue "K ARG 384": "NH1" <-> "NH2" Residue "K ASP 407": "OD1" <-> "OD2" Residue "K PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 244": "NH1" <-> "NH2" Residue "L TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 381": "OD1" <-> "OD2" Residue "L GLU 383": "OE1" <-> "OE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "L ASP 407": "OD1" <-> "OD2" Residue "L PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 244": "NH1" <-> "NH2" Residue "M TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 381": "OD1" <-> "OD2" Residue "M GLU 383": "OE1" <-> "OE2" Residue "M ARG 384": "NH1" <-> "NH2" Residue "M ASP 407": "OD1" <-> "OD2" Residue "M PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 244": "NH1" <-> "NH2" Residue "N TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 381": "OD1" <-> "OD2" Residue "N GLU 383": "OE1" <-> "OE2" Residue "N ARG 384": "NH1" <-> "NH2" Residue "N ASP 407": "OD1" <-> "OD2" Residue "N PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 244": "NH1" <-> "NH2" Residue "O TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 381": "OD1" <-> "OD2" Residue "O GLU 383": "OE1" <-> "OE2" Residue "O ARG 384": "NH1" <-> "NH2" Residue "O ASP 407": "OD1" <-> "OD2" Residue "O PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 244": "NH1" <-> "NH2" Residue "P TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 381": "OD1" <-> "OD2" Residue "P GLU 383": "OE1" <-> "OE2" Residue "P ARG 384": "NH1" <-> "NH2" Residue "P ASP 407": "OD1" <-> "OD2" Residue "P PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 244": "NH1" <-> "NH2" Residue "Q TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 381": "OD1" <-> "OD2" Residue "Q GLU 383": "OE1" <-> "OE2" Residue "Q ARG 384": "NH1" <-> "NH2" Residue "Q ASP 407": "OD1" <-> "OD2" Residue "Q PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 244": "NH1" <-> "NH2" Residue "R TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 381": "OD1" <-> "OD2" Residue "R GLU 383": "OE1" <-> "OE2" Residue "R ARG 384": "NH1" <-> "NH2" Residue "R ASP 407": "OD1" <-> "OD2" Residue "R PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 381": "OD1" <-> "OD2" Residue "S GLU 383": "OE1" <-> "OE2" Residue "S ARG 384": "NH1" <-> "NH2" Residue "S ASP 407": "OD1" <-> "OD2" Residue "S PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 244": "NH1" <-> "NH2" Residue "T TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 381": "OD1" <-> "OD2" Residue "T GLU 383": "OE1" <-> "OE2" Residue "T ARG 384": "NH1" <-> "NH2" Residue "T ASP 407": "OD1" <-> "OD2" Residue "T PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 244": "NH1" <-> "NH2" Residue "U TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 381": "OD1" <-> "OD2" Residue "U GLU 383": "OE1" <-> "OE2" Residue "U ARG 384": "NH1" <-> "NH2" Residue "U ASP 407": "OD1" <-> "OD2" Residue "U PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 244": "NH1" <-> "NH2" Residue "V TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 381": "OD1" <-> "OD2" Residue "V GLU 383": "OE1" <-> "OE2" Residue "V ARG 384": "NH1" <-> "NH2" Residue "V ASP 407": "OD1" <-> "OD2" Residue "V PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 244": "NH1" <-> "NH2" Residue "W TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 381": "OD1" <-> "OD2" Residue "W GLU 383": "OE1" <-> "OE2" Residue "W ARG 384": "NH1" <-> "NH2" Residue "W ASP 407": "OD1" <-> "OD2" Residue "W PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 244": "NH1" <-> "NH2" Residue "X TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 381": "OD1" <-> "OD2" Residue "X GLU 383": "OE1" <-> "OE2" Residue "X ARG 384": "NH1" <-> "NH2" Residue "X ASP 407": "OD1" <-> "OD2" Residue "X PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 244": "NH1" <-> "NH2" Residue "Y TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 381": "OD1" <-> "OD2" Residue "Y GLU 383": "OE1" <-> "OE2" Residue "Y ARG 384": "NH1" <-> "NH2" Residue "Y ASP 407": "OD1" <-> "OD2" Residue "Y PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 244": "NH1" <-> "NH2" Residue "Z TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 381": "OD1" <-> "OD2" Residue "Z GLU 383": "OE1" <-> "OE2" Residue "Z ARG 384": "NH1" <-> "NH2" Residue "Z ASP 407": "OD1" <-> "OD2" Residue "Z PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 244": "NH1" <-> "NH2" Residue "1 TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 381": "OD1" <-> "OD2" Residue "1 GLU 383": "OE1" <-> "OE2" Residue "1 ARG 384": "NH1" <-> "NH2" Residue "1 ASP 407": "OD1" <-> "OD2" Residue "1 PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 244": "NH1" <-> "NH2" Residue "2 TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 381": "OD1" <-> "OD2" Residue "2 GLU 383": "OE1" <-> "OE2" Residue "2 ARG 384": "NH1" <-> "NH2" Residue "2 ASP 407": "OD1" <-> "OD2" Residue "2 PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 244": "NH1" <-> "NH2" Residue "3 TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 381": "OD1" <-> "OD2" Residue "3 GLU 383": "OE1" <-> "OE2" Residue "3 ARG 384": "NH1" <-> "NH2" Residue "3 ASP 407": "OD1" <-> "OD2" Residue "3 PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 244": "NH1" <-> "NH2" Residue "4 TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 381": "OD1" <-> "OD2" Residue "4 GLU 383": "OE1" <-> "OE2" Residue "4 ARG 384": "NH1" <-> "NH2" Residue "4 ASP 407": "OD1" <-> "OD2" Residue "4 PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 244": "NH1" <-> "NH2" Residue "5 TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 381": "OD1" <-> "OD2" Residue "5 GLU 383": "OE1" <-> "OE2" Residue "5 ARG 384": "NH1" <-> "NH2" Residue "5 ASP 407": "OD1" <-> "OD2" Residue "5 PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 244": "NH1" <-> "NH2" Residue "6 TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 381": "OD1" <-> "OD2" Residue "6 GLU 383": "OE1" <-> "OE2" Residue "6 ARG 384": "NH1" <-> "NH2" Residue "6 ASP 407": "OD1" <-> "OD2" Residue "6 PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38176 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "B" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "C" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "D" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "E" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "F" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "G" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "H" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "I" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "J" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "K" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "L" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "M" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "N" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "O" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "P" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "Q" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "R" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "S" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "T" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "U" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "V" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "W" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "X" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "Y" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "Z" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "1" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "2" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "3" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "4" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "5" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "6" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Time building chain proxies: 18.74, per 1000 atoms: 0.49 Number of scatterers: 38176 At special positions: 0 Unit cell: (239.202, 239.202, 97.818, 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 96 16.00 O 7712 8.00 N 7136 7.00 C 23232 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: 13.46 Conformation dependent library (CDL) restraints added in 6.7 seconds 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9280 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 97 sheets defined 29.1% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'A' and resid 232 through 258 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 258 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 258 Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 258 Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY D 421 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 258 Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY E 421 " --> pdb=" O ARG E 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 258 Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY F 421 " --> pdb=" O ARG F 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 258 Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY G 421 " --> pdb=" O ARG G 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 258 Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY H 421 " --> pdb=" O ARG H 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 258 Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY I 421 " --> pdb=" O ARG I 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 258 Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY J 421 " --> pdb=" O ARG J 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 258 Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY K 421 " --> pdb=" O ARG K 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 258 Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY L 421 " --> pdb=" O ARG L 417 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 258 Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY M 421 " --> pdb=" O ARG M 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 258 Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY N 421 " --> pdb=" O ARG N 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 258 Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY O 421 " --> pdb=" O ARG O 417 " (cutoff:3.500A) Processing helix chain 'P' and resid 232 through 258 Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY P 421 " --> pdb=" O ARG P 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 258 Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY Q 421 " --> pdb=" O ARG Q 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 258 Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY R 421 " --> pdb=" O ARG R 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 232 through 258 Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY S 421 " --> pdb=" O ARG S 417 " (cutoff:3.500A) Processing helix chain 'T' and resid 232 through 258 Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY T 421 " --> pdb=" O ARG T 417 " (cutoff:3.500A) Processing helix chain 'U' and resid 232 through 258 Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY U 421 " --> pdb=" O ARG U 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 232 through 258 Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY V 421 " --> pdb=" O ARG V 417 " (cutoff:3.500A) Processing helix chain 'W' and resid 232 through 258 Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY W 421 " --> pdb=" O ARG W 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 232 through 258 Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY X 421 " --> pdb=" O ARG X 417 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 258 Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY Y 421 " --> pdb=" O ARG Y 417 " (cutoff:3.500A) Processing helix chain 'Z' and resid 232 through 258 Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY Z 421 " --> pdb=" O ARG Z 417 " (cutoff:3.500A) Processing helix chain '1' and resid 232 through 258 Proline residue: 1 255 - end of helix Processing helix chain '1' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY 1 421 " --> pdb=" O ARG 1 417 " (cutoff:3.500A) Processing helix chain '2' and resid 232 through 258 Proline residue: 2 255 - end of helix Processing helix chain '2' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY 2 421 " --> pdb=" O ARG 2 417 " (cutoff:3.500A) Processing helix chain '3' and resid 232 through 258 Proline residue: 3 255 - end of helix Processing helix chain '3' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY 3 421 " --> pdb=" O ARG 3 417 " (cutoff:3.500A) Processing helix chain '4' and resid 232 through 258 Proline residue: 4 255 - end of helix Processing helix chain '4' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY 4 421 " --> pdb=" O ARG 4 417 " (cutoff:3.500A) Processing helix chain '5' and resid 232 through 258 Proline residue: 5 255 - end of helix Processing helix chain '5' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY 5 421 " --> pdb=" O ARG 5 417 " (cutoff:3.500A) Processing helix chain '6' and resid 232 through 258 Proline residue: 6 255 - end of helix Processing helix chain '6' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY 6 421 " --> pdb=" O ARG 6 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP A 271 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE A 382 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 277 removed outlier: 3.782A pdb=" N HIS A 374 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 276 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN B 274 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HIS B 374 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 276 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN C 274 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS C 374 " --> pdb=" O GLU D 276 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU D 276 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN D 274 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS D 374 " --> pdb=" O GLU E 276 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 276 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN E 274 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS E 374 " --> pdb=" O GLU F 276 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU F 276 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN F 274 " --> pdb=" O LYS E 376 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS F 374 " --> pdb=" O GLU G 276 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU G 276 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN G 274 " --> pdb=" O LYS F 376 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS G 374 " --> pdb=" O GLU H 276 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN H 274 " --> pdb=" O LYS G 376 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN I 274 " --> pdb=" O LYS H 376 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN J 274 " --> pdb=" O LYS I 376 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS J 374 " --> pdb=" O GLU K 276 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU K 276 " --> pdb=" O HIS J 374 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN K 274 " --> pdb=" O LYS J 376 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN L 274 " --> pdb=" O LYS K 376 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS L 374 " --> pdb=" O GLU M 276 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU M 276 " --> pdb=" O HIS L 374 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN M 274 " --> pdb=" O LYS L 376 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN N 274 " --> pdb=" O LYS M 376 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS N 374 " --> pdb=" O GLU O 276 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU O 276 " --> pdb=" O HIS N 374 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN O 274 " --> pdb=" O LYS N 376 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS O 374 " --> pdb=" O GLU P 276 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN P 274 " --> pdb=" O LYS O 376 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN Q 274 " --> pdb=" O LYS P 376 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN R 274 " --> pdb=" O LYS Q 376 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN S 274 " --> pdb=" O LYS R 376 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN T 274 " --> pdb=" O LYS S 376 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN U 274 " --> pdb=" O LYS T 376 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS U 374 " --> pdb=" O GLU V 276 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU V 276 " --> pdb=" O HIS U 374 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN V 274 " --> pdb=" O LYS U 376 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS V 374 " --> pdb=" O GLU W 276 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU W 276 " --> pdb=" O HIS V 374 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN W 274 " --> pdb=" O LYS V 376 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN X 274 " --> pdb=" O LYS W 376 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN Y 274 " --> pdb=" O LYS X 376 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS Y 374 " --> pdb=" O GLU Z 276 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU Z 276 " --> pdb=" O HIS Y 374 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN Z 274 " --> pdb=" O LYS Y 376 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN 1 274 " --> pdb=" O LYS Z 376 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS 1 374 " --> pdb=" O GLU 2 276 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU 2 276 " --> pdb=" O HIS 1 374 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN 2 274 " --> pdb=" O LYS 1 376 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS 2 374 " --> pdb=" O GLU 3 276 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU 3 276 " --> pdb=" O HIS 2 374 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN 3 274 " --> pdb=" O LYS 2 376 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN 4 274 " --> pdb=" O LYS 3 376 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS 4 374 " --> pdb=" O GLU 5 276 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU 5 276 " --> pdb=" O HIS 4 374 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN 5 274 " --> pdb=" O LYS 4 376 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS 5 374 " --> pdb=" O GLU 6 276 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU 6 276 " --> pdb=" O HIS 5 374 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN 6 274 " --> pdb=" O LYS 5 376 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS 6 374 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AA4, first strand: chain 'A' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN A 365 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP B 271 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE B 382 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 281 through 282 Processing sheet with id=AA7, first strand: chain 'B' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN B 365 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP C 271 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE C 382 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AB1, first strand: chain 'C' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN C 365 " --> pdb=" O ARG C 294 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP D 271 " --> pdb=" O ILE D 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE D 382 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 281 through 282 Processing sheet with id=AB4, first strand: chain 'D' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN D 365 " --> pdb=" O ARG D 294 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP E 271 " --> pdb=" O ILE E 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE E 382 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 281 through 282 Processing sheet with id=AB7, first strand: chain 'E' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN E 365 " --> pdb=" O ARG E 294 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP F 271 " --> pdb=" O ILE F 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE F 382 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 281 through 282 Processing sheet with id=AC1, first strand: chain 'F' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN F 365 " --> pdb=" O ARG F 294 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP G 271 " --> pdb=" O ILE G 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE G 382 " --> pdb=" O ASP G 271 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 281 through 282 Processing sheet with id=AC4, first strand: chain 'G' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN G 365 " --> pdb=" O ARG G 294 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP H 271 " --> pdb=" O ILE H 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE H 382 " --> pdb=" O ASP H 271 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 281 through 282 Processing sheet with id=AC7, first strand: chain 'H' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN H 365 " --> pdb=" O ARG H 294 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP I 271 " --> pdb=" O ILE I 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE I 382 " --> pdb=" O ASP I 271 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 281 through 282 Processing sheet with id=AD1, first strand: chain 'I' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN I 365 " --> pdb=" O ARG I 294 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP J 271 " --> pdb=" O ILE J 382 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE J 382 " --> pdb=" O ASP J 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 281 through 282 Processing sheet with id=AD4, first strand: chain 'J' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN J 365 " --> pdb=" O ARG J 294 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP K 271 " --> pdb=" O ILE K 382 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE K 382 " --> pdb=" O ASP K 271 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 281 through 282 Processing sheet with id=AD7, first strand: chain 'K' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN K 365 " --> pdb=" O ARG K 294 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP L 271 " --> pdb=" O ILE L 382 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE L 382 " --> pdb=" O ASP L 271 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 281 through 282 Processing sheet with id=AE1, first strand: chain 'L' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN L 365 " --> pdb=" O ARG L 294 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP M 271 " --> pdb=" O ILE M 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE M 382 " --> pdb=" O ASP M 271 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 281 through 282 Processing sheet with id=AE4, first strand: chain 'M' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN M 365 " --> pdb=" O ARG M 294 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP N 271 " --> pdb=" O ILE N 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE N 382 " --> pdb=" O ASP N 271 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 281 through 282 Processing sheet with id=AE7, first strand: chain 'N' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN N 365 " --> pdb=" O ARG N 294 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP O 271 " --> pdb=" O ILE O 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE O 382 " --> pdb=" O ASP O 271 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 281 through 282 Processing sheet with id=AF1, first strand: chain 'O' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN O 365 " --> pdb=" O ARG O 294 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP P 271 " --> pdb=" O ILE P 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE P 382 " --> pdb=" O ASP P 271 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 281 through 282 Processing sheet with id=AF4, first strand: chain 'P' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN P 365 " --> pdb=" O ARG P 294 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP Q 271 " --> pdb=" O ILE Q 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE Q 382 " --> pdb=" O ASP Q 271 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 281 through 282 Processing sheet with id=AF7, first strand: chain 'Q' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN Q 365 " --> pdb=" O ARG Q 294 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP R 271 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE R 382 " --> pdb=" O ASP R 271 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 281 through 282 Processing sheet with id=AG1, first strand: chain 'R' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN R 365 " --> pdb=" O ARG R 294 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP S 271 " --> pdb=" O ILE S 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE S 382 " --> pdb=" O ASP S 271 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 281 through 282 Processing sheet with id=AG4, first strand: chain 'S' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN S 365 " --> pdb=" O ARG S 294 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP T 271 " --> pdb=" O ILE T 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE T 382 " --> pdb=" O ASP T 271 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'T' and resid 281 through 282 Processing sheet with id=AG7, first strand: chain 'T' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN T 365 " --> pdb=" O ARG T 294 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP U 271 " --> pdb=" O ILE U 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE U 382 " --> pdb=" O ASP U 271 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'U' and resid 281 through 282 Processing sheet with id=AH1, first strand: chain 'U' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN U 365 " --> pdb=" O ARG U 294 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP V 271 " --> pdb=" O ILE V 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE V 382 " --> pdb=" O ASP V 271 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'V' and resid 281 through 282 Processing sheet with id=AH4, first strand: chain 'V' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN V 365 " --> pdb=" O ARG V 294 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'W' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP W 271 " --> pdb=" O ILE W 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE W 382 " --> pdb=" O ASP W 271 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 281 through 282 Processing sheet with id=AH7, first strand: chain 'W' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN W 365 " --> pdb=" O ARG W 294 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP X 271 " --> pdb=" O ILE X 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE X 382 " --> pdb=" O ASP X 271 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 281 through 282 Processing sheet with id=AI1, first strand: chain 'X' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN X 365 " --> pdb=" O ARG X 294 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP Y 271 " --> pdb=" O ILE Y 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE Y 382 " --> pdb=" O ASP Y 271 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Y' and resid 281 through 282 Processing sheet with id=AI4, first strand: chain 'Y' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN Y 365 " --> pdb=" O ARG Y 294 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Z' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP Z 271 " --> pdb=" O ILE Z 382 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE Z 382 " --> pdb=" O ASP Z 271 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Z' and resid 281 through 282 Processing sheet with id=AI7, first strand: chain 'Z' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN Z 365 " --> pdb=" O ARG Z 294 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain '1' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP 1 271 " --> pdb=" O ILE 1 382 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE 1 382 " --> pdb=" O ASP 1 271 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain '1' and resid 281 through 282 Processing sheet with id=AJ1, first strand: chain '1' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN 1 365 " --> pdb=" O ARG 1 294 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain '2' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP 2 271 " --> pdb=" O ILE 2 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE 2 382 " --> pdb=" O ASP 2 271 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain '2' and resid 281 through 282 Processing sheet with id=AJ4, first strand: chain '2' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN 2 365 " --> pdb=" O ARG 2 294 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain '3' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP 3 271 " --> pdb=" O ILE 3 382 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE 3 382 " --> pdb=" O ASP 3 271 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain '3' and resid 281 through 282 Processing sheet with id=AJ7, first strand: chain '3' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN 3 365 " --> pdb=" O ARG 3 294 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain '4' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP 4 271 " --> pdb=" O ILE 4 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE 4 382 " --> pdb=" O ASP 4 271 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain '4' and resid 281 through 282 Processing sheet with id=AK1, first strand: chain '4' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN 4 365 " --> pdb=" O ARG 4 294 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain '5' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP 5 271 " --> pdb=" O ILE 5 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE 5 382 " --> pdb=" O ASP 5 271 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain '5' and resid 281 through 282 Processing sheet with id=AK4, first strand: chain '5' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN 5 365 " --> pdb=" O ARG 5 294 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain '6' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP 6 271 " --> pdb=" O ILE 6 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE 6 382 " --> pdb=" O ASP 6 271 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain '6' and resid 281 through 282 Processing sheet with id=AK7, first strand: chain '6' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN 6 365 " --> pdb=" O ARG 6 294 " (cutoff:3.500A) 1668 hydrogen bonds defined for protein. 4770 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: 11.36 Time building geometry restraints manager: 14.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13728 1.34 - 1.45: 4786 1.45 - 1.57: 19854 1.57 - 1.68: 0 1.68 - 1.80: 192 Bond restraints: 38560 Sorted by residual: bond pdb=" C TYR A 282 " pdb=" N SER A 283 " ideal model delta sigma weight residual 1.331 1.296 0.035 2.07e-02 2.33e+03 2.84e+00 bond pdb=" C TYR S 282 " pdb=" N SER S 283 " ideal model delta sigma weight residual 1.331 1.296 0.035 2.07e-02 2.33e+03 2.83e+00 bond pdb=" C TYR G 282 " pdb=" N SER G 283 " ideal model delta sigma weight residual 1.331 1.296 0.035 2.07e-02 2.33e+03 2.82e+00 bond pdb=" C TYR L 282 " pdb=" N SER L 283 " ideal model delta sigma weight residual 1.331 1.296 0.035 2.07e-02 2.33e+03 2.82e+00 bond pdb=" C TYR B 282 " pdb=" N SER B 283 " ideal model delta sigma weight residual 1.331 1.296 0.035 2.07e-02 2.33e+03 2.80e+00 ... (remaining 38555 not shown) Histogram of bond angle deviations from ideal: 100.91 - 107.00: 902 107.00 - 113.08: 21652 113.08 - 119.17: 9793 119.17 - 125.26: 19397 125.26 - 131.34: 224 Bond angle restraints: 51968 Sorted by residual: angle pdb=" N ARG E 294 " pdb=" CA ARG E 294 " pdb=" C ARG E 294 " ideal model delta sigma weight residual 114.31 110.00 4.31 1.29e+00 6.01e-01 1.12e+01 angle pdb=" N ARG C 294 " pdb=" CA ARG C 294 " pdb=" C ARG C 294 " ideal model delta sigma weight residual 114.31 110.00 4.31 1.29e+00 6.01e-01 1.11e+01 angle pdb=" N ARG P 294 " pdb=" CA ARG P 294 " pdb=" C ARG P 294 " ideal model delta sigma weight residual 114.31 110.01 4.30 1.29e+00 6.01e-01 1.11e+01 angle pdb=" N ARG D 294 " pdb=" CA ARG D 294 " pdb=" C ARG D 294 " ideal model delta sigma weight residual 114.31 110.01 4.30 1.29e+00 6.01e-01 1.11e+01 angle pdb=" N ARG F 294 " pdb=" CA ARG F 294 " pdb=" C ARG F 294 " ideal model delta sigma weight residual 114.31 110.01 4.30 1.29e+00 6.01e-01 1.11e+01 ... (remaining 51963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.36: 19296 11.36 - 22.72: 3066 22.72 - 34.08: 1094 34.08 - 45.44: 480 45.44 - 56.79: 160 Dihedral angle restraints: 24096 sinusoidal: 9984 harmonic: 14112 Sorted by residual: dihedral pdb=" CA GLN J 297 " pdb=" C GLN J 297 " pdb=" N LEU J 298 " pdb=" CA LEU J 298 " ideal model delta harmonic sigma weight residual -180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA GLN 3 297 " pdb=" C GLN 3 297 " pdb=" N LEU 3 298 " pdb=" CA LEU 3 298 " ideal model delta harmonic sigma weight residual 180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA GLN W 297 " pdb=" C GLN W 297 " pdb=" N LEU W 298 " pdb=" CA LEU W 298 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 24093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2831 0.025 - 0.050: 1894 0.050 - 0.076: 718 0.076 - 0.101: 358 0.101 - 0.126: 151 Chirality restraints: 5952 Sorted by residual: chirality pdb=" CA ILE 4 382 " pdb=" N ILE 4 382 " pdb=" C ILE 4 382 " pdb=" CB ILE 4 382 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE 1 382 " pdb=" N ILE 1 382 " pdb=" C ILE 1 382 " pdb=" CB ILE 1 382 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA ILE H 382 " pdb=" N ILE H 382 " pdb=" C ILE H 382 " pdb=" CB ILE H 382 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 5949 not shown) Planarity restraints: 6976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 300 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C ILE C 300 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE C 300 " -0.011 2.00e-02 2.50e+03 pdb=" N SER C 301 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE Y 300 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C ILE Y 300 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE Y 300 " 0.011 2.00e-02 2.50e+03 pdb=" N SER Y 301 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE 1 300 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C ILE 1 300 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE 1 300 " -0.011 2.00e-02 2.50e+03 pdb=" N SER 1 301 " -0.010 2.00e-02 2.50e+03 ... (remaining 6973 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 870 2.59 - 3.17: 33027 3.17 - 3.75: 52231 3.75 - 4.32: 80878 4.32 - 4.90: 140393 Nonbonded interactions: 307399 Sorted by model distance: nonbonded pdb=" OE1 GLU L 418 " pdb=" OG1 THR M 429 " model vdw 2.016 2.440 nonbonded pdb=" OE1 GLU E 418 " pdb=" OG1 THR F 429 " model vdw 2.032 2.440 nonbonded pdb=" OE1 GLU 4 418 " pdb=" OG1 THR 5 429 " model vdw 2.077 2.440 nonbonded pdb=" O ASN G 239 " pdb=" OG SER G 243 " model vdw 2.081 2.440 nonbonded pdb=" O ASN D 239 " pdb=" OG SER D 243 " model vdw 2.081 2.440 ... (remaining 307394 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 5.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 17.870 Check model and map are aligned: 0.630 Set scattering table: 0.380 Process input model: 89.100 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.450 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.048 38560 Z= 0.591 Angle : 0.886 7.073 51968 Z= 0.525 Chirality : 0.043 0.126 5952 Planarity : 0.005 0.029 6976 Dihedral : 14.700 56.794 14816 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 11.33 % Allowed : 14.11 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.12), residues: 4640 helix: -0.64 (0.12), residues: 1280 sheet: -2.44 (0.11), residues: 2208 loop : -2.92 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS T 263 PHE 0.013 0.002 PHE D 422 TYR 0.005 0.001 TYR D 393 ARG 0.003 0.000 ARG D 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1667 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 486 poor density : 1181 time to evaluate : 4.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 SER cc_start: 0.9033 (OUTLIER) cc_final: 0.8613 (t) REVERT: E 301 SER cc_start: 0.8032 (t) cc_final: 0.7757 (m) REVERT: E 376 LYS cc_start: 0.8181 (tttt) cc_final: 0.7966 (tttm) REVERT: F 232 ASP cc_start: 0.7661 (t0) cc_final: 0.7390 (t0) REVERT: F 431 ASN cc_start: 0.7986 (t0) cc_final: 0.7772 (t0) REVERT: I 271 ASP cc_start: 0.7836 (t0) cc_final: 0.7529 (t0) REVERT: I 386 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8406 (p) REVERT: I 425 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8344 (ttpt) REVERT: J 376 LYS cc_start: 0.7818 (tttt) cc_final: 0.7545 (ttmm) REVERT: J 425 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8445 (ttpt) REVERT: J 435 SER cc_start: 0.7896 (OUTLIER) cc_final: 0.7633 (m) REVERT: K 386 SER cc_start: 0.9235 (OUTLIER) cc_final: 0.8711 (p) REVERT: K 425 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8448 (ttpt) REVERT: K 434 ASN cc_start: 0.7385 (t0) cc_final: 0.7163 (p0) REVERT: K 435 SER cc_start: 0.7972 (OUTLIER) cc_final: 0.7683 (m) REVERT: L 386 SER cc_start: 0.9220 (OUTLIER) cc_final: 0.8512 (p) REVERT: M 376 LYS cc_start: 0.8259 (tttt) cc_final: 0.8023 (tttm) REVERT: N 376 LYS cc_start: 0.8038 (tttt) cc_final: 0.7370 (tttp) REVERT: N 425 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8452 (ttpt) REVERT: O 425 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8394 (ttpt) REVERT: P 418 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7498 (mt-10) REVERT: P 435 SER cc_start: 0.7992 (OUTLIER) cc_final: 0.7752 (m) REVERT: Q 376 LYS cc_start: 0.7617 (tttt) cc_final: 0.7236 (tttp) REVERT: Q 386 SER cc_start: 0.8921 (OUTLIER) cc_final: 0.8407 (p) REVERT: Q 423 SER cc_start: 0.8093 (OUTLIER) cc_final: 0.7857 (p) REVERT: Q 425 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8507 (ttpt) REVERT: R 425 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8483 (ttpt) REVERT: S 423 SER cc_start: 0.8202 (OUTLIER) cc_final: 0.7932 (p) REVERT: S 425 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8457 (ttpt) REVERT: T 271 ASP cc_start: 0.7843 (t0) cc_final: 0.7575 (t0) REVERT: T 425 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8411 (ttpt) REVERT: W 271 ASP cc_start: 0.7713 (t0) cc_final: 0.7399 (t0) REVERT: W 425 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8344 (ttpt) REVERT: Y 303 GLN cc_start: 0.7246 (mt0) cc_final: 0.6950 (mp10) REVERT: Z 386 SER cc_start: 0.9133 (OUTLIER) cc_final: 0.8800 (t) REVERT: Z 425 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8298 (ttpt) REVERT: 1 409 MET cc_start: 0.8113 (mmm) cc_final: 0.7895 (mmm) REVERT: 1 413 GLU cc_start: 0.8137 (tt0) cc_final: 0.7765 (mt-10) REVERT: 3 232 ASP cc_start: 0.7635 (t0) cc_final: 0.7380 (t0) REVERT: 3 299 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7425 (m-40) REVERT: 3 376 LYS cc_start: 0.8306 (tttt) cc_final: 0.8100 (tttt) REVERT: 4 425 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8374 (ttpt) REVERT: 5 417 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7778 (ttm110) REVERT: 6 425 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8284 (ttmm) outliers start: 486 outliers final: 315 residues processed: 1563 average time/residue: 0.4816 time to fit residues: 1203.9156 Evaluate side-chains 1246 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 906 time to evaluate : 4.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 357 SER Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 423 SER Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 289 SER Chi-restraints excluded: chain H residue 299 ASN Chi-restraints excluded: chain H residue 357 SER Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 423 SER Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 357 SER Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain I residue 386 SER Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 423 SER Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain I residue 425 LYS Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain J residue 231 ASN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 357 SER Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 416 THR Chi-restraints excluded: chain J residue 423 SER Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain J residue 425 LYS Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 231 ASN Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 357 SER Chi-restraints excluded: chain K residue 358 THR Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 423 SER Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain K residue 425 LYS Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain K residue 435 SER Chi-restraints excluded: chain L residue 289 SER Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 357 SER Chi-restraints excluded: chain L residue 358 THR Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 386 SER Chi-restraints excluded: chain L residue 423 SER Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain M residue 243 SER Chi-restraints excluded: chain M residue 289 SER Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 381 ASP Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain M residue 429 THR Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain N residue 289 SER Chi-restraints excluded: chain N residue 357 SER Chi-restraints excluded: chain N residue 358 THR Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 386 SER Chi-restraints excluded: chain N residue 416 THR Chi-restraints excluded: chain N residue 423 SER Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain N residue 425 LYS Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 357 SER Chi-restraints excluded: chain O residue 358 THR Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 386 SER Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain O residue 423 SER Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain O residue 425 LYS Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain P residue 289 SER Chi-restraints excluded: chain P residue 357 SER Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 386 SER Chi-restraints excluded: chain P residue 416 THR Chi-restraints excluded: chain P residue 423 SER Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 435 SER Chi-restraints excluded: chain Q residue 231 ASN Chi-restraints excluded: chain Q residue 299 ASN Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 386 SER Chi-restraints excluded: chain Q residue 416 THR Chi-restraints excluded: chain Q residue 423 SER Chi-restraints excluded: chain Q residue 424 ASP Chi-restraints excluded: chain Q residue 425 LYS Chi-restraints excluded: chain R residue 231 ASN Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 289 SER Chi-restraints excluded: chain R residue 299 ASN Chi-restraints excluded: chain R residue 357 SER Chi-restraints excluded: chain R residue 358 THR Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 386 SER Chi-restraints excluded: chain R residue 423 SER Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain R residue 425 LYS Chi-restraints excluded: chain S residue 231 ASN Chi-restraints excluded: chain S residue 243 SER Chi-restraints excluded: chain S residue 289 SER Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 357 SER Chi-restraints excluded: chain S residue 358 THR Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 381 ASP Chi-restraints excluded: chain S residue 386 SER Chi-restraints excluded: chain S residue 423 SER Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain S residue 425 LYS Chi-restraints excluded: chain S residue 430 LEU Chi-restraints excluded: chain T residue 231 ASN Chi-restraints excluded: chain T residue 243 SER Chi-restraints excluded: chain T residue 289 SER Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 358 THR Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 386 SER Chi-restraints excluded: chain T residue 423 SER Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain T residue 425 LYS Chi-restraints excluded: chain T residue 429 THR Chi-restraints excluded: chain U residue 243 SER Chi-restraints excluded: chain U residue 289 SER Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 358 THR Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 386 SER Chi-restraints excluded: chain U residue 423 SER Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain U residue 430 LEU Chi-restraints excluded: chain V residue 243 SER Chi-restraints excluded: chain V residue 289 SER Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 358 THR Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 386 SER Chi-restraints excluded: chain V residue 416 THR Chi-restraints excluded: chain V residue 423 SER Chi-restraints excluded: chain V residue 424 ASP Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 289 SER Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 357 SER Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 386 SER Chi-restraints excluded: chain W residue 416 THR Chi-restraints excluded: chain W residue 423 SER Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain W residue 425 LYS Chi-restraints excluded: chain W residue 429 THR Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain X residue 289 SER Chi-restraints excluded: chain X residue 299 ASN Chi-restraints excluded: chain X residue 357 SER Chi-restraints excluded: chain X residue 358 THR Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 416 THR Chi-restraints excluded: chain X residue 423 SER Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain X residue 430 LEU Chi-restraints excluded: chain Y residue 289 SER Chi-restraints excluded: chain Y residue 299 ASN Chi-restraints excluded: chain Y residue 357 SER Chi-restraints excluded: chain Y residue 358 THR Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 386 SER Chi-restraints excluded: chain Y residue 416 THR Chi-restraints excluded: chain Y residue 423 SER Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 231 ASN Chi-restraints excluded: chain Z residue 289 SER Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 357 SER Chi-restraints excluded: chain Z residue 358 THR Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 381 ASP Chi-restraints excluded: chain Z residue 386 SER Chi-restraints excluded: chain Z residue 416 THR Chi-restraints excluded: chain Z residue 423 SER Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain Z residue 425 LYS Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain 1 residue 243 SER Chi-restraints excluded: chain 1 residue 289 SER Chi-restraints excluded: chain 1 residue 299 ASN Chi-restraints excluded: chain 1 residue 357 SER Chi-restraints excluded: chain 1 residue 358 THR Chi-restraints excluded: chain 1 residue 369 ASP Chi-restraints excluded: chain 1 residue 416 THR Chi-restraints excluded: chain 1 residue 423 SER Chi-restraints excluded: chain 1 residue 424 ASP Chi-restraints excluded: chain 1 residue 429 THR Chi-restraints excluded: chain 1 residue 430 LEU Chi-restraints excluded: chain 2 residue 243 SER Chi-restraints excluded: chain 2 residue 289 SER Chi-restraints excluded: chain 2 residue 299 ASN Chi-restraints excluded: chain 2 residue 358 THR Chi-restraints excluded: chain 2 residue 369 ASP Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 423 SER Chi-restraints excluded: chain 2 residue 424 ASP Chi-restraints excluded: chain 2 residue 429 THR Chi-restraints excluded: chain 3 residue 243 SER Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 299 ASN Chi-restraints excluded: chain 3 residue 357 SER Chi-restraints excluded: chain 3 residue 358 THR Chi-restraints excluded: chain 3 residue 369 ASP Chi-restraints excluded: chain 3 residue 416 THR Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 429 THR Chi-restraints excluded: chain 3 residue 430 LEU Chi-restraints excluded: chain 4 residue 289 SER Chi-restraints excluded: chain 4 residue 299 ASN Chi-restraints excluded: chain 4 residue 357 SER Chi-restraints excluded: chain 4 residue 358 THR Chi-restraints excluded: chain 4 residue 369 ASP Chi-restraints excluded: chain 4 residue 386 SER Chi-restraints excluded: chain 4 residue 416 THR Chi-restraints excluded: chain 4 residue 423 SER Chi-restraints excluded: chain 4 residue 424 ASP Chi-restraints excluded: chain 4 residue 425 LYS Chi-restraints excluded: chain 4 residue 429 THR Chi-restraints excluded: chain 5 residue 243 SER Chi-restraints excluded: chain 5 residue 299 ASN Chi-restraints excluded: chain 5 residue 357 SER Chi-restraints excluded: chain 5 residue 358 THR Chi-restraints excluded: chain 5 residue 369 ASP Chi-restraints excluded: chain 5 residue 416 THR Chi-restraints excluded: chain 5 residue 423 SER Chi-restraints excluded: chain 5 residue 424 ASP Chi-restraints excluded: chain 5 residue 429 THR Chi-restraints excluded: chain 6 residue 289 SER Chi-restraints excluded: chain 6 residue 299 ASN Chi-restraints excluded: chain 6 residue 357 SER Chi-restraints excluded: chain 6 residue 358 THR Chi-restraints excluded: chain 6 residue 369 ASP Chi-restraints excluded: chain 6 residue 381 ASP Chi-restraints excluded: chain 6 residue 416 THR Chi-restraints excluded: chain 6 residue 423 SER Chi-restraints excluded: chain 6 residue 424 ASP Chi-restraints excluded: chain 6 residue 425 LYS Chi-restraints excluded: chain 6 residue 429 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 4.9990 chunk 363 optimal weight: 5.9990 chunk 201 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 245 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 376 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 228 optimal weight: 7.9990 chunk 280 optimal weight: 1.9990 chunk 435 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN A 234 GLN A 365 ASN A 434 ASN B 365 ASN B 411 GLN B 434 ASN C 365 ASN C 434 ASN D 231 ASN D 263 HIS D 365 ASN D 411 GLN D 434 ASN E 365 ASN E 434 ASN F 234 GLN F 365 ASN F 411 GLN F 431 ASN F 434 ASN G 365 ASN G 434 ASN H 234 GLN H 263 HIS H 365 ASN I 231 ASN I 234 GLN I 263 HIS I 365 ASN I 434 ASN J 231 ASN J 234 GLN J 263 HIS J 365 ASN J 411 GLN J 434 ASN K 231 ASN K 234 GLN K 263 HIS K 365 ASN K 434 ASN L 263 HIS L 365 ASN L 434 ASN M 234 GLN M 365 ASN M 434 ASN N 263 HIS N 365 ASN N 411 GLN N 434 ASN O 263 HIS O 365 ASN O 411 GLN O 434 ASN P 234 GLN P 263 HIS P 365 ASN ** P 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 231 ASN Q 234 GLN Q 261 ASN Q 263 HIS Q 365 ASN Q 411 GLN R 231 ASN R 234 GLN R 263 HIS R 365 ASN R 411 GLN S 231 ASN S 263 HIS S 365 ASN S 411 GLN T 231 ASN T 234 GLN T 263 HIS T 365 ASN T 411 GLN U 231 ASN U 234 GLN ** U 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 263 HIS U 365 ASN U 411 GLN V 234 GLN V 263 HIS V 365 ASN V 434 ASN W 234 GLN W 263 HIS W 365 ASN W 434 ASN X 234 GLN ** X 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 HIS X 365 ASN X 434 ASN Y 231 ASN Y 234 GLN Y 263 HIS Y 365 ASN Y 411 GLN Y 434 ASN Z 231 ASN Z 234 GLN Z 263 HIS Z 365 ASN Z 434 ASN 1 263 HIS 1 365 ASN 1 411 GLN 1 434 ASN 2 231 ASN 2 234 GLN 2 365 ASN 2 411 GLN 2 434 ASN 3 234 GLN 3 365 ASN 3 434 ASN 4 263 HIS 4 365 ASN 4 411 GLN 4 434 ASN 5 234 GLN 5 365 ASN 5 411 GLN 5 434 ASN 6 365 ASN 6 434 ASN Total number of N/Q/H flips: 129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 38560 Z= 0.192 Angle : 0.615 8.731 51968 Z= 0.313 Chirality : 0.039 0.118 5952 Planarity : 0.004 0.031 6976 Dihedral : 7.942 59.640 5712 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 6.90 % Allowed : 16.51 % Favored : 76.59 % 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: -1.57 (0.13), residues: 4640 helix: 1.78 (0.14), residues: 1280 sheet: -1.90 (0.12), residues: 2336 loop : -2.06 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS O 374 PHE 0.023 0.001 PHE A 422 TYR 0.014 0.001 TYR 6 393 ARG 0.008 0.001 ARG 6 417 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 926 time to evaluate : 4.272 Fit side-chains REVERT: A 394 LYS cc_start: 0.5499 (OUTLIER) cc_final: 0.5210 (pttt) REVERT: B 377 MET cc_start: 0.8027 (mmm) cc_final: 0.7823 (mmm) REVERT: B 393 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.6935 (m-10) REVERT: D 237 PHE cc_start: 0.7776 (t80) cc_final: 0.7235 (t80) REVERT: D 393 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7743 (m-10) REVERT: E 376 LYS cc_start: 0.7998 (tttt) cc_final: 0.7778 (tttt) REVERT: G 393 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.7401 (m-10) REVERT: H 409 MET cc_start: 0.8405 (mmm) cc_final: 0.8172 (mmm) REVERT: H 418 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7208 (mm-30) REVERT: I 369 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.7032 (m-30) REVERT: I 376 LYS cc_start: 0.7593 (tttt) cc_final: 0.7079 (tttp) REVERT: I 386 SER cc_start: 0.8901 (m) cc_final: 0.7960 (p) REVERT: I 409 MET cc_start: 0.8478 (mmm) cc_final: 0.8058 (mmm) REVERT: I 413 GLU cc_start: 0.7916 (tt0) cc_final: 0.7704 (mt-10) REVERT: M 376 LYS cc_start: 0.8041 (tttt) cc_final: 0.7826 (tttt) REVERT: N 409 MET cc_start: 0.8522 (mmm) cc_final: 0.8312 (mmm) REVERT: N 413 GLU cc_start: 0.7950 (tt0) cc_final: 0.7630 (mt-10) REVERT: O 409 MET cc_start: 0.8651 (mmm) cc_final: 0.8394 (mmm) REVERT: Q 303 GLN cc_start: 0.6977 (mt0) cc_final: 0.6770 (mp10) REVERT: Q 376 LYS cc_start: 0.7798 (tttt) cc_final: 0.7195 (tttp) REVERT: Q 386 SER cc_start: 0.9044 (m) cc_final: 0.8179 (p) REVERT: Q 409 MET cc_start: 0.8114 (tpp) cc_final: 0.7585 (tpp) REVERT: R 276 GLU cc_start: 0.7428 (mp0) cc_final: 0.7208 (mp0) REVERT: R 409 MET cc_start: 0.8233 (mmm) cc_final: 0.7950 (mmm) REVERT: S 232 ASP cc_start: 0.7255 (t0) cc_final: 0.6664 (m-30) REVERT: S 386 SER cc_start: 0.9108 (m) cc_final: 0.8227 (p) REVERT: S 418 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7473 (mm-30) REVERT: S 430 LEU cc_start: 0.8623 (tp) cc_final: 0.8308 (tp) REVERT: T 356 ARG cc_start: 0.6956 (ttm-80) cc_final: 0.6741 (ttm170) REVERT: W 377 MET cc_start: 0.7915 (mmm) cc_final: 0.7699 (mmm) REVERT: W 412 ILE cc_start: 0.8298 (mm) cc_final: 0.8050 (tt) REVERT: X 409 MET cc_start: 0.8400 (mmm) cc_final: 0.8160 (mmm) REVERT: Y 356 ARG cc_start: 0.7059 (ttm-80) cc_final: 0.6780 (ttm170) REVERT: Y 386 SER cc_start: 0.9020 (m) cc_final: 0.8109 (p) REVERT: Y 412 ILE cc_start: 0.8429 (mm) cc_final: 0.8200 (tt) REVERT: Z 377 MET cc_start: 0.7887 (mmm) cc_final: 0.7636 (mmm) REVERT: Z 386 SER cc_start: 0.9125 (m) cc_final: 0.8399 (t) REVERT: 1 409 MET cc_start: 0.8100 (mmm) cc_final: 0.7831 (mmm) REVERT: 1 412 ILE cc_start: 0.8505 (mm) cc_final: 0.8217 (tt) REVERT: 1 413 GLU cc_start: 0.7938 (tt0) cc_final: 0.7719 (mt-10) REVERT: 2 386 SER cc_start: 0.9099 (m) cc_final: 0.8420 (t) REVERT: 2 393 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7656 (m-10) REVERT: 3 376 LYS cc_start: 0.8006 (tttt) cc_final: 0.7799 (tttt) REVERT: 5 393 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7667 (m-10) REVERT: 5 420 MET cc_start: 0.8298 (ptm) cc_final: 0.8055 (ptm) REVERT: 6 394 LYS cc_start: 0.4044 (OUTLIER) cc_final: 0.3829 (pttp) REVERT: 6 408 GLN cc_start: 0.7259 (tp-100) cc_final: 0.6784 (tp-100) outliers start: 296 outliers final: 221 residues processed: 1130 average time/residue: 0.4480 time to fit residues: 845.3792 Evaluate side-chains 1071 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 842 time to evaluate : 4.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 393 TYR Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 231 ASN Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 430 LEU Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 299 ASN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 381 ASP Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain I residue 231 ASN Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain I residue 381 ASP Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain J residue 231 ASN Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 411 GLN Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 430 LEU Chi-restraints excluded: chain K residue 231 ASN Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 381 ASP Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain M residue 243 SER Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 393 TYR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain M residue 429 THR Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 411 GLN Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain O residue 231 ASN Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 411 GLN Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 361 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 430 LEU Chi-restraints excluded: chain Q residue 231 ASN Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 299 ASN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 430 LEU Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 231 ASN Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 299 ASN Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 381 ASP Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain S residue 231 ASN Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 411 GLN Chi-restraints excluded: chain S residue 434 ASN Chi-restraints excluded: chain S residue 435 SER Chi-restraints excluded: chain T residue 231 ASN Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 381 ASP Chi-restraints excluded: chain T residue 411 GLN Chi-restraints excluded: chain T residue 429 THR Chi-restraints excluded: chain T residue 430 LEU Chi-restraints excluded: chain T residue 434 ASN Chi-restraints excluded: chain U residue 231 ASN Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 243 SER Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain U residue 411 GLN Chi-restraints excluded: chain U residue 415 LEU Chi-restraints excluded: chain U residue 434 ASN Chi-restraints excluded: chain V residue 242 GLU Chi-restraints excluded: chain V residue 243 SER Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 358 THR Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain V residue 424 ASP Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain V residue 430 LEU Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain W residue 429 THR Chi-restraints excluded: chain W residue 430 LEU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain X residue 299 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 381 ASP Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Y residue 231 ASN Chi-restraints excluded: chain Y residue 299 ASN Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 411 GLN Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 231 ASN Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain 1 residue 243 SER Chi-restraints excluded: chain 1 residue 299 ASN Chi-restraints excluded: chain 1 residue 369 ASP Chi-restraints excluded: chain 1 residue 411 GLN Chi-restraints excluded: chain 1 residue 424 ASP Chi-restraints excluded: chain 1 residue 429 THR Chi-restraints excluded: chain 2 residue 231 ASN Chi-restraints excluded: chain 2 residue 243 SER Chi-restraints excluded: chain 2 residue 299 ASN Chi-restraints excluded: chain 2 residue 369 ASP Chi-restraints excluded: chain 2 residue 393 TYR Chi-restraints excluded: chain 2 residue 411 GLN Chi-restraints excluded: chain 2 residue 424 ASP Chi-restraints excluded: chain 2 residue 429 THR Chi-restraints excluded: chain 2 residue 430 LEU Chi-restraints excluded: chain 3 residue 243 SER Chi-restraints excluded: chain 3 residue 299 ASN Chi-restraints excluded: chain 3 residue 369 ASP Chi-restraints excluded: chain 3 residue 381 ASP Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 429 THR Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 4 residue 299 ASN Chi-restraints excluded: chain 4 residue 369 ASP Chi-restraints excluded: chain 4 residue 393 TYR Chi-restraints excluded: chain 4 residue 411 GLN Chi-restraints excluded: chain 4 residue 424 ASP Chi-restraints excluded: chain 4 residue 429 THR Chi-restraints excluded: chain 4 residue 430 LEU Chi-restraints excluded: chain 5 residue 231 ASN Chi-restraints excluded: chain 5 residue 299 ASN Chi-restraints excluded: chain 5 residue 393 TYR Chi-restraints excluded: chain 5 residue 411 GLN Chi-restraints excluded: chain 5 residue 424 ASP Chi-restraints excluded: chain 5 residue 429 THR Chi-restraints excluded: chain 6 residue 231 ASN Chi-restraints excluded: chain 6 residue 242 GLU Chi-restraints excluded: chain 6 residue 299 ASN Chi-restraints excluded: chain 6 residue 369 ASP Chi-restraints excluded: chain 6 residue 393 TYR Chi-restraints excluded: chain 6 residue 394 LYS Chi-restraints excluded: chain 6 residue 424 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 0.6980 chunk 135 optimal weight: 7.9990 chunk 362 optimal weight: 0.0670 chunk 296 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 436 optimal weight: 0.9980 chunk 471 optimal weight: 4.9990 chunk 388 optimal weight: 0.9990 chunk 433 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 350 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 239 ASN C 239 ASN C 411 GLN D 231 ASN E 239 ASN F 239 ASN G 239 ASN I 231 ASN I 411 GLN J 234 GLN J 239 ASN K 411 GLN L 411 GLN ** M 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 411 GLN P 434 ASN R 411 GLN T 234 GLN U 231 ASN U 239 ASN W 234 GLN X 411 GLN Y 231 ASN Z 411 GLN ** 1 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 231 ASN 3 239 ASN 3 411 GLN 4 239 ASN 6 411 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 38560 Z= 0.151 Angle : 0.545 8.269 51968 Z= 0.280 Chirality : 0.038 0.132 5952 Planarity : 0.003 0.028 6976 Dihedral : 5.932 59.911 5438 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 6.04 % Allowed : 20.03 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 4640 helix: 2.66 (0.14), residues: 1280 sheet: -1.59 (0.12), residues: 2336 loop : -1.85 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS O 374 PHE 0.026 0.001 PHE 4 422 TYR 0.013 0.001 TYR 6 393 ARG 0.004 0.000 ARG F 417 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 906 time to evaluate : 4.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 237 PHE cc_start: 0.7778 (t80) cc_final: 0.7192 (t80) REVERT: G 393 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7422 (m-10) REVERT: H 409 MET cc_start: 0.8365 (mmm) cc_final: 0.8110 (mmm) REVERT: H 418 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7373 (mm-30) REVERT: I 376 LYS cc_start: 0.7367 (tttt) cc_final: 0.7133 (ttpt) REVERT: I 386 SER cc_start: 0.8885 (m) cc_final: 0.7896 (t) REVERT: I 409 MET cc_start: 0.8472 (mmm) cc_final: 0.8083 (mmm) REVERT: I 413 GLU cc_start: 0.7896 (tt0) cc_final: 0.7672 (mt-10) REVERT: J 232 ASP cc_start: 0.7168 (t0) cc_final: 0.6518 (m-30) REVERT: J 376 LYS cc_start: 0.7479 (tttt) cc_final: 0.7139 (ttmm) REVERT: K 413 GLU cc_start: 0.7686 (tt0) cc_final: 0.7115 (mt-10) REVERT: K 418 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7396 (mm-30) REVERT: M 250 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8336 (mt-10) REVERT: N 376 LYS cc_start: 0.7332 (tttt) cc_final: 0.6910 (tttp) REVERT: N 409 MET cc_start: 0.8538 (mmm) cc_final: 0.8111 (mmm) REVERT: N 413 GLU cc_start: 0.7849 (tt0) cc_final: 0.7556 (mt-10) REVERT: O 409 MET cc_start: 0.8672 (mmm) cc_final: 0.8422 (mmm) REVERT: Q 303 GLN cc_start: 0.6930 (mt0) cc_final: 0.6681 (mp10) REVERT: Q 376 LYS cc_start: 0.7638 (tttt) cc_final: 0.7069 (tttp) REVERT: Q 386 SER cc_start: 0.9009 (m) cc_final: 0.8096 (p) REVERT: Q 415 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8383 (mp) REVERT: R 276 GLU cc_start: 0.7344 (mp0) cc_final: 0.7092 (mp0) REVERT: R 418 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7622 (mm-30) REVERT: S 232 ASP cc_start: 0.7252 (t0) cc_final: 0.6621 (m-30) REVERT: S 386 SER cc_start: 0.9008 (m) cc_final: 0.8147 (p) REVERT: S 418 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7412 (mm-30) REVERT: S 435 SER cc_start: 0.8120 (OUTLIER) cc_final: 0.7603 (m) REVERT: U 231 ASN cc_start: 0.6080 (OUTLIER) cc_final: 0.5726 (m110) REVERT: V 232 ASP cc_start: 0.7415 (t0) cc_final: 0.7153 (t0) REVERT: W 412 ILE cc_start: 0.8408 (mm) cc_final: 0.8175 (tt) REVERT: X 242 GLU cc_start: 0.6952 (pt0) cc_final: 0.6669 (tt0) REVERT: X 409 MET cc_start: 0.8372 (mmm) cc_final: 0.8155 (mmm) REVERT: X 418 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7174 (mm-30) REVERT: Y 231 ASN cc_start: 0.6066 (OUTLIER) cc_final: 0.5789 (m110) REVERT: Y 376 LYS cc_start: 0.7428 (tttt) cc_final: 0.6858 (mtpp) REVERT: Y 386 SER cc_start: 0.8945 (m) cc_final: 0.7988 (t) REVERT: Y 409 MET cc_start: 0.8297 (mmm) cc_final: 0.7986 (tpt) REVERT: Z 232 ASP cc_start: 0.7307 (t0) cc_final: 0.6508 (m-30) REVERT: 1 431 ASN cc_start: 0.8352 (t0) cc_final: 0.8024 (t0) REVERT: 2 393 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7479 (m-10) REVERT: 3 376 LYS cc_start: 0.7924 (tttt) cc_final: 0.7712 (tttt) REVERT: 5 393 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.7743 (m-10) REVERT: 6 408 GLN cc_start: 0.7137 (tp-100) cc_final: 0.6902 (tp-100) outliers start: 259 outliers final: 183 residues processed: 1064 average time/residue: 0.4327 time to fit residues: 775.7792 Evaluate side-chains 1069 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 879 time to evaluate : 3.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 411 GLN Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 231 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 393 TYR Chi-restraints excluded: chain G residue 231 ASN Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain H residue 231 ASN Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 299 ASN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain I residue 231 ASN Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 381 ASP Chi-restraints excluded: chain I residue 411 GLN Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 410 LYS Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 430 LEU Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 411 GLN Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 411 GLN Chi-restraints excluded: chain M residue 231 ASN Chi-restraints excluded: chain M residue 243 SER Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 231 ASN Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain O residue 231 ASN Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 430 LEU Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 299 ASN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain Q residue 424 ASP Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 299 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 381 ASP Chi-restraints excluded: chain R residue 386 SER Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain R residue 434 ASN Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain S residue 434 ASN Chi-restraints excluded: chain S residue 435 SER Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 410 LYS Chi-restraints excluded: chain T residue 416 THR Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain T residue 429 THR Chi-restraints excluded: chain T residue 434 ASN Chi-restraints excluded: chain U residue 231 ASN Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 243 SER Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 357 SER Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 410 LYS Chi-restraints excluded: chain U residue 414 ASP Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain U residue 434 ASN Chi-restraints excluded: chain V residue 231 ASN Chi-restraints excluded: chain V residue 243 SER Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain V residue 416 THR Chi-restraints excluded: chain V residue 434 ASN Chi-restraints excluded: chain W residue 231 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 416 THR Chi-restraints excluded: chain W residue 429 THR Chi-restraints excluded: chain X residue 231 ASN Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain X residue 299 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 411 GLN Chi-restraints excluded: chain X residue 416 THR Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Y residue 231 ASN Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 299 ASN Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 411 GLN Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain 1 residue 231 ASN Chi-restraints excluded: chain 1 residue 243 SER Chi-restraints excluded: chain 1 residue 299 ASN Chi-restraints excluded: chain 1 residue 369 ASP Chi-restraints excluded: chain 1 residue 429 THR Chi-restraints excluded: chain 2 residue 231 ASN Chi-restraints excluded: chain 2 residue 243 SER Chi-restraints excluded: chain 2 residue 299 ASN Chi-restraints excluded: chain 2 residue 357 SER Chi-restraints excluded: chain 2 residue 369 ASP Chi-restraints excluded: chain 2 residue 393 TYR Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 3 residue 231 ASN Chi-restraints excluded: chain 3 residue 243 SER Chi-restraints excluded: chain 3 residue 299 ASN Chi-restraints excluded: chain 3 residue 369 ASP Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 3 residue 411 GLN Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 4 residue 231 ASN Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 4 residue 299 ASN Chi-restraints excluded: chain 4 residue 369 ASP Chi-restraints excluded: chain 4 residue 416 THR Chi-restraints excluded: chain 5 residue 231 ASN Chi-restraints excluded: chain 5 residue 289 SER Chi-restraints excluded: chain 5 residue 299 ASN Chi-restraints excluded: chain 5 residue 393 TYR Chi-restraints excluded: chain 5 residue 416 THR Chi-restraints excluded: chain 6 residue 242 GLU Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain 6 residue 299 ASN Chi-restraints excluded: chain 6 residue 369 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 0.5980 chunk 328 optimal weight: 0.9990 chunk 226 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 208 optimal weight: 7.9990 chunk 293 optimal weight: 4.9990 chunk 438 optimal weight: 10.0000 chunk 463 optimal weight: 2.9990 chunk 228 optimal weight: 8.9990 chunk 415 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN C 239 ASN C 285 ASN E 239 ASN F 239 ASN G 239 ASN H 239 ASN H 411 GLN I 231 ASN I 239 ASN J 234 GLN J 411 GLN K 239 ASN M 239 ASN N 411 GLN O 411 GLN Q 411 GLN R 239 ASN S 411 GLN T 239 ASN T 411 GLN U 231 ASN U 239 ASN U 411 GLN X 239 ASN Z 239 ASN 1 239 ASN 2 231 ASN ** 2 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 239 ASN 6 239 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 38560 Z= 0.307 Angle : 0.638 8.580 51968 Z= 0.323 Chirality : 0.040 0.151 5952 Planarity : 0.004 0.029 6976 Dihedral : 6.136 52.015 5353 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 8.09 % Allowed : 19.59 % Favored : 72.32 % 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: -0.91 (0.14), residues: 4640 helix: 2.50 (0.14), residues: 1280 sheet: -1.53 (0.12), residues: 2336 loop : -1.96 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS 6 374 PHE 0.020 0.002 PHE 4 422 TYR 0.012 0.001 TYR A 393 ARG 0.004 0.000 ARG I 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 893 time to evaluate : 4.744 Fit side-chains REVERT: A 393 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7900 (m-10) REVERT: B 393 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.6687 (m-10) REVERT: C 393 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.6982 (m-10) REVERT: C 423 SER cc_start: 0.8267 (t) cc_final: 0.8023 (t) REVERT: D 231 ASN cc_start: 0.6313 (OUTLIER) cc_final: 0.5737 (m110) REVERT: D 237 PHE cc_start: 0.7934 (t80) cc_final: 0.7529 (t80) REVERT: D 393 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.7664 (m-10) REVERT: E 414 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7225 (m-30) REVERT: F 232 ASP cc_start: 0.7713 (t0) cc_final: 0.7470 (t0) REVERT: F 409 MET cc_start: 0.8199 (tpp) cc_final: 0.7658 (tpp) REVERT: G 393 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7700 (m-10) REVERT: I 231 ASN cc_start: 0.5778 (OUTLIER) cc_final: 0.4930 (m110) REVERT: I 232 ASP cc_start: 0.7404 (t0) cc_final: 0.7171 (t0) REVERT: I 386 SER cc_start: 0.9052 (m) cc_final: 0.8078 (t) REVERT: I 409 MET cc_start: 0.8449 (mmm) cc_final: 0.8095 (mmm) REVERT: I 413 GLU cc_start: 0.7929 (tt0) cc_final: 0.7589 (mt-10) REVERT: K 413 GLU cc_start: 0.7760 (tt0) cc_final: 0.7215 (mt-10) REVERT: N 409 MET cc_start: 0.8616 (mmm) cc_final: 0.8128 (mmm) REVERT: N 413 GLU cc_start: 0.7940 (tt0) cc_final: 0.7560 (mt-10) REVERT: O 409 MET cc_start: 0.8585 (mmm) cc_final: 0.8300 (mmm) REVERT: Q 232 ASP cc_start: 0.7343 (t0) cc_final: 0.6585 (m-30) REVERT: Q 423 SER cc_start: 0.8302 (t) cc_final: 0.8084 (t) REVERT: U 231 ASN cc_start: 0.5820 (OUTLIER) cc_final: 0.5116 (m110) REVERT: X 409 MET cc_start: 0.8334 (mmm) cc_final: 0.8086 (mmm) REVERT: Y 231 ASN cc_start: 0.5689 (OUTLIER) cc_final: 0.4919 (m110) REVERT: Y 386 SER cc_start: 0.9187 (m) cc_final: 0.8356 (p) REVERT: Z 377 MET cc_start: 0.7999 (mmm) cc_final: 0.7780 (mmm) REVERT: 2 231 ASN cc_start: 0.6382 (OUTLIER) cc_final: 0.5740 (m110) REVERT: 2 393 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7414 (m-10) REVERT: 4 404 LEU cc_start: 0.6994 (mp) cc_final: 0.6718 (mp) REVERT: 5 393 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.8002 (m-10) outliers start: 347 outliers final: 247 residues processed: 1138 average time/residue: 0.4436 time to fit residues: 844.5046 Evaluate side-chains 1126 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 866 time to evaluate : 4.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 381 ASP Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain E residue 231 ASN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 393 TYR Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 231 ASN Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 430 LEU Chi-restraints excluded: chain H residue 231 ASN Chi-restraints excluded: chain H residue 299 ASN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 381 ASP Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 411 GLN Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain I residue 231 ASN Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 381 ASP Chi-restraints excluded: chain I residue 410 LYS Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain J residue 231 ASN Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 410 LYS Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 430 LEU Chi-restraints excluded: chain K residue 231 ASN Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 381 ASP Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 381 ASP Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain M residue 231 ASN Chi-restraints excluded: chain M residue 289 SER Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 393 TYR Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 231 ASN Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 411 GLN Chi-restraints excluded: chain N residue 415 LEU Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain O residue 231 ASN Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 381 ASP Chi-restraints excluded: chain O residue 411 GLN Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain O residue 430 LEU Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain P residue 361 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 430 LEU Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 299 ASN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 424 ASP Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 231 ASN Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 299 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 381 ASP Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain R residue 434 ASN Chi-restraints excluded: chain S residue 231 ASN Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 411 GLN Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain S residue 434 ASN Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 357 SER Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 381 ASP Chi-restraints excluded: chain T residue 416 THR Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain T residue 429 THR Chi-restraints excluded: chain T residue 434 ASN Chi-restraints excluded: chain U residue 231 ASN Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 357 SER Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain U residue 414 ASP Chi-restraints excluded: chain U residue 415 LEU Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain U residue 434 ASN Chi-restraints excluded: chain V residue 231 ASN Chi-restraints excluded: chain V residue 242 GLU Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain V residue 416 THR Chi-restraints excluded: chain V residue 424 ASP Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain V residue 434 ASN Chi-restraints excluded: chain W residue 231 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 429 THR Chi-restraints excluded: chain X residue 231 ASN Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 299 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 381 ASP Chi-restraints excluded: chain X residue 410 LYS Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain X residue 430 LEU Chi-restraints excluded: chain Y residue 231 ASN Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 299 ASN Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 231 ASN Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 410 LYS Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain 1 residue 231 ASN Chi-restraints excluded: chain 1 residue 299 ASN Chi-restraints excluded: chain 1 residue 369 ASP Chi-restraints excluded: chain 1 residue 416 THR Chi-restraints excluded: chain 1 residue 429 THR Chi-restraints excluded: chain 2 residue 231 ASN Chi-restraints excluded: chain 2 residue 243 SER Chi-restraints excluded: chain 2 residue 289 SER Chi-restraints excluded: chain 2 residue 299 ASN Chi-restraints excluded: chain 2 residue 357 SER Chi-restraints excluded: chain 2 residue 369 ASP Chi-restraints excluded: chain 2 residue 393 TYR Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 424 ASP Chi-restraints excluded: chain 2 residue 429 THR Chi-restraints excluded: chain 3 residue 231 ASN Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 299 ASN Chi-restraints excluded: chain 3 residue 369 ASP Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 429 THR Chi-restraints excluded: chain 4 residue 231 ASN Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 4 residue 289 SER Chi-restraints excluded: chain 4 residue 299 ASN Chi-restraints excluded: chain 4 residue 369 ASP Chi-restraints excluded: chain 4 residue 381 ASP Chi-restraints excluded: chain 4 residue 393 TYR Chi-restraints excluded: chain 4 residue 424 ASP Chi-restraints excluded: chain 4 residue 430 LEU Chi-restraints excluded: chain 5 residue 231 ASN Chi-restraints excluded: chain 5 residue 289 SER Chi-restraints excluded: chain 5 residue 299 ASN Chi-restraints excluded: chain 5 residue 381 ASP Chi-restraints excluded: chain 5 residue 393 TYR Chi-restraints excluded: chain 5 residue 424 ASP Chi-restraints excluded: chain 5 residue 430 LEU Chi-restraints excluded: chain 6 residue 231 ASN Chi-restraints excluded: chain 6 residue 242 GLU Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain 6 residue 289 SER Chi-restraints excluded: chain 6 residue 299 ASN Chi-restraints excluded: chain 6 residue 369 ASP Chi-restraints excluded: chain 6 residue 393 TYR Chi-restraints excluded: chain 6 residue 424 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 345 optimal weight: 2.9990 chunk 191 optimal weight: 0.0060 chunk 395 optimal weight: 3.9990 chunk 320 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 0.5980 chunk 416 optimal weight: 0.0570 chunk 117 optimal weight: 2.9990 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 411 GLN C 239 ASN D 411 GLN E 239 ASN G 239 ASN G 411 GLN H 239 ASN I 231 ASN J 234 GLN K 239 ASN L 239 ASN M 239 ASN M 263 HIS N 239 ASN N 411 GLN O 239 ASN O 411 GLN P 239 ASN Q 239 ASN Q 411 GLN R 239 ASN S 239 ASN S 411 GLN T 239 ASN U 231 ASN V 239 ASN V 411 GLN W 411 GLN 1 239 ASN 2 231 ASN 2 239 ASN 2 263 HIS 3 239 ASN 5 411 GLN 6 239 ASN 6 408 GLN 6 411 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 38560 Z= 0.139 Angle : 0.530 6.965 51968 Z= 0.271 Chirality : 0.039 0.141 5952 Planarity : 0.003 0.022 6976 Dihedral : 5.159 23.619 5345 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 6.18 % Allowed : 21.78 % Favored : 72.04 % 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: -0.59 (0.14), residues: 4640 helix: 3.04 (0.14), residues: 1280 sheet: -1.47 (0.12), residues: 2336 loop : -1.86 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 374 PHE 0.018 0.001 PHE 4 422 TYR 0.009 0.001 TYR C 393 ARG 0.005 0.000 ARG R 417 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 933 time to evaluate : 4.392 Fit side-chains revert: symmetry clash REVERT: D 231 ASN cc_start: 0.6260 (OUTLIER) cc_final: 0.5698 (m110) REVERT: D 237 PHE cc_start: 0.7835 (t80) cc_final: 0.7404 (t80) REVERT: E 244 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6217 (ttt-90) REVERT: E 414 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7149 (m-30) REVERT: F 232 ASP cc_start: 0.7695 (t0) cc_final: 0.7434 (t0) REVERT: F 409 MET cc_start: 0.8198 (tpp) cc_final: 0.7177 (tpp) REVERT: F 413 GLU cc_start: 0.7998 (tt0) cc_final: 0.7664 (mt-10) REVERT: G 242 GLU cc_start: 0.7548 (tt0) cc_final: 0.7091 (tt0) REVERT: G 393 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7808 (m-10) REVERT: H 418 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7378 (mm-30) REVERT: H 431 ASN cc_start: 0.8265 (t0) cc_final: 0.7969 (t0) REVERT: I 376 LYS cc_start: 0.7345 (tttt) cc_final: 0.7083 (ttpt) REVERT: I 409 MET cc_start: 0.8444 (mmm) cc_final: 0.7905 (mmm) REVERT: I 413 GLU cc_start: 0.7851 (tt0) cc_final: 0.7570 (mt-10) REVERT: J 232 ASP cc_start: 0.7409 (t0) cc_final: 0.6698 (m-30) REVERT: J 376 LYS cc_start: 0.7482 (tttt) cc_final: 0.7125 (ttmm) REVERT: K 237 PHE cc_start: 0.7845 (t80) cc_final: 0.7166 (t80) REVERT: K 413 GLU cc_start: 0.7733 (tt0) cc_final: 0.7205 (mt-10) REVERT: L 231 ASN cc_start: 0.5863 (OUTLIER) cc_final: 0.5564 (m110) REVERT: L 237 PHE cc_start: 0.7842 (t80) cc_final: 0.7234 (t80) REVERT: M 409 MET cc_start: 0.8184 (mmm) cc_final: 0.7843 (tpt) REVERT: N 376 LYS cc_start: 0.7318 (tttt) cc_final: 0.6875 (tttp) REVERT: N 409 MET cc_start: 0.8596 (mmm) cc_final: 0.8351 (mmm) REVERT: O 409 MET cc_start: 0.8648 (mmm) cc_final: 0.8402 (mmm) REVERT: P 418 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7709 (mm-30) REVERT: Q 376 LYS cc_start: 0.7376 (tttt) cc_final: 0.6768 (mtpp) REVERT: S 231 ASN cc_start: 0.6075 (OUTLIER) cc_final: 0.5786 (p0) REVERT: S 232 ASP cc_start: 0.7274 (t0) cc_final: 0.6733 (m-30) REVERT: S 242 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6695 (tt0) REVERT: T 232 ASP cc_start: 0.7345 (t0) cc_final: 0.6704 (m-30) REVERT: T 237 PHE cc_start: 0.7794 (t80) cc_final: 0.7143 (t80) REVERT: U 232 ASP cc_start: 0.7158 (t0) cc_final: 0.6612 (m-30) REVERT: V 376 LYS cc_start: 0.7349 (tttt) cc_final: 0.6909 (ttmm) REVERT: W 242 GLU cc_start: 0.7444 (tt0) cc_final: 0.7010 (tt0) REVERT: X 409 MET cc_start: 0.8327 (mmm) cc_final: 0.8118 (mmm) REVERT: X 418 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7219 (mm-30) REVERT: Y 231 ASN cc_start: 0.5644 (OUTLIER) cc_final: 0.4831 (m110) REVERT: Y 232 ASP cc_start: 0.7223 (t0) cc_final: 0.6994 (t0) REVERT: Y 376 LYS cc_start: 0.7358 (tttt) cc_final: 0.7089 (ttpt) REVERT: Y 386 SER cc_start: 0.9007 (m) cc_final: 0.8003 (t) REVERT: Z 377 MET cc_start: 0.7934 (mmm) cc_final: 0.7713 (mmm) REVERT: 1 431 ASN cc_start: 0.8355 (t0) cc_final: 0.8068 (t0) REVERT: 4 376 LYS cc_start: 0.7451 (tttt) cc_final: 0.6989 (tttp) REVERT: 6 412 ILE cc_start: 0.8666 (mm) cc_final: 0.8317 (tt) outliers start: 265 outliers final: 175 residues processed: 1088 average time/residue: 0.4121 time to fit residues: 773.9890 Evaluate side-chains 1101 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 918 time to evaluate : 4.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain E residue 231 ASN Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 393 TYR Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain G residue 231 ASN Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 411 GLN Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 299 ASN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain I residue 231 ASN Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 381 ASP Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 411 GLN Chi-restraints excluded: chain K residue 231 ASN Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain M residue 231 ASN Chi-restraints excluded: chain M residue 289 SER Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 429 THR Chi-restraints excluded: chain N residue 231 ASN Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 386 SER Chi-restraints excluded: chain N residue 411 GLN Chi-restraints excluded: chain O residue 231 ASN Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 411 GLN Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain O residue 430 LEU Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain Q residue 299 ASN Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 411 GLN Chi-restraints excluded: chain Q residue 424 ASP Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 381 ASP Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain R residue 434 ASN Chi-restraints excluded: chain S residue 231 ASN Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 411 GLN Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain S residue 434 ASN Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 411 GLN Chi-restraints excluded: chain T residue 416 THR Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain U residue 231 ASN Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 411 GLN Chi-restraints excluded: chain U residue 414 ASP Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain U residue 434 ASN Chi-restraints excluded: chain V residue 231 ASN Chi-restraints excluded: chain V residue 242 GLU Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain V residue 416 THR Chi-restraints excluded: chain V residue 424 ASP Chi-restraints excluded: chain V residue 434 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 411 GLN Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain W residue 430 LEU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 299 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 381 ASP Chi-restraints excluded: chain X residue 416 THR Chi-restraints excluded: chain Y residue 231 ASN Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 299 ASN Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 416 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain 1 residue 299 ASN Chi-restraints excluded: chain 1 residue 369 ASP Chi-restraints excluded: chain 1 residue 416 THR Chi-restraints excluded: chain 1 residue 424 ASP Chi-restraints excluded: chain 2 residue 231 ASN Chi-restraints excluded: chain 2 residue 289 SER Chi-restraints excluded: chain 2 residue 299 ASN Chi-restraints excluded: chain 2 residue 357 SER Chi-restraints excluded: chain 2 residue 369 ASP Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 424 ASP Chi-restraints excluded: chain 2 residue 429 THR Chi-restraints excluded: chain 3 residue 231 ASN Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 299 ASN Chi-restraints excluded: chain 3 residue 369 ASP Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 4 residue 231 ASN Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 4 residue 243 SER Chi-restraints excluded: chain 4 residue 289 SER Chi-restraints excluded: chain 4 residue 299 ASN Chi-restraints excluded: chain 4 residue 369 ASP Chi-restraints excluded: chain 4 residue 393 TYR Chi-restraints excluded: chain 4 residue 430 LEU Chi-restraints excluded: chain 5 residue 231 ASN Chi-restraints excluded: chain 5 residue 289 SER Chi-restraints excluded: chain 5 residue 299 ASN Chi-restraints excluded: chain 5 residue 411 GLN Chi-restraints excluded: chain 5 residue 424 ASP Chi-restraints excluded: chain 6 residue 231 ASN Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain 6 residue 299 ASN Chi-restraints excluded: chain 6 residue 369 ASP Chi-restraints excluded: chain 6 residue 393 TYR Chi-restraints excluded: chain 6 residue 411 GLN Chi-restraints excluded: chain 6 residue 424 ASP Chi-restraints excluded: chain 6 residue 429 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 0.0020 chunk 417 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 272 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 464 optimal weight: 9.9990 chunk 385 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 243 optimal weight: 8.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 GLN C 239 ASN D 239 ASN D 411 GLN E 239 ASN F 411 GLN G 411 GLN H 239 ASN I 231 ASN I 239 ASN K 239 ASN L 239 ASN M 239 ASN N 239 ASN N 411 GLN O 239 ASN O 411 GLN P 239 ASN Q 411 GLN R 239 ASN S 239 ASN S 411 GLN T 239 ASN U 231 ASN U 239 ASN V 239 ASN V 411 GLN W 411 GLN Y 239 ASN Y 411 GLN 1 239 ASN 1 411 GLN 2 231 ASN 2 239 ASN 2 411 GLN 3 239 ASN 5 411 GLN 6 239 ASN 6 411 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 38560 Z= 0.183 Angle : 0.543 8.593 51968 Z= 0.278 Chirality : 0.039 0.219 5952 Planarity : 0.003 0.023 6976 Dihedral : 5.081 20.852 5324 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 6.88 % Allowed : 21.64 % Favored : 71.48 % 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: -0.62 (0.14), residues: 4640 helix: 2.97 (0.14), residues: 1280 sheet: -1.45 (0.12), residues: 2336 loop : -1.90 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 374 PHE 0.018 0.001 PHE 1 237 TYR 0.012 0.001 TYR 5 393 ARG 0.004 0.000 ARG R 417 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1216 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 921 time to evaluate : 4.368 Fit side-chains REVERT: B 232 ASP cc_start: 0.7538 (t0) cc_final: 0.7330 (t0) REVERT: C 393 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.6664 (m-10) REVERT: D 231 ASN cc_start: 0.6251 (OUTLIER) cc_final: 0.5687 (m110) REVERT: D 237 PHE cc_start: 0.7844 (t80) cc_final: 0.7423 (t80) REVERT: E 244 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6293 (ttt-90) REVERT: E 414 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7096 (m-30) REVERT: F 232 ASP cc_start: 0.7749 (t0) cc_final: 0.7530 (t0) REVERT: F 376 LYS cc_start: 0.7366 (tttt) cc_final: 0.6923 (tttp) REVERT: F 404 LEU cc_start: 0.6996 (mp) cc_final: 0.6696 (mp) REVERT: F 409 MET cc_start: 0.8183 (tpp) cc_final: 0.7831 (tpp) REVERT: G 242 GLU cc_start: 0.7542 (tt0) cc_final: 0.7138 (tt0) REVERT: G 393 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7917 (m-10) REVERT: G 414 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7116 (m-30) REVERT: H 418 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7380 (mm-30) REVERT: H 431 ASN cc_start: 0.8343 (t0) cc_final: 0.8009 (t0) REVERT: I 231 ASN cc_start: 0.5761 (OUTLIER) cc_final: 0.4680 (m110) REVERT: I 376 LYS cc_start: 0.7391 (tttt) cc_final: 0.7124 (ttpt) REVERT: I 413 GLU cc_start: 0.7867 (tt0) cc_final: 0.7621 (mt-10) REVERT: J 232 ASP cc_start: 0.7315 (t0) cc_final: 0.6587 (m-30) REVERT: J 242 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: J 376 LYS cc_start: 0.7539 (tttt) cc_final: 0.7179 (ttmm) REVERT: K 237 PHE cc_start: 0.7821 (t80) cc_final: 0.7195 (t80) REVERT: K 413 GLU cc_start: 0.7781 (tt0) cc_final: 0.7407 (mt-10) REVERT: L 231 ASN cc_start: 0.5911 (OUTLIER) cc_final: 0.5621 (m110) REVERT: L 237 PHE cc_start: 0.7860 (t80) cc_final: 0.7272 (t80) REVERT: N 376 LYS cc_start: 0.7464 (tttt) cc_final: 0.7042 (tttp) REVERT: N 409 MET cc_start: 0.8592 (mmm) cc_final: 0.8169 (tpp) REVERT: O 409 MET cc_start: 0.8690 (mmm) cc_final: 0.8439 (mmm) REVERT: P 418 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7672 (mm-30) REVERT: Q 232 ASP cc_start: 0.7215 (t0) cc_final: 0.6702 (m-30) REVERT: Q 376 LYS cc_start: 0.7414 (tttt) cc_final: 0.6813 (mtpp) REVERT: S 231 ASN cc_start: 0.6029 (OUTLIER) cc_final: 0.5801 (p0) REVERT: S 232 ASP cc_start: 0.7336 (t0) cc_final: 0.6701 (m-30) REVERT: S 237 PHE cc_start: 0.7844 (t80) cc_final: 0.7137 (t80) REVERT: S 242 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6719 (tt0) REVERT: T 237 PHE cc_start: 0.7866 (t80) cc_final: 0.7226 (t80) REVERT: U 231 ASN cc_start: 0.5591 (OUTLIER) cc_final: 0.4476 (m110) REVERT: U 232 ASP cc_start: 0.7311 (t0) cc_final: 0.7102 (t0) REVERT: U 242 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6922 (tt0) REVERT: V 376 LYS cc_start: 0.7456 (tttt) cc_final: 0.7007 (ttmm) REVERT: V 413 GLU cc_start: 0.7888 (tt0) cc_final: 0.7502 (mt-10) REVERT: W 242 GLU cc_start: 0.7472 (tt0) cc_final: 0.7074 (tt0) REVERT: X 418 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7295 (mm-30) REVERT: Y 231 ASN cc_start: 0.5688 (OUTLIER) cc_final: 0.4836 (m110) REVERT: Y 232 ASP cc_start: 0.7318 (t0) cc_final: 0.7059 (t0) REVERT: Z 231 ASN cc_start: 0.6813 (OUTLIER) cc_final: 0.6574 (p0) REVERT: Z 232 ASP cc_start: 0.7201 (t0) cc_final: 0.6529 (m-30) REVERT: Z 377 MET cc_start: 0.7943 (mmm) cc_final: 0.7735 (mmm) REVERT: 1 431 ASN cc_start: 0.8381 (t0) cc_final: 0.8090 (t0) REVERT: 2 231 ASN cc_start: 0.6285 (OUTLIER) cc_final: 0.5262 (m110) REVERT: 3 413 GLU cc_start: 0.7971 (tt0) cc_final: 0.7552 (mt-10) REVERT: 4 376 LYS cc_start: 0.7491 (tttt) cc_final: 0.7018 (tttp) REVERT: 4 404 LEU cc_start: 0.6842 (mp) cc_final: 0.6574 (mp) REVERT: 4 413 GLU cc_start: 0.7980 (tt0) cc_final: 0.7552 (mt-10) REVERT: 5 242 GLU cc_start: 0.7568 (tt0) cc_final: 0.7134 (tt0) REVERT: 5 414 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7039 (m-30) REVERT: 6 412 ILE cc_start: 0.8592 (mm) cc_final: 0.8383 (tt) outliers start: 295 outliers final: 195 residues processed: 1105 average time/residue: 0.4246 time to fit residues: 801.8985 Evaluate side-chains 1126 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 914 time to evaluate : 4.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 393 TYR Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 411 GLN Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 299 ASN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 231 ASN Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 411 GLN Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 231 ASN Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 381 ASP Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain M residue 289 SER Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 411 GLN Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 411 GLN Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 299 ASN Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 411 GLN Chi-restraints excluded: chain Q residue 424 ASP Chi-restraints excluded: chain Q residue 430 LEU Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 231 ASN Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 299 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 381 ASP Chi-restraints excluded: chain R residue 416 THR Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain R residue 434 ASN Chi-restraints excluded: chain S residue 231 ASN Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 411 GLN Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain S residue 434 ASN Chi-restraints excluded: chain T residue 231 ASN Chi-restraints excluded: chain T residue 243 SER Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 411 GLN Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain U residue 231 ASN Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 357 SER Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain U residue 411 GLN Chi-restraints excluded: chain U residue 414 ASP Chi-restraints excluded: chain U residue 415 LEU Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain U residue 434 ASN Chi-restraints excluded: chain V residue 242 GLU Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain V residue 416 THR Chi-restraints excluded: chain V residue 424 ASP Chi-restraints excluded: chain V residue 434 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 411 GLN Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 299 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 381 ASP Chi-restraints excluded: chain X residue 391 VAL Chi-restraints excluded: chain X residue 416 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Y residue 231 ASN Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 299 ASN Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 411 GLN Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 231 ASN Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 416 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain 1 residue 231 ASN Chi-restraints excluded: chain 1 residue 299 ASN Chi-restraints excluded: chain 1 residue 369 ASP Chi-restraints excluded: chain 1 residue 411 GLN Chi-restraints excluded: chain 1 residue 424 ASP Chi-restraints excluded: chain 2 residue 231 ASN Chi-restraints excluded: chain 2 residue 289 SER Chi-restraints excluded: chain 2 residue 299 ASN Chi-restraints excluded: chain 2 residue 357 SER Chi-restraints excluded: chain 2 residue 369 ASP Chi-restraints excluded: chain 2 residue 411 GLN Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 424 ASP Chi-restraints excluded: chain 2 residue 429 THR Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 299 ASN Chi-restraints excluded: chain 3 residue 369 ASP Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 4 residue 243 SER Chi-restraints excluded: chain 4 residue 289 SER Chi-restraints excluded: chain 4 residue 299 ASN Chi-restraints excluded: chain 4 residue 369 ASP Chi-restraints excluded: chain 4 residue 393 TYR Chi-restraints excluded: chain 4 residue 416 THR Chi-restraints excluded: chain 4 residue 424 ASP Chi-restraints excluded: chain 4 residue 429 THR Chi-restraints excluded: chain 4 residue 430 LEU Chi-restraints excluded: chain 5 residue 289 SER Chi-restraints excluded: chain 5 residue 299 ASN Chi-restraints excluded: chain 5 residue 411 GLN Chi-restraints excluded: chain 5 residue 414 ASP Chi-restraints excluded: chain 5 residue 424 ASP Chi-restraints excluded: chain 6 residue 231 ASN Chi-restraints excluded: chain 6 residue 242 GLU Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain 6 residue 289 SER Chi-restraints excluded: chain 6 residue 299 ASN Chi-restraints excluded: chain 6 residue 369 ASP Chi-restraints excluded: chain 6 residue 393 TYR Chi-restraints excluded: chain 6 residue 411 GLN Chi-restraints excluded: chain 6 residue 424 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 264 optimal weight: 4.9990 chunk 339 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 390 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 462 optimal weight: 0.9990 chunk 289 optimal weight: 1.9990 chunk 282 optimal weight: 0.8980 chunk 213 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN B 239 ASN B 411 GLN C 239 ASN D 239 ASN D 411 GLN E 239 ASN E 411 GLN F 411 GLN G 411 GLN H 239 ASN I 231 ASN I 239 ASN J 239 ASN K 239 ASN L 239 ASN L 411 GLN M 239 ASN N 239 ASN N 411 GLN O 239 ASN O 411 GLN P 239 ASN P 411 GLN Q 411 GLN R 239 ASN S 239 ASN S 411 GLN T 239 ASN U 231 ASN U 239 ASN V 239 ASN Y 239 ASN 1 239 ASN 1 411 GLN 2 231 ASN 2 239 ASN 2 411 GLN 3 239 ASN 4 239 ASN 5 411 GLN 6 239 ASN 6 411 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 38560 Z= 0.213 Angle : 0.558 7.764 51968 Z= 0.286 Chirality : 0.039 0.202 5952 Planarity : 0.003 0.028 6976 Dihedral : 5.161 22.100 5324 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 7.04 % Allowed : 22.13 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 4640 helix: 2.86 (0.14), residues: 1280 sheet: -1.48 (0.12), residues: 2336 loop : -1.91 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS 6 374 PHE 0.023 0.001 PHE 1 237 TYR 0.012 0.001 TYR 5 393 ARG 0.007 0.000 ARG 4 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 903 time to evaluate : 4.317 Fit side-chains REVERT: A 413 GLU cc_start: 0.7967 (tt0) cc_final: 0.7540 (mt-10) REVERT: C 393 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.6610 (m-10) REVERT: D 231 ASN cc_start: 0.6299 (OUTLIER) cc_final: 0.5722 (m110) REVERT: D 237 PHE cc_start: 0.7860 (t80) cc_final: 0.7461 (t80) REVERT: D 393 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7474 (m-10) REVERT: E 244 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6380 (ttt-90) REVERT: E 414 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7234 (m-30) REVERT: F 242 GLU cc_start: 0.7488 (tt0) cc_final: 0.7237 (tt0) REVERT: F 376 LYS cc_start: 0.7441 (tttt) cc_final: 0.7001 (tttp) REVERT: F 409 MET cc_start: 0.8170 (tpp) cc_final: 0.7825 (tpp) REVERT: G 242 GLU cc_start: 0.7574 (tt0) cc_final: 0.7185 (tt0) REVERT: G 393 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.8006 (m-10) REVERT: H 418 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7389 (mm-30) REVERT: H 431 ASN cc_start: 0.8341 (t0) cc_final: 0.7991 (t0) REVERT: I 231 ASN cc_start: 0.6131 (OUTLIER) cc_final: 0.4648 (m-40) REVERT: J 413 GLU cc_start: 0.7706 (tt0) cc_final: 0.7419 (mt-10) REVERT: K 237 PHE cc_start: 0.7853 (t80) cc_final: 0.7247 (t80) REVERT: K 413 GLU cc_start: 0.7798 (tt0) cc_final: 0.7424 (mt-10) REVERT: L 231 ASN cc_start: 0.5957 (OUTLIER) cc_final: 0.5654 (m110) REVERT: L 237 PHE cc_start: 0.7869 (t80) cc_final: 0.7288 (t80) REVERT: M 413 GLU cc_start: 0.7929 (tt0) cc_final: 0.7655 (mt-10) REVERT: N 376 LYS cc_start: 0.7474 (tttt) cc_final: 0.7040 (tttp) REVERT: O 409 MET cc_start: 0.8691 (mmm) cc_final: 0.8449 (mmm) REVERT: P 418 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7646 (mm-30) REVERT: Q 376 LYS cc_start: 0.7431 (tttt) cc_final: 0.7146 (ttpt) REVERT: Q 435 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8230 (m) REVERT: R 242 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6654 (tt0) REVERT: S 231 ASN cc_start: 0.6077 (OUTLIER) cc_final: 0.5822 (p0) REVERT: S 232 ASP cc_start: 0.7329 (t0) cc_final: 0.6622 (m-30) REVERT: S 237 PHE cc_start: 0.7926 (t80) cc_final: 0.7195 (t80) REVERT: T 237 PHE cc_start: 0.7913 (t80) cc_final: 0.7266 (t80) REVERT: U 231 ASN cc_start: 0.5963 (OUTLIER) cc_final: 0.4432 (m110) REVERT: U 232 ASP cc_start: 0.7344 (t0) cc_final: 0.7113 (t0) REVERT: U 242 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6938 (tt0) REVERT: V 376 LYS cc_start: 0.7488 (tttt) cc_final: 0.6994 (tttp) REVERT: V 410 LYS cc_start: 0.8976 (tptt) cc_final: 0.8586 (tptt) REVERT: W 242 GLU cc_start: 0.7505 (tt0) cc_final: 0.7110 (tt0) REVERT: W 413 GLU cc_start: 0.7870 (tt0) cc_final: 0.7598 (mt-10) REVERT: X 418 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7287 (mm-30) REVERT: Y 231 ASN cc_start: 0.5737 (OUTLIER) cc_final: 0.4932 (m110) REVERT: Y 232 ASP cc_start: 0.7328 (t0) cc_final: 0.7066 (t0) REVERT: Y 393 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7764 (m-10) REVERT: Z 231 ASN cc_start: 0.6595 (OUTLIER) cc_final: 0.6364 (p0) REVERT: Z 232 ASP cc_start: 0.7301 (t0) cc_final: 0.6607 (m-30) REVERT: Z 409 MET cc_start: 0.8565 (mmm) cc_final: 0.8261 (tpp) REVERT: 1 431 ASN cc_start: 0.8354 (t0) cc_final: 0.8071 (t0) REVERT: 2 231 ASN cc_start: 0.6456 (OUTLIER) cc_final: 0.5469 (m110) REVERT: 2 413 GLU cc_start: 0.7896 (tt0) cc_final: 0.7579 (mt-10) REVERT: 3 413 GLU cc_start: 0.7950 (tt0) cc_final: 0.7552 (mt-10) REVERT: 4 376 LYS cc_start: 0.7548 (tttt) cc_final: 0.7067 (tttp) REVERT: 4 404 LEU cc_start: 0.7003 (mp) cc_final: 0.6770 (mp) REVERT: 5 242 GLU cc_start: 0.7538 (tt0) cc_final: 0.7100 (tt0) REVERT: 6 404 LEU cc_start: 0.6288 (mp) cc_final: 0.6036 (mp) REVERT: 6 412 ILE cc_start: 0.8593 (mm) cc_final: 0.8351 (tt) outliers start: 302 outliers final: 208 residues processed: 1107 average time/residue: 0.4166 time to fit residues: 790.3115 Evaluate side-chains 1126 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 901 time to evaluate : 4.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 231 ASN Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 393 TYR Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 411 GLN Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 299 ASN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 231 ASN Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 381 ASP Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 231 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 231 ASN Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 381 ASP Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain M residue 231 ASN Chi-restraints excluded: chain M residue 289 SER Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 429 THR Chi-restraints excluded: chain N residue 231 ASN Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 411 GLN Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 411 GLN Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 411 GLN Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 231 ASN Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 299 ASN Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 411 GLN Chi-restraints excluded: chain Q residue 424 ASP Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 231 ASN Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 299 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 381 ASP Chi-restraints excluded: chain R residue 416 THR Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain R residue 434 ASN Chi-restraints excluded: chain S residue 231 ASN Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 411 GLN Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain S residue 434 ASN Chi-restraints excluded: chain T residue 231 ASN Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 243 SER Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 411 GLN Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain U residue 231 ASN Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 357 SER Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain U residue 411 GLN Chi-restraints excluded: chain U residue 414 ASP Chi-restraints excluded: chain U residue 415 LEU Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain U residue 434 ASN Chi-restraints excluded: chain V residue 231 ASN Chi-restraints excluded: chain V residue 242 GLU Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain V residue 416 THR Chi-restraints excluded: chain V residue 424 ASP Chi-restraints excluded: chain V residue 434 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 299 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 381 ASP Chi-restraints excluded: chain X residue 416 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Y residue 231 ASN Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 243 SER Chi-restraints excluded: chain Y residue 299 ASN Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 393 TYR Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 231 ASN Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 416 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain 1 residue 231 ASN Chi-restraints excluded: chain 1 residue 299 ASN Chi-restraints excluded: chain 1 residue 369 ASP Chi-restraints excluded: chain 1 residue 411 GLN Chi-restraints excluded: chain 1 residue 424 ASP Chi-restraints excluded: chain 2 residue 231 ASN Chi-restraints excluded: chain 2 residue 289 SER Chi-restraints excluded: chain 2 residue 299 ASN Chi-restraints excluded: chain 2 residue 357 SER Chi-restraints excluded: chain 2 residue 369 ASP Chi-restraints excluded: chain 2 residue 411 GLN Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 424 ASP Chi-restraints excluded: chain 3 residue 231 ASN Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 299 ASN Chi-restraints excluded: chain 3 residue 369 ASP Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 3 residue 429 THR Chi-restraints excluded: chain 4 residue 231 ASN Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 4 residue 243 SER Chi-restraints excluded: chain 4 residue 289 SER Chi-restraints excluded: chain 4 residue 299 ASN Chi-restraints excluded: chain 4 residue 369 ASP Chi-restraints excluded: chain 4 residue 393 TYR Chi-restraints excluded: chain 4 residue 416 THR Chi-restraints excluded: chain 4 residue 424 ASP Chi-restraints excluded: chain 4 residue 430 LEU Chi-restraints excluded: chain 5 residue 289 SER Chi-restraints excluded: chain 5 residue 299 ASN Chi-restraints excluded: chain 5 residue 411 GLN Chi-restraints excluded: chain 5 residue 424 ASP Chi-restraints excluded: chain 6 residue 231 ASN Chi-restraints excluded: chain 6 residue 242 GLU Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain 6 residue 289 SER Chi-restraints excluded: chain 6 residue 299 ASN Chi-restraints excluded: chain 6 residue 369 ASP Chi-restraints excluded: chain 6 residue 411 GLN Chi-restraints excluded: chain 6 residue 424 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 276 optimal weight: 0.9980 chunk 139 optimal weight: 0.4980 chunk 90 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 294 optimal weight: 1.9990 chunk 315 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 363 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 411 GLN B 239 ASN B 411 GLN C 239 ASN D 239 ASN D 411 GLN E 239 ASN E 411 GLN G 411 GLN H 239 ASN H 411 GLN I 231 ASN I 239 ASN J 239 ASN J 411 GLN K 239 ASN L 239 ASN M 239 ASN M 411 GLN N 411 GLN O 239 ASN O 411 GLN P 239 ASN P 411 GLN Q 411 GLN R 239 ASN S 239 ASN S 411 GLN T 239 ASN U 231 ASN V 239 ASN Y 239 ASN Z 239 ASN 1 239 ASN 2 231 ASN 2 239 ASN 3 239 ASN 5 411 GLN 6 239 ASN 6 411 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 38560 Z= 0.240 Angle : 0.580 9.731 51968 Z= 0.296 Chirality : 0.040 0.275 5952 Planarity : 0.003 0.024 6976 Dihedral : 5.265 23.265 5324 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 6.93 % Allowed : 22.85 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 4640 helix: 2.74 (0.14), residues: 1280 sheet: -1.51 (0.12), residues: 2336 loop : -1.91 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS 6 374 PHE 0.022 0.001 PHE 1 237 TYR 0.010 0.001 TYR 5 393 ARG 0.006 0.000 ARG 4 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 890 time to evaluate : 4.327 Fit side-chains REVERT: A 413 GLU cc_start: 0.7912 (tt0) cc_final: 0.7577 (mt-10) REVERT: B 232 ASP cc_start: 0.7505 (t0) cc_final: 0.7265 (t0) REVERT: C 393 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.6615 (m-10) REVERT: D 231 ASN cc_start: 0.6356 (OUTLIER) cc_final: 0.5783 (m110) REVERT: D 237 PHE cc_start: 0.7885 (t80) cc_final: 0.7474 (t80) REVERT: D 393 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7424 (m-10) REVERT: E 244 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6354 (ttt-90) REVERT: E 414 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7272 (m-30) REVERT: F 242 GLU cc_start: 0.7439 (tt0) cc_final: 0.7192 (tt0) REVERT: F 376 LYS cc_start: 0.7543 (tttt) cc_final: 0.7074 (tttp) REVERT: F 404 LEU cc_start: 0.6867 (mp) cc_final: 0.6586 (mp) REVERT: F 409 MET cc_start: 0.8207 (tpp) cc_final: 0.7841 (tpp) REVERT: G 242 GLU cc_start: 0.7599 (tt0) cc_final: 0.7211 (tt0) REVERT: G 393 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.8003 (m-10) REVERT: H 418 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7393 (mm-30) REVERT: H 431 ASN cc_start: 0.8344 (t0) cc_final: 0.8000 (t0) REVERT: I 231 ASN cc_start: 0.6588 (OUTLIER) cc_final: 0.5170 (m110) REVERT: I 386 SER cc_start: 0.8900 (m) cc_final: 0.7845 (t) REVERT: J 413 GLU cc_start: 0.7691 (tt0) cc_final: 0.7211 (mt-10) REVERT: J 432 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8731 (p) REVERT: K 237 PHE cc_start: 0.7865 (t80) cc_final: 0.7301 (t80) REVERT: K 413 GLU cc_start: 0.7805 (tt0) cc_final: 0.7401 (mt-10) REVERT: L 231 ASN cc_start: 0.6020 (OUTLIER) cc_final: 0.5738 (m110) REVERT: L 237 PHE cc_start: 0.7906 (t80) cc_final: 0.7318 (t80) REVERT: M 409 MET cc_start: 0.8247 (mmm) cc_final: 0.7476 (tpt) REVERT: M 413 GLU cc_start: 0.7907 (tt0) cc_final: 0.7631 (mt-10) REVERT: N 376 LYS cc_start: 0.7557 (tttt) cc_final: 0.7084 (tttp) REVERT: O 409 MET cc_start: 0.8695 (mmm) cc_final: 0.8389 (mmm) REVERT: P 418 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7651 (mm-30) REVERT: Q 376 LYS cc_start: 0.7461 (tttt) cc_final: 0.7164 (ttpt) REVERT: R 242 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6668 (tt0) REVERT: T 237 PHE cc_start: 0.7937 (t80) cc_final: 0.7274 (t80) REVERT: U 231 ASN cc_start: 0.6168 (OUTLIER) cc_final: 0.4534 (m110) REVERT: U 242 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: V 376 LYS cc_start: 0.7515 (tttt) cc_final: 0.7027 (tttp) REVERT: W 242 GLU cc_start: 0.7537 (tt0) cc_final: 0.7172 (tt0) REVERT: W 413 GLU cc_start: 0.7831 (tt0) cc_final: 0.7617 (mt-10) REVERT: X 418 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7315 (mm-30) REVERT: Y 231 ASN cc_start: 0.5899 (OUTLIER) cc_final: 0.5113 (m110) REVERT: Y 232 ASP cc_start: 0.7371 (t0) cc_final: 0.7103 (t0) REVERT: Y 393 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7786 (m-10) REVERT: Y 409 MET cc_start: 0.8485 (mmm) cc_final: 0.8202 (tpp) REVERT: Z 231 ASN cc_start: 0.6564 (OUTLIER) cc_final: 0.6351 (p0) REVERT: Z 232 ASP cc_start: 0.7251 (t0) cc_final: 0.6584 (m-30) REVERT: Z 409 MET cc_start: 0.8571 (mmm) cc_final: 0.8265 (tpp) REVERT: 2 231 ASN cc_start: 0.6377 (OUTLIER) cc_final: 0.5551 (m110) REVERT: 2 409 MET cc_start: 0.8220 (mmm) cc_final: 0.7528 (tpt) REVERT: 2 413 GLU cc_start: 0.7913 (tt0) cc_final: 0.7569 (mt-10) REVERT: 3 409 MET cc_start: 0.8183 (tpp) cc_final: 0.7454 (tpp) REVERT: 3 413 GLU cc_start: 0.7927 (tt0) cc_final: 0.7583 (mt-10) REVERT: 4 404 LEU cc_start: 0.6933 (mp) cc_final: 0.6704 (mp) REVERT: 4 409 MET cc_start: 0.8268 (tpp) cc_final: 0.7416 (tpp) REVERT: 5 242 GLU cc_start: 0.7578 (tt0) cc_final: 0.7163 (tt0) REVERT: 6 404 LEU cc_start: 0.6260 (mp) cc_final: 0.6030 (mp) outliers start: 297 outliers final: 216 residues processed: 1104 average time/residue: 0.4200 time to fit residues: 793.3563 Evaluate side-chains 1117 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 885 time to evaluate : 4.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 231 ASN Chi-restraints excluded: chain E residue 244 ARG Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 393 TYR Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain G residue 231 ASN Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 411 GLN Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 299 ASN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 381 ASP Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 231 ASN Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 381 ASP Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 231 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain K residue 231 ASN Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 381 ASP Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain M residue 231 ASN Chi-restraints excluded: chain M residue 289 SER Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 393 TYR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain M residue 429 THR Chi-restraints excluded: chain N residue 231 ASN Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 243 SER Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 411 GLN Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 411 GLN Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 411 GLN Chi-restraints excluded: chain P residue 416 THR Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 231 ASN Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 299 ASN Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 411 GLN Chi-restraints excluded: chain Q residue 424 ASP Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain R residue 231 ASN Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 299 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 381 ASP Chi-restraints excluded: chain R residue 416 THR Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain R residue 434 ASN Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 411 GLN Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain S residue 434 ASN Chi-restraints excluded: chain T residue 231 ASN Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 243 SER Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 357 SER Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 381 ASP Chi-restraints excluded: chain T residue 411 GLN Chi-restraints excluded: chain T residue 416 THR Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain U residue 231 ASN Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 357 SER Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain U residue 411 GLN Chi-restraints excluded: chain U residue 414 ASP Chi-restraints excluded: chain U residue 415 LEU Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain U residue 434 ASN Chi-restraints excluded: chain V residue 242 GLU Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain V residue 416 THR Chi-restraints excluded: chain V residue 424 ASP Chi-restraints excluded: chain V residue 434 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 299 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 381 ASP Chi-restraints excluded: chain X residue 391 VAL Chi-restraints excluded: chain X residue 416 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Y residue 231 ASN Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 243 SER Chi-restraints excluded: chain Y residue 299 ASN Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 393 TYR Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 231 ASN Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 416 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain 1 residue 231 ASN Chi-restraints excluded: chain 1 residue 299 ASN Chi-restraints excluded: chain 1 residue 369 ASP Chi-restraints excluded: chain 1 residue 424 ASP Chi-restraints excluded: chain 2 residue 231 ASN Chi-restraints excluded: chain 2 residue 289 SER Chi-restraints excluded: chain 2 residue 299 ASN Chi-restraints excluded: chain 2 residue 357 SER Chi-restraints excluded: chain 2 residue 369 ASP Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 424 ASP Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 299 ASN Chi-restraints excluded: chain 3 residue 369 ASP Chi-restraints excluded: chain 3 residue 381 ASP Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 4 residue 231 ASN Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 4 residue 243 SER Chi-restraints excluded: chain 4 residue 289 SER Chi-restraints excluded: chain 4 residue 299 ASN Chi-restraints excluded: chain 4 residue 369 ASP Chi-restraints excluded: chain 4 residue 393 TYR Chi-restraints excluded: chain 4 residue 416 THR Chi-restraints excluded: chain 4 residue 424 ASP Chi-restraints excluded: chain 4 residue 430 LEU Chi-restraints excluded: chain 5 residue 289 SER Chi-restraints excluded: chain 5 residue 299 ASN Chi-restraints excluded: chain 5 residue 411 GLN Chi-restraints excluded: chain 5 residue 424 ASP Chi-restraints excluded: chain 6 residue 231 ASN Chi-restraints excluded: chain 6 residue 242 GLU Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain 6 residue 289 SER Chi-restraints excluded: chain 6 residue 299 ASN Chi-restraints excluded: chain 6 residue 369 ASP Chi-restraints excluded: chain 6 residue 411 GLN Chi-restraints excluded: chain 6 residue 424 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 6.9990 chunk 443 optimal weight: 2.9990 chunk 404 optimal weight: 9.9990 chunk 431 optimal weight: 0.8980 chunk 259 optimal weight: 1.9990 chunk 187 optimal weight: 0.2980 chunk 338 optimal weight: 6.9990 chunk 132 optimal weight: 0.5980 chunk 389 optimal weight: 4.9990 chunk 407 optimal weight: 2.9990 chunk 429 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 239 ASN B 411 GLN C 239 ASN D 239 ASN E 239 ASN E 263 HIS F 263 HIS G 411 GLN H 239 ASN I 231 ASN I 239 ASN J 239 ASN K 239 ASN L 239 ASN M 239 ASN M 411 GLN N 411 GLN O 239 ASN O 411 GLN P 239 ASN Q 411 GLN R 239 ASN S 239 ASN S 411 GLN T 239 ASN U 231 ASN W 411 GLN Y 239 ASN 1 239 ASN 2 231 ASN 2 239 ASN 3 239 ASN 5 411 GLN 6 239 ASN 6 411 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 38560 Z= 0.248 Angle : 0.594 8.935 51968 Z= 0.304 Chirality : 0.040 0.251 5952 Planarity : 0.003 0.055 6976 Dihedral : 5.340 23.795 5324 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 6.53 % Allowed : 23.39 % Favored : 70.08 % 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: -0.78 (0.14), residues: 4640 helix: 2.73 (0.14), residues: 1280 sheet: -1.53 (0.12), residues: 2336 loop : -1.87 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 374 PHE 0.022 0.001 PHE F 237 TYR 0.010 0.001 TYR 5 393 ARG 0.012 0.000 ARG L 417 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 896 time to evaluate : 4.635 Fit side-chains REVERT: A 409 MET cc_start: 0.8145 (tpp) cc_final: 0.7543 (tpp) REVERT: B 232 ASP cc_start: 0.7532 (t0) cc_final: 0.7286 (t0) REVERT: C 393 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.6594 (m-10) REVERT: D 231 ASN cc_start: 0.6347 (OUTLIER) cc_final: 0.5745 (m110) REVERT: D 237 PHE cc_start: 0.7909 (t80) cc_final: 0.7501 (t80) REVERT: D 393 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7327 (m-10) REVERT: D 413 GLU cc_start: 0.7841 (tt0) cc_final: 0.7301 (mt-10) REVERT: E 409 MET cc_start: 0.8218 (mmm) cc_final: 0.7529 (tpt) REVERT: E 413 GLU cc_start: 0.7884 (tt0) cc_final: 0.7518 (mt-10) REVERT: E 414 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7226 (m-30) REVERT: F 242 GLU cc_start: 0.7439 (tt0) cc_final: 0.7161 (tt0) REVERT: F 376 LYS cc_start: 0.7581 (tttt) cc_final: 0.7104 (tttp) REVERT: F 404 LEU cc_start: 0.6903 (mp) cc_final: 0.6637 (mp) REVERT: F 409 MET cc_start: 0.8225 (tpp) cc_final: 0.7836 (tpp) REVERT: G 242 GLU cc_start: 0.7605 (tt0) cc_final: 0.7211 (tt0) REVERT: G 393 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.8065 (m-10) REVERT: H 413 GLU cc_start: 0.7990 (tt0) cc_final: 0.7591 (mt-10) REVERT: H 418 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7336 (mm-30) REVERT: H 431 ASN cc_start: 0.8361 (t0) cc_final: 0.7984 (t0) REVERT: I 231 ASN cc_start: 0.6602 (OUTLIER) cc_final: 0.5320 (m-40) REVERT: I 386 SER cc_start: 0.8907 (m) cc_final: 0.7871 (t) REVERT: J 413 GLU cc_start: 0.7683 (tt0) cc_final: 0.7197 (mt-10) REVERT: K 237 PHE cc_start: 0.7891 (t80) cc_final: 0.7376 (t80) REVERT: K 413 GLU cc_start: 0.7830 (tt0) cc_final: 0.7399 (mt-10) REVERT: L 231 ASN cc_start: 0.6119 (OUTLIER) cc_final: 0.5786 (m110) REVERT: L 237 PHE cc_start: 0.7884 (t80) cc_final: 0.7320 (t80) REVERT: L 417 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7848 (ttm110) REVERT: M 409 MET cc_start: 0.8210 (mmm) cc_final: 0.7519 (tpt) REVERT: M 413 GLU cc_start: 0.7905 (tt0) cc_final: 0.7659 (mt-10) REVERT: N 376 LYS cc_start: 0.7578 (tttt) cc_final: 0.7101 (tttp) REVERT: O 409 MET cc_start: 0.8700 (mmm) cc_final: 0.8385 (mmm) REVERT: P 418 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7695 (mm-30) REVERT: Q 376 LYS cc_start: 0.7461 (tttt) cc_final: 0.6969 (tttp) REVERT: R 242 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6655 (tt0) REVERT: T 237 PHE cc_start: 0.7937 (t80) cc_final: 0.7305 (t80) REVERT: U 231 ASN cc_start: 0.6418 (OUTLIER) cc_final: 0.4913 (m-40) REVERT: V 376 LYS cc_start: 0.7536 (tttt) cc_final: 0.7048 (tttp) REVERT: W 242 GLU cc_start: 0.7559 (tt0) cc_final: 0.7189 (tt0) REVERT: W 409 MET cc_start: 0.8516 (mmm) cc_final: 0.7941 (tpp) REVERT: X 418 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7360 (mm-30) REVERT: Y 231 ASN cc_start: 0.5972 (OUTLIER) cc_final: 0.5215 (m110) REVERT: Y 232 ASP cc_start: 0.7394 (t0) cc_final: 0.7124 (t0) REVERT: Y 393 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7739 (m-10) REVERT: Y 409 MET cc_start: 0.8488 (mmm) cc_final: 0.8128 (tpt) REVERT: Z 231 ASN cc_start: 0.6535 (OUTLIER) cc_final: 0.6330 (p0) REVERT: Z 232 ASP cc_start: 0.7219 (t0) cc_final: 0.6471 (m-30) REVERT: Z 409 MET cc_start: 0.8594 (mmm) cc_final: 0.8089 (tpp) REVERT: Z 413 GLU cc_start: 0.7861 (tt0) cc_final: 0.7611 (mt-10) REVERT: 2 231 ASN cc_start: 0.6653 (OUTLIER) cc_final: 0.5923 (m-40) REVERT: 2 409 MET cc_start: 0.8182 (mmm) cc_final: 0.7790 (tpt) REVERT: 3 409 MET cc_start: 0.8159 (tpp) cc_final: 0.7397 (tpp) REVERT: 3 413 GLU cc_start: 0.7919 (tt0) cc_final: 0.7543 (mt-10) REVERT: 5 242 GLU cc_start: 0.7604 (tt0) cc_final: 0.7210 (tt0) outliers start: 280 outliers final: 210 residues processed: 1101 average time/residue: 0.4206 time to fit residues: 792.1511 Evaluate side-chains 1107 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 884 time to evaluate : 4.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 231 ASN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain G residue 231 ASN Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 411 GLN Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 299 ASN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 381 ASP Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 231 ASN Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 381 ASP Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain J residue 231 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 231 ASN Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 381 ASP Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain M residue 289 SER Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 393 TYR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain M residue 429 THR Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 243 SER Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 411 GLN Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 381 ASP Chi-restraints excluded: chain O residue 411 GLN Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 299 ASN Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 411 GLN Chi-restraints excluded: chain Q residue 424 ASP Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain R residue 231 ASN Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 299 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 381 ASP Chi-restraints excluded: chain R residue 416 THR Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain R residue 434 ASN Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 411 GLN Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain S residue 434 ASN Chi-restraints excluded: chain T residue 231 ASN Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 243 SER Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 357 SER Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 381 ASP Chi-restraints excluded: chain T residue 411 GLN Chi-restraints excluded: chain T residue 416 THR Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain T residue 434 ASN Chi-restraints excluded: chain U residue 231 ASN Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 357 SER Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain U residue 411 GLN Chi-restraints excluded: chain U residue 414 ASP Chi-restraints excluded: chain U residue 415 LEU Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain U residue 434 ASN Chi-restraints excluded: chain V residue 231 ASN Chi-restraints excluded: chain V residue 242 GLU Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain V residue 416 THR Chi-restraints excluded: chain V residue 424 ASP Chi-restraints excluded: chain V residue 430 LEU Chi-restraints excluded: chain V residue 434 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 299 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 381 ASP Chi-restraints excluded: chain X residue 391 VAL Chi-restraints excluded: chain X residue 416 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Y residue 231 ASN Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 243 SER Chi-restraints excluded: chain Y residue 299 ASN Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 393 TYR Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 231 ASN Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 416 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain 1 residue 231 ASN Chi-restraints excluded: chain 1 residue 299 ASN Chi-restraints excluded: chain 1 residue 369 ASP Chi-restraints excluded: chain 1 residue 424 ASP Chi-restraints excluded: chain 2 residue 231 ASN Chi-restraints excluded: chain 2 residue 289 SER Chi-restraints excluded: chain 2 residue 299 ASN Chi-restraints excluded: chain 2 residue 357 SER Chi-restraints excluded: chain 2 residue 369 ASP Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 424 ASP Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 299 ASN Chi-restraints excluded: chain 3 residue 369 ASP Chi-restraints excluded: chain 3 residue 381 ASP Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 4 residue 231 ASN Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 4 residue 243 SER Chi-restraints excluded: chain 4 residue 289 SER Chi-restraints excluded: chain 4 residue 299 ASN Chi-restraints excluded: chain 4 residue 369 ASP Chi-restraints excluded: chain 4 residue 424 ASP Chi-restraints excluded: chain 4 residue 430 LEU Chi-restraints excluded: chain 5 residue 231 ASN Chi-restraints excluded: chain 5 residue 289 SER Chi-restraints excluded: chain 5 residue 299 ASN Chi-restraints excluded: chain 5 residue 411 GLN Chi-restraints excluded: chain 5 residue 424 ASP Chi-restraints excluded: chain 5 residue 430 LEU Chi-restraints excluded: chain 6 residue 231 ASN Chi-restraints excluded: chain 6 residue 242 GLU Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain 6 residue 289 SER Chi-restraints excluded: chain 6 residue 299 ASN Chi-restraints excluded: chain 6 residue 369 ASP Chi-restraints excluded: chain 6 residue 411 GLN Chi-restraints excluded: chain 6 residue 424 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 3.9990 chunk 455 optimal weight: 0.9980 chunk 278 optimal weight: 6.9990 chunk 216 optimal weight: 0.9990 chunk 316 optimal weight: 2.9990 chunk 478 optimal weight: 6.9990 chunk 440 optimal weight: 0.7980 chunk 380 optimal weight: 0.0770 chunk 39 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 263 HIS B 411 GLN C 239 ASN C 263 HIS D 239 ASN D 411 GLN E 239 ASN F 411 GLN G 411 GLN H 239 ASN I 231 ASN I 239 ASN J 239 ASN K 239 ASN L 239 ASN M 239 ASN N 239 ASN N 411 GLN O 411 GLN P 239 ASN Q 411 GLN R 239 ASN S 239 ASN S 261 ASN S 411 GLN T 239 ASN U 231 ASN W 411 GLN X 411 GLN Y 239 ASN 1 239 ASN 2 231 ASN 2 239 ASN 3 239 ASN 4 239 ASN 4 411 GLN 5 411 GLN 6 239 ASN 6 411 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 38560 Z= 0.212 Angle : 0.578 8.676 51968 Z= 0.296 Chirality : 0.040 0.273 5952 Planarity : 0.003 0.053 6976 Dihedral : 5.160 21.865 5324 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 6.04 % Allowed : 24.04 % Favored : 69.92 % 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: -0.74 (0.14), residues: 4640 helix: 2.82 (0.14), residues: 1280 sheet: -1.54 (0.12), residues: 2336 loop : -1.83 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS 6 374 PHE 0.021 0.001 PHE 1 237 TYR 0.008 0.001 TYR 5 393 ARG 0.012 0.000 ARG L 417 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 895 time to evaluate : 4.526 Fit side-chains REVERT: A 232 ASP cc_start: 0.7171 (t0) cc_final: 0.6741 (m-30) REVERT: A 409 MET cc_start: 0.8109 (tpp) cc_final: 0.7877 (tpt) REVERT: B 232 ASP cc_start: 0.7519 (t0) cc_final: 0.7279 (t0) REVERT: C 393 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.6548 (m-10) REVERT: C 413 GLU cc_start: 0.7852 (tt0) cc_final: 0.7396 (mt-10) REVERT: D 231 ASN cc_start: 0.6288 (OUTLIER) cc_final: 0.5695 (m110) REVERT: D 237 PHE cc_start: 0.7894 (t80) cc_final: 0.7478 (t80) REVERT: D 393 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7339 (m-10) REVERT: D 413 GLU cc_start: 0.7842 (tt0) cc_final: 0.7319 (mt-10) REVERT: E 409 MET cc_start: 0.8199 (mmm) cc_final: 0.7759 (tpt) REVERT: E 414 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7215 (m-30) REVERT: F 242 GLU cc_start: 0.7412 (tt0) cc_final: 0.7176 (tt0) REVERT: F 376 LYS cc_start: 0.7525 (tttt) cc_final: 0.7040 (tttp) REVERT: F 404 LEU cc_start: 0.6948 (mp) cc_final: 0.6714 (mp) REVERT: F 409 MET cc_start: 0.8242 (tpp) cc_final: 0.7904 (tpp) REVERT: G 242 GLU cc_start: 0.7597 (tt0) cc_final: 0.7196 (tt0) REVERT: H 242 GLU cc_start: 0.7351 (tt0) cc_final: 0.7065 (tt0) REVERT: H 413 GLU cc_start: 0.8029 (tt0) cc_final: 0.7639 (mt-10) REVERT: H 418 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7314 (mm-30) REVERT: I 231 ASN cc_start: 0.6657 (OUTLIER) cc_final: 0.5419 (m-40) REVERT: I 386 SER cc_start: 0.8900 (m) cc_final: 0.7865 (t) REVERT: J 232 ASP cc_start: 0.7227 (t0) cc_final: 0.6627 (m-30) REVERT: J 413 GLU cc_start: 0.7674 (tt0) cc_final: 0.7416 (mt-10) REVERT: K 237 PHE cc_start: 0.7866 (t80) cc_final: 0.7340 (t80) REVERT: K 409 MET cc_start: 0.8584 (mmm) cc_final: 0.8151 (tpt) REVERT: K 413 GLU cc_start: 0.7807 (tt0) cc_final: 0.7384 (mt-10) REVERT: L 231 ASN cc_start: 0.6088 (OUTLIER) cc_final: 0.5716 (m110) REVERT: L 237 PHE cc_start: 0.7868 (t80) cc_final: 0.7301 (t80) REVERT: L 417 ARG cc_start: 0.8204 (ttm110) cc_final: 0.7823 (ttm110) REVERT: N 376 LYS cc_start: 0.7507 (tttt) cc_final: 0.7031 (tttp) REVERT: O 409 MET cc_start: 0.8695 (mmm) cc_final: 0.8383 (mmm) REVERT: P 418 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7679 (mm-30) REVERT: Q 376 LYS cc_start: 0.7409 (tttt) cc_final: 0.7107 (ttpt) REVERT: R 242 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6649 (tt0) REVERT: S 237 PHE cc_start: 0.7918 (t80) cc_final: 0.7297 (t80) REVERT: T 237 PHE cc_start: 0.7906 (t80) cc_final: 0.7278 (t80) REVERT: U 231 ASN cc_start: 0.6431 (OUTLIER) cc_final: 0.5062 (m-40) REVERT: U 242 GLU cc_start: 0.7181 (pt0) cc_final: 0.6978 (tt0) REVERT: V 232 ASP cc_start: 0.7049 (t0) cc_final: 0.6672 (m-30) REVERT: V 376 LYS cc_start: 0.7455 (tttt) cc_final: 0.6972 (tttp) REVERT: W 242 GLU cc_start: 0.7518 (tt0) cc_final: 0.7172 (tt0) REVERT: W 409 MET cc_start: 0.8436 (mmm) cc_final: 0.8141 (tpp) REVERT: X 418 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7318 (mm-30) REVERT: Y 231 ASN cc_start: 0.6107 (OUTLIER) cc_final: 0.5327 (m110) REVERT: Y 232 ASP cc_start: 0.7369 (t0) cc_final: 0.7098 (t0) REVERT: Y 376 LYS cc_start: 0.7490 (tttt) cc_final: 0.6999 (tttp) REVERT: Y 393 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7803 (m-10) REVERT: Y 409 MET cc_start: 0.8478 (mmm) cc_final: 0.8195 (tpp) REVERT: Z 232 ASP cc_start: 0.7117 (t0) cc_final: 0.6455 (m-30) REVERT: Z 409 MET cc_start: 0.8583 (mmm) cc_final: 0.8286 (tpp) REVERT: 2 231 ASN cc_start: 0.6596 (OUTLIER) cc_final: 0.5957 (m-40) REVERT: 3 409 MET cc_start: 0.8138 (tpp) cc_final: 0.7755 (tpp) REVERT: 5 242 GLU cc_start: 0.7511 (tt0) cc_final: 0.7111 (tt0) outliers start: 259 outliers final: 204 residues processed: 1085 average time/residue: 0.4237 time to fit residues: 792.2109 Evaluate side-chains 1103 residues out of total 4288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 888 time to evaluate : 4.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 231 ASN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain G residue 231 ASN Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 411 GLN Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 299 ASN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 381 ASP Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 231 ASN Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 381 ASP Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain J residue 231 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 381 ASP Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain M residue 231 ASN Chi-restraints excluded: chain M residue 289 SER Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain M residue 429 THR Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 391 VAL Chi-restraints excluded: chain N residue 411 GLN Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 381 ASP Chi-restraints excluded: chain O residue 411 GLN Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 299 ASN Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 411 GLN Chi-restraints excluded: chain Q residue 424 ASP Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain R residue 231 ASN Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 381 ASP Chi-restraints excluded: chain R residue 416 THR Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain R residue 434 ASN Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 411 GLN Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain S residue 434 ASN Chi-restraints excluded: chain T residue 231 ASN Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 243 SER Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 357 SER Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 381 ASP Chi-restraints excluded: chain T residue 411 GLN Chi-restraints excluded: chain T residue 416 THR Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain T residue 434 ASN Chi-restraints excluded: chain U residue 231 ASN Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 357 SER Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain U residue 411 GLN Chi-restraints excluded: chain U residue 414 ASP Chi-restraints excluded: chain U residue 415 LEU Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain U residue 434 ASN Chi-restraints excluded: chain V residue 231 ASN Chi-restraints excluded: chain V residue 242 GLU Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain V residue 424 ASP Chi-restraints excluded: chain V residue 430 LEU Chi-restraints excluded: chain V residue 434 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 299 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 381 ASP Chi-restraints excluded: chain X residue 391 VAL Chi-restraints excluded: chain X residue 416 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Y residue 231 ASN Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 243 SER Chi-restraints excluded: chain Y residue 299 ASN Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 393 TYR Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 416 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain 1 residue 231 ASN Chi-restraints excluded: chain 1 residue 299 ASN Chi-restraints excluded: chain 1 residue 369 ASP Chi-restraints excluded: chain 1 residue 424 ASP Chi-restraints excluded: chain 2 residue 231 ASN Chi-restraints excluded: chain 2 residue 289 SER Chi-restraints excluded: chain 2 residue 299 ASN Chi-restraints excluded: chain 2 residue 357 SER Chi-restraints excluded: chain 2 residue 369 ASP Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 424 ASP Chi-restraints excluded: chain 2 residue 430 LEU Chi-restraints excluded: chain 3 residue 231 ASN Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 299 ASN Chi-restraints excluded: chain 3 residue 369 ASP Chi-restraints excluded: chain 3 residue 381 ASP Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 4 residue 231 ASN Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 4 residue 243 SER Chi-restraints excluded: chain 4 residue 289 SER Chi-restraints excluded: chain 4 residue 299 ASN Chi-restraints excluded: chain 4 residue 369 ASP Chi-restraints excluded: chain 4 residue 416 THR Chi-restraints excluded: chain 4 residue 424 ASP Chi-restraints excluded: chain 5 residue 289 SER Chi-restraints excluded: chain 5 residue 299 ASN Chi-restraints excluded: chain 5 residue 411 GLN Chi-restraints excluded: chain 5 residue 424 ASP Chi-restraints excluded: chain 6 residue 242 GLU Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain 6 residue 289 SER Chi-restraints excluded: chain 6 residue 299 ASN Chi-restraints excluded: chain 6 residue 369 ASP Chi-restraints excluded: chain 6 residue 411 GLN Chi-restraints excluded: chain 6 residue 424 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 2.9990 chunk 405 optimal weight: 3.9990 chunk 116 optimal weight: 0.0370 chunk 351 optimal weight: 0.2980 chunk 56 optimal weight: 0.0670 chunk 105 optimal weight: 1.9990 chunk 381 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 391 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN C 239 ASN D 239 ASN D 411 GLN E 239 ASN E 411 GLN G 411 GLN H 239 ASN I 231 ASN I 239 ASN J 239 ASN K 239 ASN L 239 ASN M 239 ASN N 239 ASN N 411 GLN O 411 GLN P 239 ASN Q 411 GLN R 239 ASN S 239 ASN S 411 GLN T 239 ASN U 231 ASN Y 239 ASN Y 411 GLN 1 239 ASN 2 231 ASN 2 239 ASN 2 411 GLN 3 239 ASN 3 263 HIS 4 239 ASN 5 411 GLN 6 239 ASN 6 411 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.184595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.148442 restraints weight = 38726.462| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.77 r_work: 0.3899 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 38560 Z= 0.182 Angle : 0.558 8.413 51968 Z= 0.287 Chirality : 0.040 0.286 5952 Planarity : 0.003 0.052 6976 Dihedral : 4.915 19.998 5324 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.60 % Allowed : 24.32 % Favored : 70.08 % 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: -0.68 (0.14), residues: 4640 helix: 2.90 (0.14), residues: 1280 sheet: -1.52 (0.12), residues: 2336 loop : -1.80 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS O 374 PHE 0.021 0.001 PHE 1 237 TYR 0.015 0.001 TYR G 393 ARG 0.012 0.000 ARG L 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13187.94 seconds wall clock time: 234 minutes 22.63 seconds (14062.63 seconds total)