Starting phenix.real_space_refine on Sat Jul 27 12:21:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt4_19478/07_2024/8rt4_19478.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt4_19478/07_2024/8rt4_19478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt4_19478/07_2024/8rt4_19478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt4_19478/07_2024/8rt4_19478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt4_19478/07_2024/8rt4_19478.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt4_19478/07_2024/8rt4_19478.cif" } resolution = 2.46 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= 0.020 sd= 0.068 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 140 5.16 5 C 23996 2.51 5 N 6972 2.21 5 O 7350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B ASP 243": "OD1" <-> "OD2" Residue "B ASP 250": "OD1" <-> "OD2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ASP 236": "OD1" <-> "OD2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ASP 303": "OD1" <-> "OD2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "E ARG 141": "NH1" <-> "NH2" Residue "E GLU 149": "OE1" <-> "OE2" Residue "E ASP 197": "OD1" <-> "OD2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "E ARG 233": "NH1" <-> "NH2" Residue "E ASP 243": "OD1" <-> "OD2" Residue "E ASP 250": "OD1" <-> "OD2" Residue "E ARG 259": "NH1" <-> "NH2" Residue "E ARG 260": "NH1" <-> "NH2" Residue "F PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 235": "NH1" <-> "NH2" Residue "G ASP 236": "OD1" <-> "OD2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ASP 248": "OD1" <-> "OD2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "G PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 274": "NH1" <-> "NH2" Residue "G ASP 303": "OD1" <-> "OD2" Residue "G ARG 304": "NH1" <-> "NH2" Residue "G ARG 372": "NH1" <-> "NH2" Residue "H ARG 141": "NH1" <-> "NH2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "H ASP 197": "OD1" <-> "OD2" Residue "H GLU 199": "OE1" <-> "OE2" Residue "H ARG 233": "NH1" <-> "NH2" Residue "H ASP 243": "OD1" <-> "OD2" Residue "H ASP 250": "OD1" <-> "OD2" Residue "H ARG 259": "NH1" <-> "NH2" Residue "H ARG 260": "NH1" <-> "NH2" Residue "I PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 235": "NH1" <-> "NH2" Residue "J ASP 236": "OD1" <-> "OD2" Residue "J ARG 243": "NH1" <-> "NH2" Residue "J ASP 248": "OD1" <-> "OD2" Residue "J ARG 249": "NH1" <-> "NH2" Residue "J PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 274": "NH1" <-> "NH2" Residue "J ASP 303": "OD1" <-> "OD2" Residue "J ARG 304": "NH1" <-> "NH2" Residue "J ARG 372": "NH1" <-> "NH2" Residue "K ARG 141": "NH1" <-> "NH2" Residue "K GLU 149": "OE1" <-> "OE2" Residue "K ASP 197": "OD1" <-> "OD2" Residue "K GLU 199": "OE1" <-> "OE2" Residue "K ARG 233": "NH1" <-> "NH2" Residue "K ASP 243": "OD1" <-> "OD2" Residue "K ASP 250": "OD1" <-> "OD2" Residue "K ARG 259": "NH1" <-> "NH2" Residue "K ARG 260": "NH1" <-> "NH2" Residue "L PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 235": "NH1" <-> "NH2" Residue "M ASP 236": "OD1" <-> "OD2" Residue "M ARG 243": "NH1" <-> "NH2" Residue "M ASP 248": "OD1" <-> "OD2" Residue "M ARG 249": "NH1" <-> "NH2" Residue "M PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 274": "NH1" <-> "NH2" Residue "M ASP 303": "OD1" <-> "OD2" Residue "M ARG 304": "NH1" <-> "NH2" Residue "M ARG 372": "NH1" <-> "NH2" Residue "N ARG 141": "NH1" <-> "NH2" Residue "N GLU 149": "OE1" <-> "OE2" Residue "N ASP 197": "OD1" <-> "OD2" Residue "N GLU 199": "OE1" <-> "OE2" Residue "N ARG 233": "NH1" <-> "NH2" Residue "N ASP 243": "OD1" <-> "OD2" Residue "N ASP 250": "OD1" <-> "OD2" Residue "N ARG 259": "NH1" <-> "NH2" Residue "N ARG 260": "NH1" <-> "NH2" Residue "O PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P ASP 236": "OD1" <-> "OD2" Residue "P ARG 243": "NH1" <-> "NH2" Residue "P ASP 248": "OD1" <-> "OD2" Residue "P ARG 249": "NH1" <-> "NH2" Residue "P PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 274": "NH1" <-> "NH2" Residue "P ASP 303": "OD1" <-> "OD2" Residue "P ARG 304": "NH1" <-> "NH2" Residue "P ARG 372": "NH1" <-> "NH2" Residue "Q ARG 141": "NH1" <-> "NH2" Residue "Q GLU 149": "OE1" <-> "OE2" Residue "Q ASP 197": "OD1" <-> "OD2" Residue "Q GLU 199": "OE1" <-> "OE2" Residue "Q ARG 233": "NH1" <-> "NH2" Residue "Q ASP 243": "OD1" <-> "OD2" Residue "Q ASP 250": "OD1" <-> "OD2" Residue "Q ARG 259": "NH1" <-> "NH2" Residue "Q ARG 260": "NH1" <-> "NH2" Residue "R PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 235": "NH1" <-> "NH2" Residue "S ASP 236": "OD1" <-> "OD2" Residue "S ARG 243": "NH1" <-> "NH2" Residue "S ASP 248": "OD1" <-> "OD2" Residue "S ARG 249": "NH1" <-> "NH2" Residue "S PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 274": "NH1" <-> "NH2" Residue "S ASP 303": "OD1" <-> "OD2" Residue "S ARG 304": "NH1" <-> "NH2" Residue "S ARG 372": "NH1" <-> "NH2" Residue "T ARG 141": "NH1" <-> "NH2" Residue "T GLU 149": "OE1" <-> "OE2" Residue "T ASP 197": "OD1" <-> "OD2" Residue "T GLU 199": "OE1" <-> "OE2" Residue "T ARG 233": "NH1" <-> "NH2" Residue "T ASP 243": "OD1" <-> "OD2" Residue "T ASP 250": "OD1" <-> "OD2" Residue "T ARG 259": "NH1" <-> "NH2" Residue "T ARG 260": "NH1" <-> "NH2" Residue "U PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 235": "NH1" <-> "NH2" Residue "V ASP 236": "OD1" <-> "OD2" Residue "V ARG 243": "NH1" <-> "NH2" Residue "V ASP 248": "OD1" <-> "OD2" Residue "V ARG 249": "NH1" <-> "NH2" Residue "V PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 274": "NH1" <-> "NH2" Residue "V ASP 303": "OD1" <-> "OD2" Residue "V ARG 304": "NH1" <-> "NH2" Residue "V ARG 372": "NH1" <-> "NH2" Residue "W ARG 141": "NH1" <-> "NH2" Residue "W GLU 149": "OE1" <-> "OE2" Residue "W ASP 197": "OD1" <-> "OD2" Residue "W GLU 199": "OE1" <-> "OE2" Residue "W ARG 233": "NH1" <-> "NH2" Residue "W ASP 243": "OD1" <-> "OD2" Residue "W ASP 250": "OD1" <-> "OD2" Residue "W ARG 259": "NH1" <-> "NH2" Residue "W ARG 260": "NH1" <-> "NH2" Residue "X PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 235": "NH1" <-> "NH2" Residue "Y ASP 236": "OD1" <-> "OD2" Residue "Y ARG 243": "NH1" <-> "NH2" Residue "Y ASP 248": "OD1" <-> "OD2" Residue "Y ARG 249": "NH1" <-> "NH2" Residue "Y PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 274": "NH1" <-> "NH2" Residue "Y ASP 303": "OD1" <-> "OD2" Residue "Y ARG 304": "NH1" <-> "NH2" Residue "Y ARG 372": "NH1" <-> "NH2" Residue "Z ARG 141": "NH1" <-> "NH2" Residue "Z GLU 149": "OE1" <-> "OE2" Residue "Z ASP 197": "OD1" <-> "OD2" Residue "Z GLU 199": "OE1" <-> "OE2" Residue "Z ARG 233": "NH1" <-> "NH2" Residue "Z ASP 243": "OD1" <-> "OD2" Residue "Z ASP 250": "OD1" <-> "OD2" Residue "Z ARG 259": "NH1" <-> "NH2" Residue "Z ARG 260": "NH1" <-> "NH2" Residue "a PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 235": "NH1" <-> "NH2" Residue "b ASP 236": "OD1" <-> "OD2" Residue "b ARG 243": "NH1" <-> "NH2" Residue "b ASP 248": "OD1" <-> "OD2" Residue "b ARG 249": "NH1" <-> "NH2" Residue "b PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 274": "NH1" <-> "NH2" Residue "b ASP 303": "OD1" <-> "OD2" Residue "b ARG 304": "NH1" <-> "NH2" Residue "b ARG 372": "NH1" <-> "NH2" Residue "c ARG 141": "NH1" <-> "NH2" Residue "c GLU 149": "OE1" <-> "OE2" Residue "c ASP 197": "OD1" <-> "OD2" Residue "c GLU 199": "OE1" <-> "OE2" Residue "c ARG 233": "NH1" <-> "NH2" Residue "c ASP 243": "OD1" <-> "OD2" Residue "c ASP 250": "OD1" <-> "OD2" Residue "c ARG 259": "NH1" <-> "NH2" Residue "c ARG 260": "NH1" <-> "NH2" Residue "d PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 235": "NH1" <-> "NH2" Residue "e ASP 236": "OD1" <-> "OD2" Residue "e ARG 243": "NH1" <-> "NH2" Residue "e ASP 248": "OD1" <-> "OD2" Residue "e ARG 249": "NH1" <-> "NH2" Residue "e PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 274": "NH1" <-> "NH2" Residue "e ASP 303": "OD1" <-> "OD2" Residue "e ARG 304": "NH1" <-> "NH2" Residue "e ARG 372": "NH1" <-> "NH2" Residue "f ARG 141": "NH1" <-> "NH2" Residue "f GLU 149": "OE1" <-> "OE2" Residue "f ASP 197": "OD1" <-> "OD2" Residue "f GLU 199": "OE1" <-> "OE2" Residue "f ARG 233": "NH1" <-> "NH2" Residue "f ASP 243": "OD1" <-> "OD2" Residue "f ASP 250": "OD1" <-> "OD2" Residue "f ARG 259": "NH1" <-> "NH2" Residue "f ARG 260": "NH1" <-> "NH2" Residue "g PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 235": "NH1" <-> "NH2" Residue "h ASP 236": "OD1" <-> "OD2" Residue "h ARG 243": "NH1" <-> "NH2" Residue "h ASP 248": "OD1" <-> "OD2" Residue "h ARG 249": "NH1" <-> "NH2" Residue "h PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 274": "NH1" <-> "NH2" Residue "h ASP 303": "OD1" <-> "OD2" Residue "h ARG 304": "NH1" <-> "NH2" Residue "h ARG 372": "NH1" <-> "NH2" Residue "i ARG 141": "NH1" <-> "NH2" Residue "i GLU 149": "OE1" <-> "OE2" Residue "i ASP 197": "OD1" <-> "OD2" Residue "i GLU 199": "OE1" <-> "OE2" Residue "i ARG 233": "NH1" <-> "NH2" Residue "i ASP 243": "OD1" <-> "OD2" Residue "i ASP 250": "OD1" <-> "OD2" Residue "i ARG 259": "NH1" <-> "NH2" Residue "i ARG 260": "NH1" <-> "NH2" Residue "j PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 235": "NH1" <-> "NH2" Residue "k ASP 236": "OD1" <-> "OD2" Residue "k ARG 243": "NH1" <-> "NH2" Residue "k ASP 248": "OD1" <-> "OD2" Residue "k ARG 249": "NH1" <-> "NH2" Residue "k PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 274": "NH1" <-> "NH2" Residue "k ASP 303": "OD1" <-> "OD2" Residue "k ARG 304": "NH1" <-> "NH2" Residue "k ARG 372": "NH1" <-> "NH2" Residue "l ARG 141": "NH1" <-> "NH2" Residue "l GLU 149": "OE1" <-> "OE2" Residue "l ASP 197": "OD1" <-> "OD2" Residue "l GLU 199": "OE1" <-> "OE2" Residue "l ARG 233": "NH1" <-> "NH2" Residue "l ASP 243": "OD1" <-> "OD2" Residue "l ASP 250": "OD1" <-> "OD2" Residue "l ARG 259": "NH1" <-> "NH2" Residue "l ARG 260": "NH1" <-> "NH2" Residue "m PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 235": "NH1" <-> "NH2" Residue "n ASP 236": "OD1" <-> "OD2" Residue "n ARG 243": "NH1" <-> "NH2" Residue "n ASP 248": "OD1" <-> "OD2" Residue "n ARG 249": "NH1" <-> "NH2" Residue "n PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 274": "NH1" <-> "NH2" Residue "n ASP 303": "OD1" <-> "OD2" Residue "n ARG 304": "NH1" <-> "NH2" Residue "n ARG 372": "NH1" <-> "NH2" Residue "o ARG 141": "NH1" <-> "NH2" Residue "o GLU 149": "OE1" <-> "OE2" Residue "o ASP 197": "OD1" <-> "OD2" Residue "o GLU 199": "OE1" <-> "OE2" Residue "o ARG 233": "NH1" <-> "NH2" Residue "o ASP 243": "OD1" <-> "OD2" Residue "o ASP 250": "OD1" <-> "OD2" Residue "o ARG 259": "NH1" <-> "NH2" Residue "o ARG 260": "NH1" <-> "NH2" Residue "p PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 38458 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1521 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "C" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1521 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "F" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1521 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "I" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1521 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "L" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1521 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "O" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1521 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "R" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1521 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "U" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1521 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "X" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1521 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Z" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "a" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1521 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "c" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "d" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1521 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "f" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "g" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1521 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "i" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "j" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "k" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1521 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "l" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "m" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1521 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "o" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "p" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 19.17, per 1000 atoms: 0.50 Number of scatterers: 38458 At special positions: 0 Unit cell: (193.127, 195.261, 100.298, 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 140 16.00 O 7350 8.00 N 6972 7.00 C 23996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 215 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 215 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 215 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS M 215 " - pdb=" SG CYS M 231 " distance=2.03 Simple disulfide: pdb=" SG CYS P 215 " - pdb=" SG CYS P 231 " distance=2.03 Simple disulfide: pdb=" SG CYS S 215 " - pdb=" SG CYS S 231 " distance=2.03 Simple disulfide: pdb=" SG CYS V 215 " - pdb=" SG CYS V 231 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 215 " - pdb=" SG CYS Y 231 " distance=2.03 Simple disulfide: pdb=" SG CYS b 215 " - pdb=" SG CYS b 231 " distance=2.03 Simple disulfide: pdb=" SG CYS e 215 " - pdb=" SG CYS e 231 " distance=2.03 Simple disulfide: pdb=" SG CYS h 215 " - pdb=" SG CYS h 231 " distance=2.03 Simple disulfide: pdb=" SG CYS k 215 " - pdb=" SG CYS k 231 " distance=2.03 Simple disulfide: pdb=" SG CYS n 215 " - pdb=" SG CYS n 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.66 Conformation dependent library (CDL) restraints added in 6.9 seconds 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9016 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 112 sheets defined 17.2% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.37 Creating SS restraints... Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 151 removed outlier: 4.069A pdb=" N ARG B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'D' and resid 180 through 187 Processing helix chain 'D' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 151 removed outlier: 4.069A pdb=" N ARG E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 169 Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'G' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY G 312 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA G 313 " --> pdb=" O ARG G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 359 removed outlier: 3.509A pdb=" N ASN G 357 " --> pdb=" O GLU G 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 151 removed outlier: 4.068A pdb=" N ARG H 151 " --> pdb=" O ALA H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 169 Processing helix chain 'J' and resid 180 through 187 Processing helix chain 'J' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY J 312 " --> pdb=" O GLU J 308 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA J 313 " --> pdb=" O ARG J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 359 removed outlier: 3.509A pdb=" N ASN J 357 " --> pdb=" O GLU J 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 151 removed outlier: 4.068A pdb=" N ARG K 151 " --> pdb=" O ALA K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 169 Processing helix chain 'M' and resid 180 through 187 Processing helix chain 'M' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY M 312 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA M 313 " --> pdb=" O ARG M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN M 357 " --> pdb=" O GLU M 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 151 removed outlier: 4.069A pdb=" N ARG N 151 " --> pdb=" O ALA N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 169 Processing helix chain 'P' and resid 180 through 187 Processing helix chain 'P' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY P 312 " --> pdb=" O GLU P 308 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA P 313 " --> pdb=" O ARG P 309 " (cutoff:3.500A) Processing helix chain 'P' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN P 357 " --> pdb=" O GLU P 353 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 151 removed outlier: 4.067A pdb=" N ARG Q 151 " --> pdb=" O ALA Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 166 through 169 Processing helix chain 'S' and resid 180 through 187 Processing helix chain 'S' and resid 305 through 329 removed outlier: 5.603A pdb=" N GLY S 312 " --> pdb=" O GLU S 308 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA S 313 " --> pdb=" O ARG S 309 " (cutoff:3.500A) Processing helix chain 'S' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN S 357 " --> pdb=" O GLU S 353 " (cutoff:3.500A) Processing helix chain 'T' and resid 137 through 151 removed outlier: 4.069A pdb=" N ARG T 151 " --> pdb=" O ALA T 147 " (cutoff:3.500A) Processing helix chain 'T' and resid 166 through 169 Processing helix chain 'V' and resid 180 through 187 Processing helix chain 'V' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY V 312 " --> pdb=" O GLU V 308 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA V 313 " --> pdb=" O ARG V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN V 357 " --> pdb=" O GLU V 353 " (cutoff:3.500A) Processing helix chain 'W' and resid 137 through 151 removed outlier: 4.069A pdb=" N ARG W 151 " --> pdb=" O ALA W 147 " (cutoff:3.500A) Processing helix chain 'W' and resid 166 through 169 Processing helix chain 'Y' and resid 180 through 187 Processing helix chain 'Y' and resid 305 through 329 removed outlier: 5.603A pdb=" N GLY Y 312 " --> pdb=" O GLU Y 308 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA Y 313 " --> pdb=" O ARG Y 309 " (cutoff:3.500A) Processing helix chain 'Y' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN Y 357 " --> pdb=" O GLU Y 353 " (cutoff:3.500A) Processing helix chain 'Z' and resid 137 through 151 removed outlier: 4.069A pdb=" N ARG Z 151 " --> pdb=" O ALA Z 147 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 169 Processing helix chain 'b' and resid 180 through 187 Processing helix chain 'b' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY b 312 " --> pdb=" O GLU b 308 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA b 313 " --> pdb=" O ARG b 309 " (cutoff:3.500A) Processing helix chain 'b' and resid 350 through 359 removed outlier: 3.509A pdb=" N ASN b 357 " --> pdb=" O GLU b 353 " (cutoff:3.500A) Processing helix chain 'c' and resid 137 through 151 removed outlier: 4.070A pdb=" N ARG c 151 " --> pdb=" O ALA c 147 " (cutoff:3.500A) Processing helix chain 'c' and resid 166 through 169 Processing helix chain 'e' and resid 180 through 187 Processing helix chain 'e' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA e 313 " --> pdb=" O ARG e 309 " (cutoff:3.500A) Processing helix chain 'e' and resid 350 through 359 removed outlier: 3.511A pdb=" N ASN e 357 " --> pdb=" O GLU e 353 " (cutoff:3.500A) Processing helix chain 'f' and resid 137 through 151 removed outlier: 4.071A pdb=" N ARG f 151 " --> pdb=" O ALA f 147 " (cutoff:3.500A) Processing helix chain 'f' and resid 166 through 169 Processing helix chain 'h' and resid 180 through 187 Processing helix chain 'h' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY h 312 " --> pdb=" O GLU h 308 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA h 313 " --> pdb=" O ARG h 309 " (cutoff:3.500A) Processing helix chain 'h' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN h 357 " --> pdb=" O GLU h 353 " (cutoff:3.500A) Processing helix chain 'i' and resid 137 through 151 removed outlier: 4.069A pdb=" N ARG i 151 " --> pdb=" O ALA i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 166 through 169 Processing helix chain 'k' and resid 180 through 187 Processing helix chain 'k' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY k 312 " --> pdb=" O GLU k 308 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA k 313 " --> pdb=" O ARG k 309 " (cutoff:3.500A) Processing helix chain 'k' and resid 350 through 359 removed outlier: 3.510A pdb=" N ASN k 357 " --> pdb=" O GLU k 353 " (cutoff:3.500A) Processing helix chain 'l' and resid 137 through 151 removed outlier: 4.069A pdb=" N ARG l 151 " --> pdb=" O ALA l 147 " (cutoff:3.500A) Processing helix chain 'l' and resid 166 through 169 Processing helix chain 'n' and resid 180 through 187 Processing helix chain 'n' and resid 305 through 329 removed outlier: 5.602A pdb=" N GLY n 312 " --> pdb=" O GLU n 308 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ALA n 313 " --> pdb=" O ARG n 309 " (cutoff:3.500A) Processing helix chain 'n' and resid 350 through 359 removed outlier: 3.508A pdb=" N ASN n 357 " --> pdb=" O GLU n 353 " (cutoff:3.500A) Processing helix chain 'o' and resid 137 through 151 removed outlier: 4.068A pdb=" N ARG o 151 " --> pdb=" O ALA o 147 " (cutoff:3.500A) Processing helix chain 'o' and resid 166 through 169 Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.771A pdb=" N SER A 195 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199 removed outlier: 4.828A pdb=" N VAL D 270 " --> pdb=" O GLY D 289 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS D 252 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE D 275 " --> pdb=" O LYS D 252 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL D 254 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 206 through 207 Processing sheet with id=AA4, first strand: chain 'n' and resid 198 through 199 removed outlier: 4.828A pdb=" N VAL A 270 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS A 252 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A 275 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 254 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 238 Processing sheet with id=AA7, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA8, first strand: chain 'A' and resid 387 through 391 Processing sheet with id=AA9, first strand: chain 'B' and resid 202 through 203 removed outlier: 4.713A pdb=" N LYS B 225 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 175 Processing sheet with id=AB2, first strand: chain 'B' and resid 258 through 262 Processing sheet with id=AB3, first strand: chain 'D' and resid 195 through 196 removed outlier: 6.776A pdb=" N SER D 195 " --> pdb=" O ASP G 382 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 198 through 199 removed outlier: 4.828A pdb=" N VAL G 270 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS G 252 " --> pdb=" O ILE G 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE G 275 " --> pdb=" O LYS G 252 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL G 254 " --> pdb=" O SER G 273 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AB6, first strand: chain 'D' and resid 237 through 238 Processing sheet with id=AB7, first strand: chain 'D' and resid 267 through 268 Processing sheet with id=AB8, first strand: chain 'D' and resid 387 through 391 Processing sheet with id=AB9, first strand: chain 'E' and resid 202 through 203 removed outlier: 4.713A pdb=" N LYS E 225 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 172 through 175 Processing sheet with id=AC2, first strand: chain 'G' and resid 195 through 196 removed outlier: 6.743A pdb=" N SER G 195 " --> pdb=" O ASP J 382 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 198 through 199 removed outlier: 4.828A pdb=" N VAL J 270 " --> pdb=" O GLY J 289 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS J 252 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE J 275 " --> pdb=" O LYS J 252 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL J 254 " --> pdb=" O SER J 273 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AC5, first strand: chain 'G' and resid 237 through 238 Processing sheet with id=AC6, first strand: chain 'G' and resid 267 through 268 Processing sheet with id=AC7, first strand: chain 'G' and resid 387 through 391 Processing sheet with id=AC8, first strand: chain 'H' and resid 202 through 203 removed outlier: 4.713A pdb=" N LYS H 225 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 172 through 175 Processing sheet with id=AD1, first strand: chain 'J' and resid 195 through 196 removed outlier: 6.754A pdb=" N SER J 195 " --> pdb=" O ASP M 382 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 198 through 199 removed outlier: 4.829A pdb=" N VAL M 270 " --> pdb=" O GLY M 289 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS M 252 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE M 275 " --> pdb=" O LYS M 252 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL M 254 " --> pdb=" O SER M 273 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 221 through 222 Processing sheet with id=AD4, first strand: chain 'J' and resid 237 through 238 Processing sheet with id=AD5, first strand: chain 'J' and resid 267 through 268 Processing sheet with id=AD6, first strand: chain 'J' and resid 387 through 391 Processing sheet with id=AD7, first strand: chain 'K' and resid 202 through 203 removed outlier: 4.713A pdb=" N LYS K 225 " --> pdb=" O VAL K 196 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 172 through 175 Processing sheet with id=AD9, first strand: chain 'M' and resid 195 through 196 removed outlier: 6.770A pdb=" N SER M 195 " --> pdb=" O ASP P 382 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 198 through 199 removed outlier: 4.827A pdb=" N VAL P 270 " --> pdb=" O GLY P 289 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS P 252 " --> pdb=" O ILE P 275 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE P 275 " --> pdb=" O LYS P 252 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL P 254 " --> pdb=" O SER P 273 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 221 through 222 Processing sheet with id=AE3, first strand: chain 'M' and resid 237 through 238 Processing sheet with id=AE4, first strand: chain 'M' and resid 267 through 268 Processing sheet with id=AE5, first strand: chain 'M' and resid 387 through 391 Processing sheet with id=AE6, first strand: chain 'N' and resid 202 through 203 removed outlier: 4.713A pdb=" N LYS N 225 " --> pdb=" O VAL N 196 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 172 through 175 Processing sheet with id=AE8, first strand: chain 'P' and resid 195 through 196 removed outlier: 6.772A pdb=" N SER P 195 " --> pdb=" O ASP S 382 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 198 through 199 removed outlier: 4.827A pdb=" N VAL S 270 " --> pdb=" O GLY S 289 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS S 252 " --> pdb=" O ILE S 275 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE S 275 " --> pdb=" O LYS S 252 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL S 254 " --> pdb=" O SER S 273 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 221 through 222 Processing sheet with id=AF2, first strand: chain 'P' and resid 237 through 238 Processing sheet with id=AF3, first strand: chain 'P' and resid 267 through 268 Processing sheet with id=AF4, first strand: chain 'P' and resid 387 through 391 Processing sheet with id=AF5, first strand: chain 'Q' and resid 202 through 203 removed outlier: 4.712A pdb=" N LYS Q 225 " --> pdb=" O VAL Q 196 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 172 through 175 Processing sheet with id=AF7, first strand: chain 'S' and resid 195 through 196 removed outlier: 6.765A pdb=" N SER S 195 " --> pdb=" O ASP V 382 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 198 through 199 removed outlier: 4.828A pdb=" N VAL V 270 " --> pdb=" O GLY V 289 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS V 252 " --> pdb=" O ILE V 275 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE V 275 " --> pdb=" O LYS V 252 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL V 254 " --> pdb=" O SER V 273 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 221 through 222 Processing sheet with id=AG1, first strand: chain 'S' and resid 237 through 238 Processing sheet with id=AG2, first strand: chain 'S' and resid 267 through 268 Processing sheet with id=AG3, first strand: chain 'S' and resid 387 through 391 Processing sheet with id=AG4, first strand: chain 'T' and resid 202 through 203 removed outlier: 4.713A pdb=" N LYS T 225 " --> pdb=" O VAL T 196 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 172 through 175 Processing sheet with id=AG6, first strand: chain 'V' and resid 195 through 196 removed outlier: 6.759A pdb=" N SER V 195 " --> pdb=" O ASP Y 382 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'V' and resid 198 through 199 removed outlier: 4.828A pdb=" N VAL Y 270 " --> pdb=" O GLY Y 289 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS Y 252 " --> pdb=" O ILE Y 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE Y 275 " --> pdb=" O LYS Y 252 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL Y 254 " --> pdb=" O SER Y 273 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'V' and resid 221 through 222 Processing sheet with id=AG9, first strand: chain 'V' and resid 237 through 238 Processing sheet with id=AH1, first strand: chain 'V' and resid 267 through 268 Processing sheet with id=AH2, first strand: chain 'V' and resid 387 through 391 Processing sheet with id=AH3, first strand: chain 'W' and resid 202 through 203 removed outlier: 4.712A pdb=" N LYS W 225 " --> pdb=" O VAL W 196 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'W' and resid 172 through 175 Processing sheet with id=AH5, first strand: chain 'Y' and resid 195 through 196 removed outlier: 6.774A pdb=" N SER Y 195 " --> pdb=" O ASP b 382 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Y' and resid 198 through 199 removed outlier: 4.828A pdb=" N VAL b 270 " --> pdb=" O GLY b 289 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS b 252 " --> pdb=" O ILE b 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE b 275 " --> pdb=" O LYS b 252 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL b 254 " --> pdb=" O SER b 273 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Y' and resid 221 through 222 Processing sheet with id=AH8, first strand: chain 'Y' and resid 237 through 238 Processing sheet with id=AH9, first strand: chain 'Y' and resid 267 through 268 Processing sheet with id=AI1, first strand: chain 'Y' and resid 387 through 391 Processing sheet with id=AI2, first strand: chain 'Z' and resid 202 through 203 removed outlier: 4.712A pdb=" N LYS Z 225 " --> pdb=" O VAL Z 196 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Z' and resid 172 through 175 Processing sheet with id=AI4, first strand: chain 'b' and resid 195 through 196 removed outlier: 6.764A pdb=" N SER b 195 " --> pdb=" O ASP e 382 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'b' and resid 198 through 199 removed outlier: 4.829A pdb=" N VAL e 270 " --> pdb=" O GLY e 289 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS e 252 " --> pdb=" O ILE e 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE e 275 " --> pdb=" O LYS e 252 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL e 254 " --> pdb=" O SER e 273 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'b' and resid 221 through 222 Processing sheet with id=AI7, first strand: chain 'b' and resid 237 through 238 Processing sheet with id=AI8, first strand: chain 'b' and resid 267 through 268 Processing sheet with id=AI9, first strand: chain 'b' and resid 387 through 391 Processing sheet with id=AJ1, first strand: chain 'c' and resid 202 through 203 removed outlier: 4.714A pdb=" N LYS c 225 " --> pdb=" O VAL c 196 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'c' and resid 172 through 175 Processing sheet with id=AJ3, first strand: chain 'e' and resid 195 through 196 removed outlier: 6.759A pdb=" N SER e 195 " --> pdb=" O ASP h 382 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'e' and resid 198 through 199 removed outlier: 4.827A pdb=" N VAL h 270 " --> pdb=" O GLY h 289 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS h 252 " --> pdb=" O ILE h 275 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE h 275 " --> pdb=" O LYS h 252 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL h 254 " --> pdb=" O SER h 273 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'e' and resid 221 through 222 Processing sheet with id=AJ6, first strand: chain 'e' and resid 237 through 238 Processing sheet with id=AJ7, first strand: chain 'e' and resid 267 through 268 Processing sheet with id=AJ8, first strand: chain 'e' and resid 387 through 391 Processing sheet with id=AJ9, first strand: chain 'f' and resid 202 through 203 removed outlier: 4.712A pdb=" N LYS f 225 " --> pdb=" O VAL f 196 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'f' and resid 172 through 175 Processing sheet with id=AK2, first strand: chain 'h' and resid 195 through 196 removed outlier: 6.762A pdb=" N SER h 195 " --> pdb=" O ASP k 382 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'h' and resid 198 through 199 removed outlier: 4.827A pdb=" N VAL k 270 " --> pdb=" O GLY k 289 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS k 252 " --> pdb=" O ILE k 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE k 275 " --> pdb=" O LYS k 252 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL k 254 " --> pdb=" O SER k 273 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'h' and resid 221 through 222 Processing sheet with id=AK5, first strand: chain 'h' and resid 237 through 238 Processing sheet with id=AK6, first strand: chain 'h' and resid 267 through 268 Processing sheet with id=AK7, first strand: chain 'h' and resid 387 through 391 Processing sheet with id=AK8, first strand: chain 'i' and resid 202 through 203 removed outlier: 4.713A pdb=" N LYS i 225 " --> pdb=" O VAL i 196 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'i' and resid 172 through 175 Processing sheet with id=AL1, first strand: chain 'k' and resid 195 through 196 removed outlier: 6.772A pdb=" N SER k 195 " --> pdb=" O ASP n 382 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'k' and resid 198 through 199 removed outlier: 4.827A pdb=" N VAL n 270 " --> pdb=" O GLY n 289 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS n 252 " --> pdb=" O ILE n 275 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE n 275 " --> pdb=" O LYS n 252 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL n 254 " --> pdb=" O SER n 273 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'k' and resid 221 through 222 Processing sheet with id=AL4, first strand: chain 'k' and resid 237 through 238 Processing sheet with id=AL5, first strand: chain 'k' and resid 267 through 268 Processing sheet with id=AL6, first strand: chain 'k' and resid 387 through 391 Processing sheet with id=AL7, first strand: chain 'l' and resid 202 through 203 removed outlier: 4.713A pdb=" N LYS l 225 " --> pdb=" O VAL l 196 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'l' and resid 172 through 175 Processing sheet with id=AL9, first strand: chain 'n' and resid 221 through 222 Processing sheet with id=AM1, first strand: chain 'n' and resid 237 through 238 Processing sheet with id=AM2, first strand: chain 'n' and resid 267 through 268 Processing sheet with id=AM3, first strand: chain 'o' and resid 202 through 203 removed outlier: 4.712A pdb=" N LYS o 225 " --> pdb=" O VAL o 196 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'o' and resid 172 through 175 1555 hydrogen bonds defined for protein. 3993 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: 17.31 Time building geometry restraints manager: 16.09 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: 13230 1.34 - 1.45: 6589 1.45 - 1.57: 19143 1.57 - 1.69: 0 1.69 - 1.81: 238 Bond restraints: 39200 Sorted by residual: bond pdb=" CA ARG Q 259 " pdb=" CB ARG Q 259 " ideal model delta sigma weight residual 1.529 1.559 -0.030 1.58e-02 4.01e+03 3.60e+00 bond pdb=" CA ARG B 259 " pdb=" CB ARG B 259 " ideal model delta sigma weight residual 1.529 1.559 -0.030 1.58e-02 4.01e+03 3.50e+00 bond pdb=" CA ARG l 259 " pdb=" CB ARG l 259 " ideal model delta sigma weight residual 1.529 1.558 -0.029 1.58e-02 4.01e+03 3.37e+00 bond pdb=" CA ARG E 259 " pdb=" CB ARG E 259 " ideal model delta sigma weight residual 1.529 1.558 -0.029 1.58e-02 4.01e+03 3.35e+00 bond pdb=" CA ARG T 259 " pdb=" CB ARG T 259 " ideal model delta sigma weight residual 1.529 1.557 -0.028 1.58e-02 4.01e+03 3.22e+00 ... (remaining 39195 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.85: 952 105.85 - 112.91: 20661 112.91 - 119.97: 12720 119.97 - 127.02: 18292 127.02 - 134.08: 505 Bond angle restraints: 53130 Sorted by residual: angle pdb=" N ARG l 259 " pdb=" CA ARG l 259 " pdb=" CB ARG l 259 " ideal model delta sigma weight residual 110.29 117.84 -7.55 1.52e+00 4.33e-01 2.47e+01 angle pdb=" N ARG N 259 " pdb=" CA ARG N 259 " pdb=" CB ARG N 259 " ideal model delta sigma weight residual 110.29 117.82 -7.53 1.52e+00 4.33e-01 2.45e+01 angle pdb=" N ARG T 259 " pdb=" CA ARG T 259 " pdb=" CB ARG T 259 " ideal model delta sigma weight residual 110.29 117.82 -7.53 1.52e+00 4.33e-01 2.45e+01 angle pdb=" N ARG o 259 " pdb=" CA ARG o 259 " pdb=" CB ARG o 259 " ideal model delta sigma weight residual 110.29 117.81 -7.52 1.52e+00 4.33e-01 2.45e+01 angle pdb=" N ARG i 259 " pdb=" CA ARG i 259 " pdb=" CB ARG i 259 " ideal model delta sigma weight residual 110.29 117.81 -7.52 1.52e+00 4.33e-01 2.45e+01 ... (remaining 53125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 21404 16.67 - 33.34: 1662 33.34 - 50.01: 328 50.01 - 66.68: 56 66.68 - 83.35: 14 Dihedral angle restraints: 23464 sinusoidal: 9310 harmonic: 14154 Sorted by residual: dihedral pdb=" CA ARG K 259 " pdb=" C ARG K 259 " pdb=" N ARG K 260 " pdb=" CA ARG K 260 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ARG o 259 " pdb=" C ARG o 259 " pdb=" N ARG o 260 " pdb=" CA ARG o 260 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ARG i 259 " pdb=" C ARG i 259 " pdb=" N ARG i 260 " pdb=" CA ARG i 260 " ideal model delta harmonic sigma weight residual 180.00 158.06 21.94 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 23461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3135 0.031 - 0.062: 1535 0.062 - 0.092: 712 0.092 - 0.123: 297 0.123 - 0.154: 117 Chirality restraints: 5796 Sorted by residual: chirality pdb=" CA VAL l 258 " pdb=" N VAL l 258 " pdb=" C VAL l 258 " pdb=" CB VAL l 258 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA VAL Q 258 " pdb=" N VAL Q 258 " pdb=" C VAL Q 258 " pdb=" CB VAL Q 258 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA VAL N 258 " pdb=" N VAL N 258 " pdb=" C VAL N 258 " pdb=" CB VAL N 258 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 5793 not shown) Planarity restraints: 7084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN N 223 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO N 224 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO N 224 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO N 224 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 223 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO B 224 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 224 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 224 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN Q 223 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO Q 224 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO Q 224 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO Q 224 " 0.025 5.00e-02 4.00e+02 ... (remaining 7081 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 6155 2.76 - 3.29: 34002 3.29 - 3.83: 64616 3.83 - 4.36: 79971 4.36 - 4.90: 141953 Nonbonded interactions: 326697 Sorted by model distance: nonbonded pdb=" OD1 ASP W 165 " pdb=" NH2 ARG W 233 " model vdw 2.224 2.520 nonbonded pdb=" OD1 ASP B 165 " pdb=" NH2 ARG B 233 " model vdw 2.224 2.520 nonbonded pdb=" OD1 ASP H 165 " pdb=" NH2 ARG H 233 " model vdw 2.224 2.520 nonbonded pdb=" OD1 ASP T 165 " pdb=" NH2 ARG T 233 " model vdw 2.224 2.520 nonbonded pdb=" OD1 ASP N 165 " pdb=" NH2 ARG N 233 " model vdw 2.225 2.520 ... (remaining 326692 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' selection = chain 'b' selection = chain 'e' selection = chain 'h' selection = chain 'k' selection = chain 'n' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'c' selection = chain 'f' selection = chain 'i' selection = chain 'l' selection = chain 'o' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'd' selection = chain 'g' selection = chain 'j' selection = chain 'm' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.030 Extract box with map and model: 1.400 Check model and map are aligned: 0.290 Set scattering table: 0.440 Process input model: 104.180 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.350 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:10.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 39200 Z= 0.534 Angle : 0.674 7.553 53130 Z= 0.387 Chirality : 0.049 0.154 5796 Planarity : 0.004 0.045 7084 Dihedral : 12.450 83.348 14406 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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 (0.11), residues: 4942 helix: 2.26 (0.19), residues: 784 sheet: 0.85 (0.15), residues: 1022 loop : -0.24 (0.10), residues: 3136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 307 HIS 0.004 0.001 HIS J 305 PHE 0.019 0.002 PHE Z 195 TYR 0.017 0.002 TYR o 194 ARG 0.019 0.001 ARG o 259 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 810 time to evaluate : 4.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 145 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8711 (mp0) REVERT: G 209 GLN cc_start: 0.8898 (mt0) cc_final: 0.8696 (mt0) REVERT: Q 145 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8593 (mp0) REVERT: l 145 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8584 (mp0) outliers start: 0 outliers final: 0 residues processed: 810 average time/residue: 2.0913 time to fit residues: 1940.8121 Evaluate side-chains 585 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 585 time to evaluate : 4.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 413 optimal weight: 5.9990 chunk 371 optimal weight: 7.9990 chunk 206 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 384 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 233 optimal weight: 4.9990 chunk 285 optimal weight: 5.9990 chunk 444 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN G 374 ASN J 188 GLN M 188 GLN ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 188 GLN e 188 GLN ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 188 GLN h 263 GLN k 374 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 39200 Z= 0.308 Angle : 0.602 6.776 53130 Z= 0.314 Chirality : 0.043 0.135 5796 Planarity : 0.005 0.040 7084 Dihedral : 4.467 14.692 5502 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.17 % Allowed : 10.18 % Favored : 87.64 % 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 (0.12), residues: 4942 helix: 2.12 (0.19), residues: 798 sheet: 0.69 (0.17), residues: 938 loop : 0.07 (0.10), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 307 HIS 0.002 0.000 HIS Z 220 PHE 0.026 0.001 PHE W 195 TYR 0.008 0.001 TYR Z 194 ARG 0.008 0.001 ARG i 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 642 time to evaluate : 4.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.6566 (pmm150) REVERT: B 250 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7700 (m-30) REVERT: E 145 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8649 (mp0) REVERT: E 250 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: H 136 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.6411 (pmm150) REVERT: H 145 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: K 145 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: N 136 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7248 (pmm150) REVERT: N 250 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7985 (m-30) REVERT: P 319 ILE cc_start: 0.9616 (OUTLIER) cc_final: 0.9296 (mp) REVERT: Q 145 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8585 (mp0) REVERT: W 136 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.6530 (pmm150) REVERT: W 250 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: Z 136 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.6312 (pmm150) REVERT: b 319 ILE cc_start: 0.9612 (OUTLIER) cc_final: 0.9327 (mp) REVERT: c 136 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.6392 (pmm150) REVERT: c 161 MET cc_start: 0.8138 (mmm) cc_final: 0.7776 (mmm) REVERT: i 136 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7239 (pmm150) REVERT: i 250 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: k 319 ILE cc_start: 0.9643 (OUTLIER) cc_final: 0.9320 (mp) REVERT: l 145 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8569 (mp0) REVERT: o 136 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.6352 (pmm150) outliers start: 88 outliers final: 15 residues processed: 678 average time/residue: 2.2255 time to fit residues: 1725.1578 Evaluate side-chains 591 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 558 time to evaluate : 4.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain H residue 136 ARG Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain K residue 250 ASP Chi-restraints excluded: chain M residue 209 GLN Chi-restraints excluded: chain N residue 136 ARG Chi-restraints excluded: chain N residue 250 ASP Chi-restraints excluded: chain P residue 209 GLN Chi-restraints excluded: chain P residue 319 ILE Chi-restraints excluded: chain Q residue 250 ASP Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain W residue 136 ARG Chi-restraints excluded: chain W residue 250 ASP Chi-restraints excluded: chain Z residue 136 ARG Chi-restraints excluded: chain Z residue 250 ASP Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain b residue 228 MET Chi-restraints excluded: chain b residue 319 ILE Chi-restraints excluded: chain c residue 136 ARG Chi-restraints excluded: chain c residue 250 ASP Chi-restraints excluded: chain e residue 209 GLN Chi-restraints excluded: chain f residue 250 ASP Chi-restraints excluded: chain h residue 209 GLN Chi-restraints excluded: chain i residue 136 ARG Chi-restraints excluded: chain i residue 250 ASP Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain l residue 250 ASP Chi-restraints excluded: chain o residue 136 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 247 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 370 optimal weight: 9.9990 chunk 303 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 445 optimal weight: 10.0000 chunk 481 optimal weight: 0.0980 chunk 397 optimal weight: 5.9990 chunk 442 optimal weight: 10.0000 chunk 151 optimal weight: 0.6980 chunk 357 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN G 374 ASN M 263 GLN M 374 ASN ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 374 ASN Y 374 ASN b 374 ASN h 263 GLN h 374 ASN ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 374 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 39200 Z= 0.245 Angle : 0.571 8.321 53130 Z= 0.296 Chirality : 0.042 0.137 5796 Planarity : 0.004 0.044 7084 Dihedral : 4.222 14.013 5502 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.15 % Allowed : 15.32 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.12), residues: 4942 helix: 2.18 (0.19), residues: 798 sheet: 0.63 (0.17), residues: 938 loop : 0.17 (0.10), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 307 HIS 0.001 0.000 HIS M 305 PHE 0.026 0.001 PHE W 195 TYR 0.013 0.001 TYR b 387 ARG 0.008 0.000 ARG H 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 599 time to evaluate : 4.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7768 (m-30) REVERT: E 145 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8657 (mp0) REVERT: E 250 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7826 (m-30) REVERT: G 308 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: H 136 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7723 (pmm-80) REVERT: K 145 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: K 161 MET cc_start: 0.8469 (mmm) cc_final: 0.8255 (mmm) REVERT: N 145 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: N 250 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: P 319 ILE cc_start: 0.9617 (OUTLIER) cc_final: 0.9331 (mp) REVERT: Q 145 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8544 (mp0) REVERT: T 145 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: W 250 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: Z 136 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7489 (pmm-80) REVERT: Z 145 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: b 308 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: c 136 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7695 (pmm-80) REVERT: f 145 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: i 145 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: i 250 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7974 (m-30) REVERT: k 319 ILE cc_start: 0.9623 (OUTLIER) cc_final: 0.9339 (mp) REVERT: l 145 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8650 (mp0) REVERT: l 183 LYS cc_start: 0.8592 (ttpt) cc_final: 0.8369 (ttmt) outliers start: 87 outliers final: 18 residues processed: 633 average time/residue: 2.2084 time to fit residues: 1594.7697 Evaluate side-chains 586 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 550 time to evaluate : 4.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain H residue 136 ARG Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain K residue 250 ASP Chi-restraints excluded: chain M residue 209 GLN Chi-restraints excluded: chain N residue 145 GLU Chi-restraints excluded: chain N residue 250 ASP Chi-restraints excluded: chain P residue 209 GLN Chi-restraints excluded: chain P residue 319 ILE Chi-restraints excluded: chain Q residue 250 ASP Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain T residue 145 GLU Chi-restraints excluded: chain W residue 250 ASP Chi-restraints excluded: chain Z residue 136 ARG Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 250 ASP Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain b residue 228 MET Chi-restraints excluded: chain b residue 308 GLU Chi-restraints excluded: chain c residue 136 ARG Chi-restraints excluded: chain c residue 250 ASP Chi-restraints excluded: chain f residue 145 GLU Chi-restraints excluded: chain f residue 250 ASP Chi-restraints excluded: chain h residue 209 GLN Chi-restraints excluded: chain i residue 145 GLU Chi-restraints excluded: chain i residue 250 ASP Chi-restraints excluded: chain k residue 209 GLN Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain l residue 250 ASP Chi-restraints excluded: chain o residue 250 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 440 optimal weight: 4.9990 chunk 335 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 299 optimal weight: 8.9990 chunk 447 optimal weight: 9.9990 chunk 473 optimal weight: 3.9990 chunk 233 optimal weight: 0.7980 chunk 424 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN G 374 ASN J 188 GLN J 374 ASN M 188 GLN M 263 GLN M 374 ASN ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 284 ASN S 374 ASN ** V 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 374 ASN b 374 ASN e 188 GLN e 374 ASN h 188 GLN h 263 GLN h 374 ASN ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 284 ASN n 374 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 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 : 0.005 0.037 39200 Z= 0.348 Angle : 0.597 9.292 53130 Z= 0.307 Chirality : 0.043 0.142 5796 Planarity : 0.004 0.042 7084 Dihedral : 4.145 15.139 5502 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.90 % Allowed : 16.31 % Favored : 81.78 % 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: 0.92 (0.12), residues: 4942 helix: 2.36 (0.19), residues: 798 sheet: 0.55 (0.17), residues: 938 loop : 0.25 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 307 HIS 0.002 0.000 HIS M 305 PHE 0.024 0.001 PHE l 195 TYR 0.015 0.001 TYR n 387 ARG 0.011 0.001 ARG N 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 572 time to evaluate : 4.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 250 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7812 (m-30) REVERT: C 24 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8682 (ttpt) REVERT: E 145 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8589 (mp0) REVERT: E 250 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: H 136 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7517 (pmm-80) REVERT: H 145 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: K 141 ARG cc_start: 0.8237 (ttp80) cc_final: 0.8032 (ttp80) REVERT: K 145 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: N 145 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: N 250 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.8034 (m-30) REVERT: W 250 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: Z 136 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7698 (pmm-80) REVERT: Z 145 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: c 145 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: f 141 ARG cc_start: 0.8250 (ttp80) cc_final: 0.8031 (ttp80) REVERT: f 145 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: i 145 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: i 250 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: l 145 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8671 (OUTLIER) outliers start: 77 outliers final: 21 residues processed: 599 average time/residue: 2.2286 time to fit residues: 1521.9183 Evaluate side-chains 569 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 534 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain H residue 136 ARG Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 155 TYR Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain K residue 250 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain N residue 145 GLU Chi-restraints excluded: chain N residue 155 TYR Chi-restraints excluded: chain N residue 250 ASP Chi-restraints excluded: chain Q residue 250 ASP Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain T residue 250 ASP Chi-restraints excluded: chain W residue 250 ASP Chi-restraints excluded: chain Z residue 136 ARG Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 250 ASP Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain b residue 228 MET Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 155 TYR Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain f residue 145 GLU Chi-restraints excluded: chain f residue 250 ASP Chi-restraints excluded: chain i residue 145 GLU Chi-restraints excluded: chain i residue 250 ASP Chi-restraints excluded: chain k residue 209 GLN Chi-restraints excluded: chain l residue 250 ASP Chi-restraints excluded: chain o residue 250 ASP Chi-restraints excluded: chain p residue 27 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 394 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 352 optimal weight: 9.9990 chunk 195 optimal weight: 8.9990 chunk 404 optimal weight: 5.9990 chunk 327 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 chunk 425 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN A 284 ASN A 374 ASN D 374 ASN E 220 HIS G 284 ASN G 374 ASN ** J 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 284 ASN ** V 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 374 ASN b 284 ASN b 374 ASN ** e 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 39200 Z= 0.525 Angle : 0.653 10.015 53130 Z= 0.336 Chirality : 0.044 0.148 5796 Planarity : 0.004 0.045 7084 Dihedral : 4.238 13.773 5502 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.13 % Allowed : 18.71 % Favored : 79.16 % 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: 0.94 (0.12), residues: 4942 helix: 2.56 (0.19), residues: 798 sheet: 0.45 (0.17), residues: 938 loop : 0.25 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 307 HIS 0.003 0.001 HIS M 305 PHE 0.023 0.001 PHE K 195 TYR 0.025 0.001 TYR n 387 ARG 0.010 0.001 ARG c 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 547 time to evaluate : 4.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 250 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: C 24 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8724 (ttpt) REVERT: D 308 GLU cc_start: 0.7872 (mp0) cc_final: 0.7667 (mp0) REVERT: E 145 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8648 (mp0) REVERT: E 250 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7912 (m-30) REVERT: K 145 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: N 250 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8102 (m-30) REVERT: P 319 ILE cc_start: 0.9630 (OUTLIER) cc_final: 0.9405 (mp) REVERT: Q 145 GLU cc_start: 0.8554 (mp0) cc_final: 0.8335 (mp0) REVERT: Q 183 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8578 (tttm) REVERT: W 250 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7979 (m-30) REVERT: Y 308 GLU cc_start: 0.7884 (mp0) cc_final: 0.7674 (mp0) REVERT: Z 136 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7942 (pmm-80) REVERT: Z 137 GLU cc_start: 0.7028 (pm20) cc_final: 0.6761 (pm20) REVERT: c 136 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7666 (pmm-80) REVERT: c 145 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8360 (mp0) REVERT: i 250 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8093 (m-30) REVERT: k 319 ILE cc_start: 0.9634 (OUTLIER) cc_final: 0.9411 (mp) REVERT: l 145 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8514 (OUTLIER) outliers start: 86 outliers final: 30 residues processed: 587 average time/residue: 2.3096 time to fit residues: 1539.1998 Evaluate side-chains 566 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 524 time to evaluate : 4.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain G residue 209 GLN Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain K residue 250 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain N residue 250 ASP Chi-restraints excluded: chain P residue 209 GLN Chi-restraints excluded: chain P residue 319 ILE Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 250 ASP Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain T residue 250 ASP Chi-restraints excluded: chain V residue 319 ILE Chi-restraints excluded: chain W residue 250 ASP Chi-restraints excluded: chain Z residue 136 ARG Chi-restraints excluded: chain Z residue 250 ASP Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain b residue 228 MET Chi-restraints excluded: chain c residue 136 ARG Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 250 ASP Chi-restraints excluded: chain f residue 250 ASP Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain i residue 155 TYR Chi-restraints excluded: chain i residue 250 ASP Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain l residue 250 ASP Chi-restraints excluded: chain n residue 277 THR Chi-restraints excluded: chain o residue 250 ASP Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 28 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 159 optimal weight: 2.9990 chunk 426 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 278 optimal weight: 20.0000 chunk 116 optimal weight: 0.7980 chunk 474 optimal weight: 4.9990 chunk 393 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 374 ASN ** G 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 GLN M 188 GLN M 212 GLN M 374 ASN ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 374 ASN ** b 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 188 GLN h 188 GLN h 212 GLN h 374 ASN ** k 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39200 Z= 0.205 Angle : 0.605 11.237 53130 Z= 0.309 Chirality : 0.042 0.150 5796 Planarity : 0.004 0.048 7084 Dihedral : 4.006 13.444 5502 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.66 % Allowed : 20.34 % Favored : 78.00 % 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: 0.88 (0.12), residues: 4942 helix: 2.39 (0.19), residues: 798 sheet: 0.46 (0.17), residues: 938 loop : 0.24 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP k 301 HIS 0.001 0.000 HIS E 220 PHE 0.023 0.001 PHE c 195 TYR 0.015 0.001 TYR n 387 ARG 0.010 0.000 ARG c 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 583 time to evaluate : 4.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 250 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7816 (m-30) REVERT: D 308 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: E 145 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8641 (mp0) REVERT: E 250 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7802 (m-30) REVERT: F 30 ASN cc_start: 0.7833 (p0) cc_final: 0.7366 (p0) REVERT: M 308 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: N 145 GLU cc_start: 0.8304 (mp0) cc_final: 0.8046 (mp0) REVERT: N 250 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7982 (m-30) REVERT: Q 145 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: W 250 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: Y 263 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8297 (mt0) REVERT: Z 145 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: a 30 ASN cc_start: 0.7791 (p0) cc_final: 0.7326 (p0) REVERT: i 145 GLU cc_start: 0.8419 (mp0) cc_final: 0.8132 (mp0) REVERT: i 250 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7976 (m-30) outliers start: 67 outliers final: 21 residues processed: 618 average time/residue: 2.2363 time to fit residues: 1594.6742 Evaluate side-chains 577 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 546 time to evaluate : 4.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain G residue 209 GLN Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain K residue 250 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain M residue 308 GLU Chi-restraints excluded: chain N residue 250 ASP Chi-restraints excluded: chain P residue 209 GLN Chi-restraints excluded: chain Q residue 145 GLU Chi-restraints excluded: chain Q residue 250 ASP Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain T residue 250 ASP Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain W residue 250 ASP Chi-restraints excluded: chain Y residue 231 CYS Chi-restraints excluded: chain Y residue 263 GLN Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 250 ASP Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain b residue 228 MET Chi-restraints excluded: chain c residue 250 ASP Chi-restraints excluded: chain f residue 250 ASP Chi-restraints excluded: chain i residue 250 ASP Chi-restraints excluded: chain l residue 250 ASP Chi-restraints excluded: chain p residue 27 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 457 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 270 optimal weight: 9.9990 chunk 346 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 399 optimal weight: 9.9990 chunk 264 optimal weight: 6.9990 chunk 472 optimal weight: 9.9990 chunk 295 optimal weight: 0.6980 chunk 287 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN B 262 ASN D 374 ASN G 284 ASN ** G 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN P 284 ASN ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 284 ASN V 284 ASN ** V 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 262 ASN ** Y 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 374 ASN b 284 ASN ** b 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 284 ASN ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 284 ASN ** n 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 39200 Z= 0.404 Angle : 0.662 13.076 53130 Z= 0.336 Chirality : 0.043 0.142 5796 Planarity : 0.004 0.046 7084 Dihedral : 4.066 14.694 5502 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.95 % Allowed : 20.42 % Favored : 77.63 % 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 (0.12), residues: 4942 helix: 2.47 (0.19), residues: 798 sheet: 0.43 (0.17), residues: 938 loop : 0.26 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 307 HIS 0.002 0.000 HIS h 305 PHE 0.023 0.001 PHE f 195 TYR 0.027 0.001 TYR n 387 ARG 0.014 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 563 time to evaluate : 4.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7893 (m-30) REVERT: D 308 GLU cc_start: 0.7882 (mp0) cc_final: 0.7657 (mp0) REVERT: E 145 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8503 (mp0) REVERT: E 250 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: K 145 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: N 250 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.8022 (m-30) REVERT: Q 145 GLU cc_start: 0.8441 (mp0) cc_final: 0.8239 (mp0) REVERT: W 250 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: Y 308 GLU cc_start: 0.7872 (mp0) cc_final: 0.7661 (mp0) REVERT: a 30 ASN cc_start: 0.7873 (p0) cc_final: 0.7448 (p0) REVERT: f 145 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: i 250 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: o 145 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8168 (mp0) outliers start: 79 outliers final: 30 residues processed: 606 average time/residue: 2.2069 time to fit residues: 1526.0522 Evaluate side-chains 585 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 547 time to evaluate : 4.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain G residue 209 GLN Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 162 MET Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain K residue 145 GLU Chi-restraints excluded: chain K residue 250 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain N residue 250 ASP Chi-restraints excluded: chain P residue 209 GLN Chi-restraints excluded: chain Q residue 250 ASP Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain S residue 284 ASN Chi-restraints excluded: chain T residue 250 ASP Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain W residue 250 ASP Chi-restraints excluded: chain Y residue 231 CYS Chi-restraints excluded: chain Z residue 250 ASP Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain b residue 228 MET Chi-restraints excluded: chain c residue 250 ASP Chi-restraints excluded: chain f residue 145 GLU Chi-restraints excluded: chain f residue 250 ASP Chi-restraints excluded: chain i residue 225 LYS Chi-restraints excluded: chain i residue 250 ASP Chi-restraints excluded: chain k residue 209 GLN Chi-restraints excluded: chain l residue 250 ASP Chi-restraints excluded: chain n residue 284 ASN Chi-restraints excluded: chain o residue 145 GLU Chi-restraints excluded: chain o residue 250 ASP Chi-restraints excluded: chain p residue 27 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 292 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 282 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 300 optimal weight: 7.9990 chunk 321 optimal weight: 0.3980 chunk 233 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 371 optimal weight: 3.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 284 ASN ** V 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 263 GLN ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 284 ASN ** n 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 39200 Z= 0.279 Angle : 0.669 13.499 53130 Z= 0.338 Chirality : 0.043 0.141 5796 Planarity : 0.004 0.050 7084 Dihedral : 3.979 14.628 5502 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.56 % Allowed : 21.16 % Favored : 77.29 % 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: 0.86 (0.12), residues: 4942 helix: 2.23 (0.19), residues: 798 sheet: 0.46 (0.17), residues: 938 loop : 0.26 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP n 301 HIS 0.001 0.000 HIS M 305 PHE 0.021 0.001 PHE Z 195 TYR 0.023 0.001 TYR S 387 ARG 0.016 0.001 ARG H 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 561 time to evaluate : 4.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 GLU cc_start: 0.8852 (tp30) cc_final: 0.8603 (tp30) REVERT: B 250 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7874 (m-30) REVERT: D 263 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8309 (mt0) REVERT: D 308 GLU cc_start: 0.7814 (mp0) cc_final: 0.7612 (mp0) REVERT: E 250 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: Y 308 GLU cc_start: 0.7833 (mp0) cc_final: 0.7621 (mp0) REVERT: a 30 ASN cc_start: 0.7878 (p0) cc_final: 0.7473 (p0) REVERT: i 250 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: l 145 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: p 24 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.8937 (ttpt) outliers start: 63 outliers final: 33 residues processed: 590 average time/residue: 2.3072 time to fit residues: 1548.8658 Evaluate side-chains 587 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 548 time to evaluate : 4.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain G residue 209 GLN Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 162 MET Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain K residue 250 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain P residue 209 GLN Chi-restraints excluded: chain Q residue 250 ASP Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain T residue 250 ASP Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain V residue 231 CYS Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain Y residue 231 CYS Chi-restraints excluded: chain Z residue 250 ASP Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain c residue 250 ASP Chi-restraints excluded: chain e residue 277 THR Chi-restraints excluded: chain f residue 250 ASP Chi-restraints excluded: chain h residue 277 THR Chi-restraints excluded: chain i residue 250 ASP Chi-restraints excluded: chain k residue 209 GLN Chi-restraints excluded: chain l residue 145 GLU Chi-restraints excluded: chain l residue 250 ASP Chi-restraints excluded: chain n residue 277 THR Chi-restraints excluded: chain o residue 250 ASP Chi-restraints excluded: chain p residue 24 LYS Chi-restraints excluded: chain p residue 27 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 429 optimal weight: 6.9990 chunk 452 optimal weight: 9.9990 chunk 412 optimal weight: 7.9990 chunk 440 optimal weight: 20.0000 chunk 264 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 345 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 397 optimal weight: 10.0000 chunk 416 optimal weight: 7.9990 chunk 438 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 271 GLN ** G 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN P 284 ASN ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 GLN ** S 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 284 ASN V 374 ASN ** Y 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 188 GLN ** b 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 209 GLN h 263 GLN k 284 ASN ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 25 GLN n 284 ASN ** n 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 39200 Z= 0.498 Angle : 0.728 14.213 53130 Z= 0.369 Chirality : 0.044 0.150 5796 Planarity : 0.005 0.088 7084 Dihedral : 4.108 14.190 5502 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.75 % Allowed : 20.86 % Favored : 77.39 % 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: 0.88 (0.12), residues: 4942 helix: 2.23 (0.19), residues: 798 sheet: 0.42 (0.17), residues: 938 loop : 0.29 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 307 HIS 0.002 0.001 HIS M 305 PHE 0.023 0.001 PHE Z 195 TYR 0.028 0.001 TYR S 387 ARG 0.019 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 543 time to evaluate : 4.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7915 (m-30) REVERT: D 308 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: E 145 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: Q 145 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8257 (mp0) REVERT: T 151 ARG cc_start: 0.6677 (tmm160) cc_final: 0.6433 (tmm160) REVERT: U 24 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.8981 (ttpt) REVERT: W 250 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: Y 308 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: o 151 ARG cc_start: 0.6847 (tmm160) cc_final: 0.6626 (tmm160) REVERT: p 24 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.8982 (ttpt) outliers start: 71 outliers final: 28 residues processed: 578 average time/residue: 2.3034 time to fit residues: 1523.1004 Evaluate side-chains 567 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 531 time to evaluate : 4.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain G residue 209 GLN Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain J residue 231 CYS Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain K residue 250 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain Q residue 145 GLU Chi-restraints excluded: chain Q residue 250 ASP Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain T residue 250 ASP Chi-restraints excluded: chain U residue 24 LYS Chi-restraints excluded: chain U residue 27 SER Chi-restraints excluded: chain V residue 231 CYS Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain W residue 250 ASP Chi-restraints excluded: chain Y residue 308 GLU Chi-restraints excluded: chain Z residue 250 ASP Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain c residue 250 ASP Chi-restraints excluded: chain e residue 277 THR Chi-restraints excluded: chain f residue 250 ASP Chi-restraints excluded: chain h residue 277 THR Chi-restraints excluded: chain l residue 250 ASP Chi-restraints excluded: chain n residue 277 THR Chi-restraints excluded: chain o residue 250 ASP Chi-restraints excluded: chain p residue 24 LYS Chi-restraints excluded: chain p residue 27 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 289 optimal weight: 0.9980 chunk 465 optimal weight: 4.9990 chunk 284 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 323 optimal weight: 3.9990 chunk 488 optimal weight: 20.0000 chunk 449 optimal weight: 3.9990 chunk 388 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 300 optimal weight: 8.9990 chunk 238 optimal weight: 0.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 374 ASN G 271 GLN G 374 ASN M 263 GLN ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 212 GLN V 374 ASN Y 374 ASN ** a 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 374 ASN ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39200 Z= 0.232 Angle : 0.701 14.117 53130 Z= 0.353 Chirality : 0.043 0.152 5796 Planarity : 0.004 0.070 7084 Dihedral : 3.892 14.665 5502 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.38 % Allowed : 21.28 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.12), residues: 4942 helix: 1.99 (0.19), residues: 798 sheet: 0.56 (0.16), residues: 1078 loop : 0.31 (0.11), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 301 HIS 0.001 0.000 HIS E 220 PHE 0.021 0.001 PHE Q 195 TYR 0.019 0.001 TYR n 387 ARG 0.021 0.000 ARG Q 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 563 time to evaluate : 4.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7883 (m-30) REVERT: H 145 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: N 145 GLU cc_start: 0.8220 (mp0) cc_final: 0.7875 (mp0) REVERT: U 24 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.8947 (ttpt) REVERT: W 250 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7887 (m-30) REVERT: c 145 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: i 145 GLU cc_start: 0.8255 (mp0) cc_final: 0.7979 (mp0) REVERT: o 145 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: p 24 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.8947 (ttpt) outliers start: 56 outliers final: 19 residues processed: 584 average time/residue: 2.2636 time to fit residues: 1503.3987 Evaluate side-chains 573 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 547 time to evaluate : 4.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain G residue 209 GLN Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain J residue 231 CYS Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain K residue 250 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain T residue 250 ASP Chi-restraints excluded: chain U residue 24 LYS Chi-restraints excluded: chain V residue 231 CYS Chi-restraints excluded: chain W residue 250 ASP Chi-restraints excluded: chain Y residue 231 CYS Chi-restraints excluded: chain Z residue 250 ASP Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain b residue 209 GLN Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 250 ASP Chi-restraints excluded: chain e residue 277 THR Chi-restraints excluded: chain f residue 250 ASP Chi-restraints excluded: chain o residue 145 GLU Chi-restraints excluded: chain o residue 250 ASP Chi-restraints excluded: chain p residue 24 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 308 optimal weight: 5.9990 chunk 414 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 358 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 389 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 399 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN P 271 GLN ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 188 GLN b 374 ASN e 209 GLN h 263 GLN ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.050954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.037629 restraints weight = 116872.842| |-----------------------------------------------------------------------------| r_work (start): 0.2542 rms_B_bonded: 3.15 r_work: 0.2400 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 39200 Z= 0.384 Angle : 0.731 14.698 53130 Z= 0.368 Chirality : 0.044 0.146 5796 Planarity : 0.005 0.067 7084 Dihedral : 3.950 13.473 5502 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.26 % Allowed : 21.38 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.12), residues: 4942 helix: 1.93 (0.19), residues: 798 sheet: 0.46 (0.17), residues: 938 loop : 0.31 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 307 HIS 0.002 0.000 HIS M 305 PHE 0.021 0.001 PHE Q 195 TYR 0.021 0.001 TYR S 387 ARG 0.021 0.001 ARG W 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20572.39 seconds wall clock time: 356 minutes 19.63 seconds (21379.63 seconds total)