Starting phenix.real_space_refine on Fri Mar 22 22:02:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxf_4668/03_2024/6qxf_4668.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxf_4668/03_2024/6qxf_4668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxf_4668/03_2024/6qxf_4668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxf_4668/03_2024/6qxf_4668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxf_4668/03_2024/6qxf_4668.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qxf_4668/03_2024/6qxf_4668.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 50 5.49 5 S 144 5.16 5 C 22240 2.51 5 N 5603 2.21 5 O 6648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 122": "OD1" <-> "OD2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 122": "OD1" <-> "OD2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 122": "OD1" <-> "OD2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 25": "NH1" <-> "NH2" Residue "I PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 93": "NH1" <-> "NH2" Residue "I PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 154": "NH1" <-> "NH2" Residue "I PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 190": "NH1" <-> "NH2" Residue "I ARG 228": "NH1" <-> "NH2" Residue "J TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 69": "OD1" <-> "OD2" Residue "J ARG 72": "NH1" <-> "NH2" Residue "J PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 154": "NH1" <-> "NH2" Residue "J PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 167": "NH1" <-> "NH2" Residue "J ARG 190": "NH1" <-> "NH2" Residue "J TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 25": "NH1" <-> "NH2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 93": "NH1" <-> "NH2" Residue "L PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 154": "NH1" <-> "NH2" Residue "L PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 190": "NH1" <-> "NH2" Residue "L ARG 228": "NH1" <-> "NH2" Residue "M TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 69": "OD1" <-> "OD2" Residue "M ARG 72": "NH1" <-> "NH2" Residue "M PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 154": "NH1" <-> "NH2" Residue "M PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 167": "NH1" <-> "NH2" Residue "M ARG 190": "NH1" <-> "NH2" Residue "M TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 93": "NH1" <-> "NH2" Residue "O PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 154": "NH1" <-> "NH2" Residue "O PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 190": "NH1" <-> "NH2" Residue "O ARG 228": "NH1" <-> "NH2" Residue "P TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 69": "OD1" <-> "OD2" Residue "P ARG 72": "NH1" <-> "NH2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 154": "NH1" <-> "NH2" Residue "P PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 167": "NH1" <-> "NH2" Residue "P ARG 190": "NH1" <-> "NH2" Residue "P TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 25": "NH1" <-> "NH2" Residue "R PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 93": "NH1" <-> "NH2" Residue "R PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 154": "NH1" <-> "NH2" Residue "R PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 190": "NH1" <-> "NH2" Residue "R ARG 228": "NH1" <-> "NH2" Residue "R TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 69": "OD1" <-> "OD2" Residue "S ARG 72": "NH1" <-> "NH2" Residue "S PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 154": "NH1" <-> "NH2" Residue "S PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 167": "NH1" <-> "NH2" Residue "S ARG 190": "NH1" <-> "NH2" Residue "S TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34693 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1787 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain: "B" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1795 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain: "C" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1787 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain: "D" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1795 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain: "E" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1787 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain: "F" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1795 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain: "G" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1787 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain: "H" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1795 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain: "I" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2369 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "J" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2369 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "K" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 95 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "L" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2369 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "M" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2369 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "N" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 95 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "O" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2369 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "P" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2369 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "Q" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 95 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "R" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2369 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "S" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2369 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "T" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 95 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "X" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 500 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "Y" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 525 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.80, per 1000 atoms: 0.54 Number of scatterers: 34693 At special positions: 0 Unit cell: (126.945, 179.025, 185.535, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 144 16.00 P 50 15.00 O 6648 8.00 N 5603 7.00 C 22240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.28 Conformation dependent library (CDL) restraints added in 5.7 seconds 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7944 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 40 sheets defined 51.1% alpha, 13.2% beta 25 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 12.18 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 72 through 90 removed outlier: 3.797A pdb=" N LYS A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 115 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 143 through 158 removed outlier: 3.535A pdb=" N PHE A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'B' and resid 24 through 37 Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.913A pdb=" N LYS B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 115 Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 143 through 155 Processing helix chain 'B' and resid 169 through 172 removed outlier: 3.705A pdb=" N TYR B 172 " --> pdb=" O SER B 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 169 through 172' Processing helix chain 'B' and resid 174 through 189 removed outlier: 3.543A pdb=" N LEU B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 37 Processing helix chain 'C' and resid 72 through 90 removed outlier: 3.796A pdb=" N LYS C 90 " --> pdb=" O GLN C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 115 Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 143 through 158 removed outlier: 3.535A pdb=" N PHE C 149 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 189 Processing helix chain 'D' and resid 24 through 37 Processing helix chain 'D' and resid 72 through 90 removed outlier: 3.914A pdb=" N LYS D 90 " --> pdb=" O GLN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 115 Processing helix chain 'D' and resid 125 through 134 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 169 through 172 removed outlier: 3.710A pdb=" N TYR D 172 " --> pdb=" O SER D 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 169 through 172' Processing helix chain 'D' and resid 174 through 189 removed outlier: 3.540A pdb=" N LEU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 37 Processing helix chain 'E' and resid 72 through 90 removed outlier: 3.797A pdb=" N LYS E 90 " --> pdb=" O GLN E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 115 Processing helix chain 'E' and resid 125 through 134 Processing helix chain 'E' and resid 143 through 158 removed outlier: 3.535A pdb=" N PHE E 149 " --> pdb=" O PHE E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 189 Processing helix chain 'F' and resid 24 through 37 Processing helix chain 'F' and resid 72 through 90 removed outlier: 3.890A pdb=" N LYS F 90 " --> pdb=" O GLN F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 115 Processing helix chain 'F' and resid 125 through 134 Processing helix chain 'F' and resid 143 through 155 Processing helix chain 'F' and resid 169 through 172 removed outlier: 3.715A pdb=" N TYR F 172 " --> pdb=" O SER F 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 169 through 172' Processing helix chain 'F' and resid 174 through 189 removed outlier: 3.536A pdb=" N LEU F 187 " --> pdb=" O GLU F 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 37 Processing helix chain 'G' and resid 72 through 90 removed outlier: 3.797A pdb=" N LYS G 90 " --> pdb=" O GLN G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 115 Processing helix chain 'G' and resid 125 through 134 Processing helix chain 'G' and resid 143 through 158 removed outlier: 3.535A pdb=" N PHE G 149 " --> pdb=" O PHE G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 189 Processing helix chain 'H' and resid 24 through 37 Processing helix chain 'H' and resid 72 through 90 removed outlier: 3.907A pdb=" N LYS H 90 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 115 Processing helix chain 'H' and resid 125 through 134 Processing helix chain 'H' and resid 143 through 155 Processing helix chain 'H' and resid 174 through 189 removed outlier: 3.538A pdb=" N LEU H 187 " --> pdb=" O GLU H 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 62 Processing helix chain 'I' and resid 85 through 96 removed outlier: 3.964A pdb=" N LEU I 89 " --> pdb=" O HIS I 85 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA I 92 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG I 93 " --> pdb=" O LEU I 89 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN I 94 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 124 Processing helix chain 'I' and resid 126 through 140 Processing helix chain 'I' and resid 147 through 162 removed outlier: 3.856A pdb=" N ARG I 154 " --> pdb=" O GLY I 150 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE I 155 " --> pdb=" O HIS I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 196 Processing helix chain 'I' and resid 212 through 219 Processing helix chain 'I' and resid 220 through 222 No H-bonds generated for 'chain 'I' and resid 220 through 222' Processing helix chain 'I' and resid 223 through 233 removed outlier: 3.712A pdb=" N ASP I 227 " --> pdb=" O ARG I 223 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE I 229 " --> pdb=" O ILE I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 247 removed outlier: 3.608A pdb=" N SER I 247 " --> pdb=" O LYS I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 279 Processing helix chain 'J' and resid 52 through 61 Processing helix chain 'J' and resid 85 through 96 removed outlier: 4.085A pdb=" N LEU J 89 " --> pdb=" O HIS J 85 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA J 92 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG J 93 " --> pdb=" O LEU J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 124 Processing helix chain 'J' and resid 126 through 140 Processing helix chain 'J' and resid 147 through 162 Processing helix chain 'J' and resid 171 through 196 Processing helix chain 'J' and resid 212 through 220 Processing helix chain 'J' and resid 222 through 234 removed outlier: 4.074A pdb=" N ILE J 226 " --> pdb=" O PHE J 222 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE J 229 " --> pdb=" O ILE J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 251 removed outlier: 3.701A pdb=" N ILE J 248 " --> pdb=" O GLU J 244 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE J 249 " --> pdb=" O LEU J 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER J 250 " --> pdb=" O PHE J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 279 Processing helix chain 'L' and resid 52 through 62 Processing helix chain 'L' and resid 85 through 96 removed outlier: 3.965A pdb=" N LEU L 89 " --> pdb=" O HIS L 85 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA L 92 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG L 93 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN L 94 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 124 Processing helix chain 'L' and resid 126 through 140 Processing helix chain 'L' and resid 147 through 162 removed outlier: 3.853A pdb=" N ARG L 154 " --> pdb=" O GLY L 150 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE L 155 " --> pdb=" O HIS L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 196 Processing helix chain 'L' and resid 212 through 219 Processing helix chain 'L' and resid 220 through 222 No H-bonds generated for 'chain 'L' and resid 220 through 222' Processing helix chain 'L' and resid 223 through 233 removed outlier: 3.710A pdb=" N ASP L 227 " --> pdb=" O ARG L 223 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE L 229 " --> pdb=" O ILE L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 246 Processing helix chain 'L' and resid 247 through 249 No H-bonds generated for 'chain 'L' and resid 247 through 249' Processing helix chain 'L' and resid 262 through 279 Processing helix chain 'M' and resid 52 through 61 Processing helix chain 'M' and resid 85 through 96 removed outlier: 4.085A pdb=" N LEU M 89 " --> pdb=" O HIS M 85 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA M 92 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG M 93 " --> pdb=" O LEU M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 124 Processing helix chain 'M' and resid 126 through 140 Processing helix chain 'M' and resid 147 through 162 Processing helix chain 'M' and resid 171 through 196 Processing helix chain 'M' and resid 212 through 220 Processing helix chain 'M' and resid 222 through 234 removed outlier: 4.074A pdb=" N ILE M 226 " --> pdb=" O PHE M 222 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE M 229 " --> pdb=" O ILE M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 251 removed outlier: 3.701A pdb=" N ILE M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE M 249 " --> pdb=" O LEU M 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER M 250 " --> pdb=" O PHE M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 262 through 279 Processing helix chain 'O' and resid 52 through 62 Processing helix chain 'O' and resid 85 through 96 removed outlier: 3.965A pdb=" N LEU O 89 " --> pdb=" O HIS O 85 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA O 92 " --> pdb=" O SER O 88 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG O 93 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN O 94 " --> pdb=" O GLN O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 124 Processing helix chain 'O' and resid 126 through 140 Processing helix chain 'O' and resid 147 through 162 removed outlier: 3.852A pdb=" N ARG O 154 " --> pdb=" O GLY O 150 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE O 155 " --> pdb=" O HIS O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 196 Processing helix chain 'O' and resid 212 through 219 Processing helix chain 'O' and resid 220 through 222 No H-bonds generated for 'chain 'O' and resid 220 through 222' Processing helix chain 'O' and resid 223 through 233 removed outlier: 3.709A pdb=" N ASP O 227 " --> pdb=" O ARG O 223 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE O 229 " --> pdb=" O ILE O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 246 Processing helix chain 'O' and resid 247 through 249 No H-bonds generated for 'chain 'O' and resid 247 through 249' Processing helix chain 'O' and resid 262 through 279 Processing helix chain 'P' and resid 52 through 61 Processing helix chain 'P' and resid 85 through 96 removed outlier: 4.085A pdb=" N LEU P 89 " --> pdb=" O HIS P 85 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA P 92 " --> pdb=" O SER P 88 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG P 93 " --> pdb=" O LEU P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 124 Processing helix chain 'P' and resid 126 through 140 Processing helix chain 'P' and resid 147 through 162 Processing helix chain 'P' and resid 171 through 196 Processing helix chain 'P' and resid 212 through 220 Processing helix chain 'P' and resid 222 through 234 removed outlier: 4.074A pdb=" N ILE P 226 " --> pdb=" O PHE P 222 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE P 229 " --> pdb=" O ILE P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 251 removed outlier: 3.701A pdb=" N ILE P 248 " --> pdb=" O GLU P 244 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE P 249 " --> pdb=" O LEU P 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER P 250 " --> pdb=" O PHE P 246 " (cutoff:3.500A) Processing helix chain 'P' and resid 262 through 279 Processing helix chain 'R' and resid 52 through 62 Processing helix chain 'R' and resid 85 through 96 removed outlier: 3.965A pdb=" N LEU R 89 " --> pdb=" O HIS R 85 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA R 92 " --> pdb=" O SER R 88 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARG R 93 " --> pdb=" O LEU R 89 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN R 94 " --> pdb=" O GLN R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 124 Processing helix chain 'R' and resid 126 through 140 Processing helix chain 'R' and resid 147 through 162 removed outlier: 3.850A pdb=" N ARG R 154 " --> pdb=" O GLY R 150 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE R 155 " --> pdb=" O HIS R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 196 Processing helix chain 'R' and resid 212 through 219 Processing helix chain 'R' and resid 220 through 222 No H-bonds generated for 'chain 'R' and resid 220 through 222' Processing helix chain 'R' and resid 223 through 233 removed outlier: 3.709A pdb=" N ASP R 227 " --> pdb=" O ARG R 223 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE R 229 " --> pdb=" O ILE R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 247 removed outlier: 3.611A pdb=" N SER R 247 " --> pdb=" O LYS R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 279 Processing helix chain 'S' and resid 52 through 61 Processing helix chain 'S' and resid 85 through 96 removed outlier: 4.084A pdb=" N LEU S 89 " --> pdb=" O HIS S 85 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA S 92 " --> pdb=" O SER S 88 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG S 93 " --> pdb=" O LEU S 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 124 Processing helix chain 'S' and resid 126 through 140 Processing helix chain 'S' and resid 147 through 162 Processing helix chain 'S' and resid 171 through 196 Processing helix chain 'S' and resid 212 through 220 Processing helix chain 'S' and resid 222 through 234 removed outlier: 4.074A pdb=" N ILE S 226 " --> pdb=" O PHE S 222 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE S 229 " --> pdb=" O ILE S 225 " (cutoff:3.500A) Processing helix chain 'S' and resid 237 through 251 removed outlier: 3.701A pdb=" N ILE S 248 " --> pdb=" O GLU S 244 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE S 249 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER S 250 " --> pdb=" O PHE S 246 " (cutoff:3.500A) Processing helix chain 'S' and resid 262 through 279 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 62 removed outlier: 3.667A pdb=" N VAL A 167 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AA5, first strand: chain 'B' and resid 59 through 62 removed outlier: 6.634A pdb=" N THR B 18 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLU B 196 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 20 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 120 Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AA8, first strand: chain 'C' and resid 59 through 62 removed outlier: 3.667A pdb=" N VAL C 167 " --> pdb=" O ILE C 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AB1, first strand: chain 'D' and resid 59 through 62 removed outlier: 6.662A pdb=" N THR D 18 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLU D 196 " --> pdb=" O THR D 18 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU D 20 " --> pdb=" O GLU D 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 12 through 13 Processing sheet with id=AB3, first strand: chain 'E' and resid 59 through 62 removed outlier: 3.666A pdb=" N VAL E 167 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'F' and resid 12 through 13 Processing sheet with id=AB6, first strand: chain 'F' and resid 59 through 62 removed outlier: 6.648A pdb=" N THR F 18 " --> pdb=" O PHE F 194 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLU F 196 " --> pdb=" O THR F 18 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU F 20 " --> pdb=" O GLU F 196 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 119 through 120 Processing sheet with id=AB8, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AB9, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.667A pdb=" N VAL G 167 " --> pdb=" O ILE G 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AC2, first strand: chain 'H' and resid 59 through 62 removed outlier: 6.649A pdb=" N THR H 18 " --> pdb=" O PHE H 194 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLU H 196 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU H 20 " --> pdb=" O GLU H 196 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 5 through 9 removed outlier: 7.379A pdb=" N ARG I 5 " --> pdb=" O ASP I 39 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU I 41 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL I 7 " --> pdb=" O LEU I 41 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LEU I 43 " --> pdb=" O VAL I 7 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL I 9 " --> pdb=" O LEU I 43 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU I 64 " --> pdb=" O ASP I 39 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL I 65 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA I 76 " --> pdb=" O PHE I 67 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE J 67 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE J 77 " --> pdb=" O VAL J 65 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL J 65 " --> pdb=" O PHE J 77 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU J 64 " --> pdb=" O ASP J 39 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG J 5 " --> pdb=" O ASP J 39 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU J 41 " --> pdb=" O ARG J 5 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL J 7 " --> pdb=" O LEU J 41 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU J 43 " --> pdb=" O VAL J 7 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL J 9 " --> pdb=" O LEU J 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 14 through 18 Processing sheet with id=AC5, first strand: chain 'I' and resid 49 through 51 removed outlier: 3.701A pdb=" N LEU I 50 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU J 50 " --> pdb=" O LEU I 50 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER J 13 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR J 51 " --> pdb=" O SER J 13 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEU J 15 " --> pdb=" O THR J 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 252 through 254 Processing sheet with id=AC7, first strand: chain 'J' and resid 252 through 254 Processing sheet with id=AC8, first strand: chain 'L' and resid 5 through 9 removed outlier: 7.376A pdb=" N ARG L 5 " --> pdb=" O ASP L 39 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU L 41 " --> pdb=" O ARG L 5 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL L 7 " --> pdb=" O LEU L 41 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU L 43 " --> pdb=" O VAL L 7 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL L 9 " --> pdb=" O LEU L 43 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU L 64 " --> pdb=" O ASP L 39 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL L 65 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA L 76 " --> pdb=" O PHE L 67 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE M 67 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE M 77 " --> pdb=" O VAL M 65 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL M 65 " --> pdb=" O PHE M 77 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU M 64 " --> pdb=" O ASP M 39 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG M 5 " --> pdb=" O ASP M 39 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU M 41 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL M 7 " --> pdb=" O LEU M 41 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU M 43 " --> pdb=" O VAL M 7 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL M 9 " --> pdb=" O LEU M 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 14 through 18 Processing sheet with id=AD1, first strand: chain 'L' and resid 49 through 51 removed outlier: 3.652A pdb=" N LEU L 50 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU M 50 " --> pdb=" O LEU L 50 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER M 13 " --> pdb=" O VAL M 49 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N THR M 51 " --> pdb=" O SER M 13 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEU M 15 " --> pdb=" O THR M 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 252 through 254 Processing sheet with id=AD3, first strand: chain 'M' and resid 252 through 254 Processing sheet with id=AD4, first strand: chain 'O' and resid 5 through 9 removed outlier: 7.367A pdb=" N ARG O 5 " --> pdb=" O ASP O 39 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU O 41 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL O 7 " --> pdb=" O LEU O 41 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LEU O 43 " --> pdb=" O VAL O 7 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL O 9 " --> pdb=" O LEU O 43 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU O 64 " --> pdb=" O ASP O 39 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL O 65 " --> pdb=" O LEU O 78 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA O 76 " --> pdb=" O PHE O 67 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE P 67 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE P 77 " --> pdb=" O VAL P 65 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL P 65 " --> pdb=" O PHE P 77 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU P 64 " --> pdb=" O ASP P 39 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG P 5 " --> pdb=" O ASP P 39 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU P 41 " --> pdb=" O ARG P 5 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL P 7 " --> pdb=" O LEU P 41 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU P 43 " --> pdb=" O VAL P 7 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL P 9 " --> pdb=" O LEU P 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 14 through 18 Processing sheet with id=AD6, first strand: chain 'O' and resid 49 through 51 removed outlier: 3.716A pdb=" N LEU O 50 " --> pdb=" O LEU P 50 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU P 50 " --> pdb=" O LEU O 50 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER P 13 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR P 51 " --> pdb=" O SER P 13 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEU P 15 " --> pdb=" O THR P 51 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 252 through 254 Processing sheet with id=AD8, first strand: chain 'P' and resid 252 through 254 Processing sheet with id=AD9, first strand: chain 'R' and resid 5 through 9 removed outlier: 7.364A pdb=" N ARG R 5 " --> pdb=" O ASP R 39 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU R 41 " --> pdb=" O ARG R 5 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL R 7 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU R 43 " --> pdb=" O VAL R 7 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL R 9 " --> pdb=" O LEU R 43 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU R 64 " --> pdb=" O ASP R 39 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N VAL R 65 " --> pdb=" O LEU R 78 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA R 76 " --> pdb=" O PHE R 67 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE S 67 " --> pdb=" O THR S 75 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE S 77 " --> pdb=" O VAL S 65 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL S 65 " --> pdb=" O PHE S 77 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU S 64 " --> pdb=" O ASP S 39 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG S 5 " --> pdb=" O ASP S 39 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU S 41 " --> pdb=" O ARG S 5 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL S 7 " --> pdb=" O LEU S 41 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU S 43 " --> pdb=" O VAL S 7 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL S 9 " --> pdb=" O LEU S 43 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 14 through 18 Processing sheet with id=AE2, first strand: chain 'R' and resid 49 through 51 removed outlier: 3.646A pdb=" N LEU R 50 " --> pdb=" O LEU S 50 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU S 50 " --> pdb=" O LEU R 50 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER S 13 " --> pdb=" O VAL S 49 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR S 51 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LEU S 15 " --> pdb=" O THR S 51 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 252 through 254 Processing sheet with id=AE4, first strand: chain 'S' and resid 252 through 254 1816 hydrogen bonds defined for protein. 5304 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 13.80 Time building geometry restraints manager: 14.37 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: 9954 1.34 - 1.45: 5479 1.45 - 1.57: 19657 1.57 - 1.69: 98 1.69 - 1.81: 232 Bond restraints: 35420 Sorted by residual: bond pdb=" N ASN I 62 " pdb=" CA ASN I 62 " ideal model delta sigma weight residual 1.458 1.474 -0.016 1.37e-02 5.33e+03 1.29e+00 bond pdb=" N ASN L 62 " pdb=" CA ASN L 62 " ideal model delta sigma weight residual 1.458 1.474 -0.015 1.37e-02 5.33e+03 1.26e+00 bond pdb=" N ASN R 62 " pdb=" CA ASN R 62 " ideal model delta sigma weight residual 1.458 1.473 -0.015 1.37e-02 5.33e+03 1.17e+00 bond pdb=" N ASN O 62 " pdb=" CA ASN O 62 " ideal model delta sigma weight residual 1.458 1.473 -0.015 1.37e-02 5.33e+03 1.12e+00 bond pdb=" N LYS I 204 " pdb=" CA LYS I 204 " ideal model delta sigma weight residual 1.459 1.448 0.011 1.23e-02 6.61e+03 8.38e-01 ... (remaining 35415 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.12: 843 107.12 - 113.83: 20057 113.83 - 120.54: 14517 120.54 - 127.25: 12396 127.25 - 133.95: 286 Bond angle restraints: 48099 Sorted by residual: angle pdb=" N ALA I 206 " pdb=" CA ALA I 206 " pdb=" C ALA I 206 " ideal model delta sigma weight residual 111.28 117.99 -6.71 1.09e+00 8.42e-01 3.79e+01 angle pdb=" N ALA L 206 " pdb=" CA ALA L 206 " pdb=" C ALA L 206 " ideal model delta sigma weight residual 111.28 117.96 -6.68 1.09e+00 8.42e-01 3.75e+01 angle pdb=" N ALA O 206 " pdb=" CA ALA O 206 " pdb=" C ALA O 206 " ideal model delta sigma weight residual 111.28 117.94 -6.66 1.09e+00 8.42e-01 3.73e+01 angle pdb=" N ALA R 206 " pdb=" CA ALA R 206 " pdb=" C ALA R 206 " ideal model delta sigma weight residual 111.28 117.84 -6.56 1.09e+00 8.42e-01 3.63e+01 angle pdb=" N ASN S 207 " pdb=" CA ASN S 207 " pdb=" C ASN S 207 " ideal model delta sigma weight residual 111.28 116.43 -5.15 1.09e+00 8.42e-01 2.23e+01 ... (remaining 48094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 20041 16.14 - 32.27: 889 32.27 - 48.41: 322 48.41 - 64.54: 102 64.54 - 80.68: 8 Dihedral angle restraints: 21362 sinusoidal: 9146 harmonic: 12216 Sorted by residual: dihedral pdb=" CA ASP M 69 " pdb=" CB ASP M 69 " pdb=" CG ASP M 69 " pdb=" OD1 ASP M 69 " ideal model delta sinusoidal sigma weight residual -30.00 -89.74 59.74 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP P 69 " pdb=" CB ASP P 69 " pdb=" CG ASP P 69 " pdb=" OD1 ASP P 69 " ideal model delta sinusoidal sigma weight residual -30.00 -89.71 59.71 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP J 69 " pdb=" CB ASP J 69 " pdb=" CG ASP J 69 " pdb=" OD1 ASP J 69 " ideal model delta sinusoidal sigma weight residual -30.00 -89.67 59.67 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 21359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4505 0.045 - 0.091: 747 0.091 - 0.136: 293 0.136 - 0.181: 11 0.181 - 0.227: 4 Chirality restraints: 5560 Sorted by residual: chirality pdb=" CA ALA I 206 " pdb=" N ALA I 206 " pdb=" C ALA I 206 " pdb=" CB ALA I 206 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ALA L 206 " pdb=" N ALA L 206 " pdb=" C ALA L 206 " pdb=" CB ALA L 206 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ALA O 206 " pdb=" N ALA O 206 " pdb=" C ALA O 206 " pdb=" CB ALA O 206 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 5557 not shown) Planarity restraints: 5886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 203 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.27e+00 pdb=" C LEU I 203 " -0.019 2.00e-02 2.50e+03 pdb=" O LEU I 203 " 0.007 2.00e-02 2.50e+03 pdb=" N LYS I 204 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 215 " -0.018 5.00e-02 4.00e+02 2.79e-02 1.25e+00 pdb=" N PRO B 216 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 216 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 216 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET F 215 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.23e+00 pdb=" N PRO F 216 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO F 216 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 216 " -0.015 5.00e-02 4.00e+02 ... (remaining 5883 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2883 2.74 - 3.28: 35522 3.28 - 3.82: 56752 3.82 - 4.36: 69125 4.36 - 4.90: 117999 Nonbonded interactions: 282281 Sorted by model distance: nonbonded pdb=" O ARG M 5 " pdb=" N ASP M 39 " model vdw 2.203 2.520 nonbonded pdb=" O ARG S 5 " pdb=" N ASP S 39 " model vdw 2.204 2.520 nonbonded pdb=" O ARG J 5 " pdb=" N ASP J 39 " model vdw 2.204 2.520 nonbonded pdb=" O ARG P 5 " pdb=" N ASP P 39 " model vdw 2.205 2.520 nonbonded pdb=" O LEU O 183 " pdb=" OG SER O 186 " model vdw 2.272 2.440 ... (remaining 282276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 218 or resid 501)) selection = chain 'C' selection = (chain 'D' and (resid 1 through 218 or resid 501)) selection = chain 'E' selection = (chain 'F' and (resid 1 through 218 or resid 501)) selection = chain 'G' selection = (chain 'H' and (resid 1 through 218 or resid 501)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 7.500 Check model and map are aligned: 0.570 Set scattering table: 0.360 Process input model: 98.840 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 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 : 0.002 0.023 35420 Z= 0.107 Angle : 0.424 6.708 48099 Z= 0.267 Chirality : 0.039 0.227 5560 Planarity : 0.002 0.028 5886 Dihedral : 11.229 80.681 13418 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.17 % Favored : 97.73 % Rotamer: Outliers : 0.73 % Allowed : 3.15 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.11), residues: 4048 helix: -1.07 (0.10), residues: 1972 sheet: 0.03 (0.18), residues: 660 loop : -0.42 (0.14), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP S 4 HIS 0.002 0.000 HIS P 12 PHE 0.009 0.001 PHE D 5 TYR 0.006 0.001 TYR J 156 ARG 0.003 0.000 ARG I 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 385 time to evaluate : 4.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8190 (p) REVERT: A 162 ARG cc_start: 0.9003 (mmm-85) cc_final: 0.8758 (mmm-85) REVERT: A 217 TYR cc_start: 0.7422 (t80) cc_final: 0.7019 (t80) REVERT: B 217 TYR cc_start: 0.8703 (t80) cc_final: 0.8315 (t80) REVERT: C 72 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8196 (p) REVERT: C 215 MET cc_start: 0.8694 (ptm) cc_final: 0.8468 (ppp) REVERT: E 72 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.8063 (p) REVERT: E 122 ASP cc_start: 0.9305 (OUTLIER) cc_final: 0.9060 (p0) REVERT: E 160 LYS cc_start: 0.9586 (mttt) cc_final: 0.9281 (tppt) REVERT: E 210 LYS cc_start: 0.9565 (pttt) cc_final: 0.9310 (mmtt) REVERT: G 120 GLU cc_start: 0.9382 (tt0) cc_final: 0.9023 (tm-30) REVERT: H 52 ARG cc_start: 0.9280 (ttt90) cc_final: 0.9076 (ptm-80) REVERT: H 122 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8620 (p0) REVERT: I 151 HIS cc_start: 0.9484 (m90) cc_final: 0.9274 (t-170) REVERT: J 260 MET cc_start: 0.7961 (mtp) cc_final: 0.7132 (mtt) REVERT: M 19 ASN cc_start: 0.9663 (m110) cc_final: 0.9392 (t0) REVERT: O 163 ASN cc_start: 0.9507 (m-40) cc_final: 0.9248 (t0) REVERT: R 41 LEU cc_start: 0.9677 (tp) cc_final: 0.9371 (mm) REVERT: R 237 ASN cc_start: 0.9569 (m-40) cc_final: 0.9297 (p0) REVERT: S 279 GLN cc_start: 0.9266 (mm-40) cc_final: 0.9021 (pt0) outliers start: 28 outliers final: 7 residues processed: 412 average time/residue: 0.5336 time to fit residues: 337.4021 Evaluate side-chains 198 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 186 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain J residue 82 TYR Chi-restraints excluded: chain M residue 82 TYR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 82 TYR Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 82 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 6.9990 chunk 303 optimal weight: 40.0000 chunk 168 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 204 optimal weight: 20.0000 chunk 161 optimal weight: 1.9990 chunk 313 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 233 optimal weight: 20.0000 chunk 363 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 86 GLN A 153 GLN C 71 ASN C 86 GLN C 153 GLN D 180 GLN E 71 ASN E 86 GLN E 153 GLN F 86 GLN F 180 GLN G 71 ASN G 86 GLN G 153 GLN H 180 GLN I 12 HIS I 90 GLN I 138 HIS I 211 GLN ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 HIS ** J 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 233 ASN J 236 ASN L 12 HIS L 90 GLN L 174 ASN L 211 GLN L 233 ASN M 12 HIS M 62 ASN M 138 HIS ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 233 ASN M 236 ASN ** O 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN O 211 GLN P 12 HIS P 62 ASN P 138 HIS ** P 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 233 ASN P 236 ASN ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS R 19 ASN R 90 GLN ** R 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 12 HIS ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 HIS S 174 ASN ** S 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 232 GLN S 233 ASN S 236 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 35420 Z= 0.305 Angle : 0.592 7.983 48099 Z= 0.309 Chirality : 0.040 0.199 5560 Planarity : 0.004 0.048 5886 Dihedral : 12.388 58.012 5056 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.14 % Favored : 98.76 % Rotamer: Outliers : 1.07 % Allowed : 7.38 % Favored : 91.55 % 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: 0.71 (0.12), residues: 4048 helix: 1.09 (0.11), residues: 2012 sheet: 0.24 (0.20), residues: 660 loop : -0.17 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 106 HIS 0.005 0.001 HIS M 34 PHE 0.031 0.002 PHE R 246 TYR 0.017 0.001 TYR P 261 ARG 0.008 0.001 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 180 time to evaluate : 4.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8392 (p) REVERT: B 217 TYR cc_start: 0.8719 (t80) cc_final: 0.8274 (t80) REVERT: C 72 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8350 (p) REVERT: C 215 MET cc_start: 0.8772 (ptm) cc_final: 0.8554 (ppp) REVERT: E 160 LYS cc_start: 0.9632 (mttt) cc_final: 0.9308 (tppt) REVERT: E 210 LYS cc_start: 0.9620 (pttt) cc_final: 0.9409 (mmtt) REVERT: F 55 ARG cc_start: 0.9338 (mmm-85) cc_final: 0.8914 (mtm-85) REVERT: G 120 GLU cc_start: 0.9235 (tt0) cc_final: 0.8825 (tm-30) REVERT: I 187 MET cc_start: 0.9086 (mtp) cc_final: 0.8883 (ttt) REVERT: R 41 LEU cc_start: 0.9620 (tp) cc_final: 0.9331 (mm) REVERT: R 237 ASN cc_start: 0.9583 (m-40) cc_final: 0.9283 (p0) REVERT: S 279 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8930 (pt0) outliers start: 41 outliers final: 24 residues processed: 213 average time/residue: 0.5053 time to fit residues: 171.8331 Evaluate side-chains 183 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 4.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 82 TYR Chi-restraints excluded: chain J residue 197 CYS Chi-restraints excluded: chain J residue 198 MET Chi-restraints excluded: chain L residue 127 PHE Chi-restraints excluded: chain M residue 82 TYR Chi-restraints excluded: chain O residue 205 HIS Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 82 TYR Chi-restraints excluded: chain P residue 131 GLN Chi-restraints excluded: chain P residue 245 LEU Chi-restraints excluded: chain S residue 82 TYR Chi-restraints excluded: chain S residue 137 TYR Chi-restraints excluded: chain T residue 108 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 201 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 302 optimal weight: 30.0000 chunk 247 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 363 optimal weight: 7.9990 chunk 393 optimal weight: 10.0000 chunk 324 optimal weight: 4.9990 chunk 360 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 291 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 ASN ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 HIS ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 GLN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 HIS O 138 HIS O 163 ASN ** P 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 279 GLN ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 35420 Z= 0.396 Angle : 0.628 9.333 48099 Z= 0.326 Chirality : 0.041 0.170 5560 Planarity : 0.004 0.045 5886 Dihedral : 12.866 62.970 5049 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.80 % Favored : 98.10 % Rotamer: Outliers : 1.59 % Allowed : 7.40 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.13), residues: 4048 helix: 1.77 (0.11), residues: 2060 sheet: 0.13 (0.20), residues: 656 loop : -0.15 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 4 HIS 0.010 0.002 HIS I 151 PHE 0.026 0.002 PHE R 209 TYR 0.032 0.002 TYR E 121 ARG 0.008 0.001 ARG P 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 150 time to evaluate : 4.205 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: A 72 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8439 (p) REVERT: C 72 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8432 (p) REVERT: C 215 MET cc_start: 0.8690 (ptm) cc_final: 0.8460 (ppp) REVERT: E 160 LYS cc_start: 0.9639 (mttt) cc_final: 0.9285 (tppt) REVERT: F 55 ARG cc_start: 0.9478 (mmm-85) cc_final: 0.9231 (mtm-85) REVERT: G 209 ASP cc_start: 0.9335 (OUTLIER) cc_final: 0.9084 (t70) REVERT: M 133 ILE cc_start: 0.5075 (OUTLIER) cc_final: 0.4665 (tt) REVERT: M 198 MET cc_start: 0.8034 (mmp) cc_final: 0.7368 (mmt) REVERT: R 41 LEU cc_start: 0.9660 (tp) cc_final: 0.9363 (mm) REVERT: R 198 MET cc_start: 0.8793 (mmm) cc_final: 0.8400 (mtm) REVERT: R 237 ASN cc_start: 0.9580 (m-40) cc_final: 0.9320 (p0) REVERT: S 134 MET cc_start: 0.8280 (ppp) cc_final: 0.7978 (ppp) outliers start: 61 outliers final: 25 residues processed: 202 average time/residue: 0.4510 time to fit residues: 151.9481 Evaluate side-chains 163 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 4.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain J residue 197 CYS Chi-restraints excluded: chain J residue 198 MET Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 82 TYR Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 197 CYS Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 82 TYR Chi-restraints excluded: chain S residue 137 TYR Chi-restraints excluded: chain S residue 235 HIS Chi-restraints excluded: chain T residue 108 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 359 optimal weight: 20.0000 chunk 273 optimal weight: 20.0000 chunk 188 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 chunk 365 optimal weight: 30.0000 chunk 386 optimal weight: 7.9990 chunk 190 optimal weight: 30.0000 chunk 346 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN D 180 GLN F 180 GLN G 71 ASN G 218 ASN ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 233 ASN ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 ASN ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 GLN ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 233 ASN ** P 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 35420 Z= 0.383 Angle : 0.605 11.468 48099 Z= 0.312 Chirality : 0.040 0.211 5560 Planarity : 0.003 0.057 5886 Dihedral : 13.012 63.038 5045 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.83 % Favored : 98.07 % Rotamer: Outliers : 1.88 % Allowed : 8.52 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.13), residues: 4048 helix: 2.00 (0.11), residues: 2044 sheet: -0.01 (0.20), residues: 656 loop : -0.17 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 106 HIS 0.008 0.001 HIS O 151 PHE 0.020 0.002 PHE M 24 TYR 0.025 0.002 TYR B 121 ARG 0.007 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 135 time to evaluate : 3.902 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: A 72 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8432 (p) REVERT: C 72 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8362 (p) REVERT: C 209 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8733 (t70) REVERT: C 215 MET cc_start: 0.8578 (ptm) cc_final: 0.8326 (ppp) REVERT: F 39 ASP cc_start: 0.9706 (OUTLIER) cc_final: 0.9426 (p0) REVERT: F 55 ARG cc_start: 0.9477 (mmm-85) cc_final: 0.9204 (mtm-85) REVERT: F 149 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: G 109 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8573 (mmp) REVERT: G 209 ASP cc_start: 0.9340 (OUTLIER) cc_final: 0.9099 (t70) REVERT: J 260 MET cc_start: 0.7747 (mtm) cc_final: 0.7381 (mtp) REVERT: M 133 ILE cc_start: 0.5015 (OUTLIER) cc_final: 0.4776 (tt) REVERT: M 203 LEU cc_start: 0.8354 (tp) cc_final: 0.8069 (tt) REVERT: O 219 MET cc_start: 0.8066 (ppp) cc_final: 0.7812 (pmm) REVERT: R 41 LEU cc_start: 0.9664 (tp) cc_final: 0.9344 (mm) REVERT: R 198 MET cc_start: 0.8668 (mmm) cc_final: 0.8326 (mtm) REVERT: R 236 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7130 (m110) REVERT: R 237 ASN cc_start: 0.9593 (m-40) cc_final: 0.9368 (p0) REVERT: S 134 MET cc_start: 0.8521 (ppp) cc_final: 0.8203 (ppp) outliers start: 72 outliers final: 30 residues processed: 199 average time/residue: 0.4497 time to fit residues: 148.5204 Evaluate side-chains 168 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 149 PHE Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 210 LYS Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 197 CYS Chi-restraints excluded: chain R residue 236 ASN Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 137 TYR Chi-restraints excluded: chain S residue 235 HIS Chi-restraints excluded: chain T residue 108 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 322 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 287 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 329 optimal weight: 20.0000 chunk 267 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 197 optimal weight: 9.9990 chunk 347 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 180 GLN G 218 ASN ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 GLN ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 35420 Z= 0.217 Angle : 0.516 12.973 48099 Z= 0.271 Chirality : 0.039 0.164 5560 Planarity : 0.003 0.038 5886 Dihedral : 12.953 64.333 5041 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.90 % Favored : 98.00 % Rotamer: Outliers : 1.54 % Allowed : 9.15 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.13), residues: 4048 helix: 2.31 (0.11), residues: 2052 sheet: 0.09 (0.21), residues: 656 loop : -0.09 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 106 HIS 0.010 0.001 HIS O 151 PHE 0.025 0.001 PHE R 209 TYR 0.014 0.001 TYR B 121 ARG 0.003 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 136 time to evaluate : 4.755 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: A 72 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8525 (p) REVERT: C 72 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8383 (p) REVERT: C 209 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8719 (t70) REVERT: C 215 MET cc_start: 0.8600 (ptm) cc_final: 0.8349 (ppp) REVERT: F 55 ARG cc_start: 0.9480 (mmm-85) cc_final: 0.9260 (mtm-85) REVERT: G 209 ASP cc_start: 0.9367 (OUTLIER) cc_final: 0.9110 (t70) REVERT: J 260 MET cc_start: 0.7794 (mtm) cc_final: 0.7291 (mtm) REVERT: M 203 LEU cc_start: 0.8340 (tp) cc_final: 0.8062 (tt) REVERT: O 219 MET cc_start: 0.8092 (ppp) cc_final: 0.7834 (pmm) REVERT: P 86 ASP cc_start: 0.9464 (OUTLIER) cc_final: 0.8958 (t0) REVERT: R 41 LEU cc_start: 0.9678 (tp) cc_final: 0.9399 (mm) REVERT: R 198 MET cc_start: 0.8666 (mmm) cc_final: 0.8353 (mtm) REVERT: R 237 ASN cc_start: 0.9596 (m-40) cc_final: 0.9382 (p0) REVERT: S 32 MET cc_start: 0.9251 (ttp) cc_final: 0.9041 (tmm) REVERT: S 134 MET cc_start: 0.8494 (ppp) cc_final: 0.8200 (ppp) outliers start: 59 outliers final: 39 residues processed: 188 average time/residue: 0.4560 time to fit residues: 143.5812 Evaluate side-chains 172 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 4.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 149 PHE Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 156 LYS Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 260 MET Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 85 HIS Chi-restraints excluded: chain M residue 226 ILE Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 197 CYS Chi-restraints excluded: chain S residue 137 TYR Chi-restraints excluded: chain S residue 235 HIS Chi-restraints excluded: chain T residue 108 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 130 optimal weight: 0.1980 chunk 348 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 387 optimal weight: 30.0000 chunk 321 optimal weight: 9.9990 chunk 179 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 180 GLN G 218 ASN I 85 HIS ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 232 GLN ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 35420 Z= 0.294 Angle : 0.558 13.890 48099 Z= 0.287 Chirality : 0.039 0.166 5560 Planarity : 0.003 0.039 5886 Dihedral : 12.920 65.352 5041 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.25 % Favored : 97.65 % Rotamer: Outliers : 1.96 % Allowed : 9.38 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.13), residues: 4048 helix: 2.42 (0.11), residues: 2032 sheet: 0.03 (0.21), residues: 656 loop : -0.08 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 106 HIS 0.010 0.001 HIS O 151 PHE 0.019 0.001 PHE M 24 TYR 0.023 0.001 TYR B 121 ARG 0.003 0.000 ARG F 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 129 time to evaluate : 3.384 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: A 72 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8528 (p) REVERT: C 72 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8394 (p) REVERT: C 209 ASP cc_start: 0.9107 (OUTLIER) cc_final: 0.8670 (t70) REVERT: C 215 MET cc_start: 0.8530 (ptm) cc_final: 0.8278 (ppp) REVERT: F 39 ASP cc_start: 0.9705 (OUTLIER) cc_final: 0.9431 (p0) REVERT: F 55 ARG cc_start: 0.9487 (mmm-85) cc_final: 0.9248 (mtm-85) REVERT: F 149 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8183 (m-80) REVERT: J 260 MET cc_start: 0.7777 (mtm) cc_final: 0.7411 (mtp) REVERT: M 198 MET cc_start: 0.7778 (mmt) cc_final: 0.7539 (mmp) REVERT: P 86 ASP cc_start: 0.9406 (OUTLIER) cc_final: 0.8853 (t0) REVERT: R 41 LEU cc_start: 0.9672 (tp) cc_final: 0.9379 (mm) REVERT: R 198 MET cc_start: 0.8634 (mmm) cc_final: 0.8314 (mtm) REVERT: R 237 ASN cc_start: 0.9585 (m-40) cc_final: 0.9383 (p0) REVERT: R 260 MET cc_start: 0.6590 (ttp) cc_final: 0.6326 (tmm) REVERT: S 134 MET cc_start: 0.8336 (ppp) cc_final: 0.8068 (ppp) outliers start: 75 outliers final: 49 residues processed: 195 average time/residue: 0.4513 time to fit residues: 147.6343 Evaluate side-chains 182 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 127 time to evaluate : 4.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 149 PHE Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 149 PHE Chi-restraints excluded: chain F residue 156 LYS Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 149 PHE Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain L residue 260 MET Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 85 HIS Chi-restraints excluded: chain M residue 226 ILE Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 137 TYR Chi-restraints excluded: chain T residue 108 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 373 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 220 optimal weight: 7.9990 chunk 282 optimal weight: 0.5980 chunk 218 optimal weight: 6.9990 chunk 325 optimal weight: 30.0000 chunk 216 optimal weight: 20.0000 chunk 385 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 235 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 264 ASN ** L 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 ASN ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 35420 Z= 0.333 Angle : 0.590 15.159 48099 Z= 0.302 Chirality : 0.040 0.172 5560 Planarity : 0.003 0.043 5886 Dihedral : 13.048 67.782 5041 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.59 % Favored : 97.31 % Rotamer: Outliers : 2.06 % Allowed : 9.49 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.13), residues: 4048 helix: 2.39 (0.11), residues: 2032 sheet: -0.07 (0.21), residues: 652 loop : -0.13 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 106 HIS 0.010 0.001 HIS O 151 PHE 0.018 0.001 PHE M 24 TYR 0.033 0.002 TYR B 121 ARG 0.003 0.000 ARG S 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 130 time to evaluate : 3.848 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: A 72 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8447 (p) REVERT: A 209 ASP cc_start: 0.9552 (OUTLIER) cc_final: 0.9206 (p0) REVERT: C 209 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8647 (t70) REVERT: C 211 ASP cc_start: 0.9674 (OUTLIER) cc_final: 0.9437 (m-30) REVERT: F 55 ARG cc_start: 0.9498 (mmm-85) cc_final: 0.9292 (mtm-85) REVERT: F 149 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: J 260 MET cc_start: 0.8066 (mtm) cc_final: 0.7749 (mtp) REVERT: M 203 LEU cc_start: 0.8188 (tp) cc_final: 0.7962 (tt) REVERT: O 219 MET cc_start: 0.8058 (ppp) cc_final: 0.7851 (pmm) REVERT: P 86 ASP cc_start: 0.9385 (OUTLIER) cc_final: 0.8751 (t0) REVERT: R 41 LEU cc_start: 0.9687 (tp) cc_final: 0.9388 (mm) REVERT: R 198 MET cc_start: 0.8660 (mmm) cc_final: 0.8351 (mtm) REVERT: R 260 MET cc_start: 0.6686 (ttp) cc_final: 0.6457 (tmm) REVERT: S 32 MET cc_start: 0.9260 (ttp) cc_final: 0.9001 (tmm) REVERT: S 134 MET cc_start: 0.8286 (ppp) cc_final: 0.8029 (ppp) outliers start: 79 outliers final: 50 residues processed: 199 average time/residue: 0.4499 time to fit residues: 149.6170 Evaluate side-chains 178 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 122 time to evaluate : 4.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 149 PHE Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 149 PHE Chi-restraints excluded: chain F residue 156 LYS Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 210 LYS Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 149 PHE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain L residue 260 MET Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 85 HIS Chi-restraints excluded: chain M residue 226 ILE Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 137 TYR Chi-restraints excluded: chain T residue 108 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 238 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 chunk 230 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 75 optimal weight: 0.0670 chunk 74 optimal weight: 0.5980 chunk 245 optimal weight: 40.0000 chunk 262 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 303 optimal weight: 3.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 213 ASN ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35420 Z= 0.135 Angle : 0.517 15.457 48099 Z= 0.267 Chirality : 0.039 0.180 5560 Planarity : 0.003 0.042 5886 Dihedral : 12.910 68.862 5040 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.08 % Favored : 97.83 % Rotamer: Outliers : 1.09 % Allowed : 10.58 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.13), residues: 4048 helix: 2.61 (0.11), residues: 2032 sheet: 0.04 (0.21), residues: 656 loop : -0.13 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 106 HIS 0.010 0.001 HIS O 151 PHE 0.018 0.001 PHE J 24 TYR 0.014 0.001 TYR B 121 ARG 0.004 0.000 ARG R 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 130 time to evaluate : 4.276 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: A 72 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8471 (p) REVERT: A 209 ASP cc_start: 0.9553 (OUTLIER) cc_final: 0.9262 (p0) REVERT: F 55 ARG cc_start: 0.9479 (mmm-85) cc_final: 0.9272 (mtm-85) REVERT: J 260 MET cc_start: 0.8095 (mtm) cc_final: 0.7815 (mtp) REVERT: M 203 LEU cc_start: 0.8194 (tp) cc_final: 0.7953 (tt) REVERT: P 32 MET cc_start: 0.9174 (ttp) cc_final: 0.8971 (tmm) REVERT: P 86 ASP cc_start: 0.9459 (OUTLIER) cc_final: 0.8920 (t0) REVERT: P 187 MET cc_start: 0.9455 (mtp) cc_final: 0.9234 (mtm) REVERT: P 198 MET cc_start: 0.6904 (mmp) cc_final: 0.6312 (mmp) REVERT: R 41 LEU cc_start: 0.9646 (tp) cc_final: 0.9316 (mm) REVERT: R 198 MET cc_start: 0.8636 (mmm) cc_final: 0.8314 (mtm) REVERT: R 260 MET cc_start: 0.6727 (ttp) cc_final: 0.6472 (tmm) REVERT: S 32 MET cc_start: 0.9288 (ttp) cc_final: 0.9013 (tmm) REVERT: S 134 MET cc_start: 0.8277 (ppp) cc_final: 0.8011 (ppp) outliers start: 42 outliers final: 28 residues processed: 166 average time/residue: 0.4731 time to fit residues: 131.8828 Evaluate side-chains 159 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 4.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 149 PHE Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 156 LYS Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 149 PHE Chi-restraints excluded: chain L residue 260 MET Chi-restraints excluded: chain M residue 85 HIS Chi-restraints excluded: chain M residue 226 ILE Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain S residue 137 TYR Chi-restraints excluded: chain T residue 108 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 350 optimal weight: 10.0000 chunk 369 optimal weight: 0.7980 chunk 336 optimal weight: 10.0000 chunk 359 optimal weight: 30.0000 chunk 216 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 282 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 324 optimal weight: 20.0000 chunk 339 optimal weight: 6.9990 chunk 358 optimal weight: 10.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 35420 Z= 0.258 Angle : 0.574 16.017 48099 Z= 0.291 Chirality : 0.039 0.206 5560 Planarity : 0.003 0.044 5886 Dihedral : 12.851 69.140 5040 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.45 % Favored : 97.46 % Rotamer: Outliers : 1.36 % Allowed : 10.51 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.13), residues: 4048 helix: 2.60 (0.11), residues: 2032 sheet: 0.01 (0.21), residues: 656 loop : -0.16 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 106 HIS 0.010 0.001 HIS O 151 PHE 0.018 0.001 PHE M 24 TYR 0.028 0.001 TYR B 121 ARG 0.002 0.000 ARG H 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 126 time to evaluate : 4.285 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: A 72 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8461 (p) REVERT: A 209 ASP cc_start: 0.9548 (OUTLIER) cc_final: 0.9229 (p0) REVERT: C 209 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8711 (t70) REVERT: F 55 ARG cc_start: 0.9492 (mmm-85) cc_final: 0.9282 (mtm-85) REVERT: F 149 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8177 (m-80) REVERT: J 260 MET cc_start: 0.8101 (mtm) cc_final: 0.7821 (mtp) REVERT: P 86 ASP cc_start: 0.9420 (OUTLIER) cc_final: 0.8829 (t0) REVERT: P 187 MET cc_start: 0.9464 (mtp) cc_final: 0.9240 (mtm) REVERT: P 198 MET cc_start: 0.6980 (mmp) cc_final: 0.6444 (mmp) REVERT: R 41 LEU cc_start: 0.9665 (tp) cc_final: 0.9335 (mm) REVERT: R 198 MET cc_start: 0.8653 (mmm) cc_final: 0.8336 (mtm) REVERT: R 260 MET cc_start: 0.6812 (ttp) cc_final: 0.6551 (tmm) REVERT: S 134 MET cc_start: 0.8239 (ppp) cc_final: 0.7983 (ppp) outliers start: 52 outliers final: 36 residues processed: 172 average time/residue: 0.4419 time to fit residues: 128.0421 Evaluate side-chains 164 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 123 time to evaluate : 4.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 149 PHE Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 149 PHE Chi-restraints excluded: chain F residue 156 LYS Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 149 PHE Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain L residue 260 MET Chi-restraints excluded: chain M residue 85 HIS Chi-restraints excluded: chain M residue 226 ILE Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 137 TYR Chi-restraints excluded: chain T residue 108 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 235 optimal weight: 9.9990 chunk 379 optimal weight: 30.0000 chunk 231 optimal weight: 5.9990 chunk 180 optimal weight: 20.0000 chunk 264 optimal weight: 10.0000 chunk 398 optimal weight: 10.0000 chunk 366 optimal weight: 20.0000 chunk 317 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 35420 Z= 0.348 Angle : 0.636 15.634 48099 Z= 0.320 Chirality : 0.040 0.192 5560 Planarity : 0.003 0.050 5886 Dihedral : 12.981 70.959 5040 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.69 % Favored : 97.21 % Rotamer: Outliers : 1.25 % Allowed : 10.74 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.13), residues: 4048 helix: 2.48 (0.11), residues: 2032 sheet: -0.07 (0.21), residues: 644 loop : -0.20 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP S 106 HIS 0.010 0.001 HIS O 151 PHE 0.019 0.001 PHE M 24 TYR 0.029 0.001 TYR B 121 ARG 0.003 0.000 ARG H 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 123 time to evaluate : 4.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8416 (p) REVERT: A 209 ASP cc_start: 0.9524 (OUTLIER) cc_final: 0.9123 (p0) REVERT: F 55 ARG cc_start: 0.9488 (mmm-85) cc_final: 0.9249 (mtm-85) REVERT: F 149 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: J 260 MET cc_start: 0.8167 (mtm) cc_final: 0.7913 (mtp) REVERT: P 86 ASP cc_start: 0.9414 (OUTLIER) cc_final: 0.8772 (t0) REVERT: P 198 MET cc_start: 0.7221 (mmp) cc_final: 0.6688 (mmt) REVERT: R 41 LEU cc_start: 0.9681 (tp) cc_final: 0.9363 (mm) REVERT: R 198 MET cc_start: 0.8586 (mmm) cc_final: 0.8300 (mtm) REVERT: R 260 MET cc_start: 0.6799 (ttp) cc_final: 0.6549 (tmm) REVERT: S 32 MET cc_start: 0.9272 (ttp) cc_final: 0.9015 (tmm) REVERT: S 134 MET cc_start: 0.8140 (ppp) cc_final: 0.7902 (ppp) outliers start: 48 outliers final: 39 residues processed: 167 average time/residue: 0.4606 time to fit residues: 129.4670 Evaluate side-chains 162 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 119 time to evaluate : 4.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 149 PHE Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 149 PHE Chi-restraints excluded: chain F residue 156 LYS Chi-restraints excluded: chain F residue 210 LYS Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 149 PHE Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain L residue 135 GLU Chi-restraints excluded: chain L residue 260 MET Chi-restraints excluded: chain M residue 85 HIS Chi-restraints excluded: chain M residue 226 ILE Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 137 TYR Chi-restraints excluded: chain T residue 108 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 252 optimal weight: 5.9990 chunk 338 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 292 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 317 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 326 optimal weight: 30.0000 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.060925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.038600 restraints weight = 216952.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.039794 restraints weight = 112059.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.040548 restraints weight = 74451.404| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35420 Z= 0.207 Angle : 0.563 15.427 48099 Z= 0.286 Chirality : 0.039 0.199 5560 Planarity : 0.003 0.051 5886 Dihedral : 12.958 72.026 5040 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.40 % Favored : 97.50 % Rotamer: Outliers : 1.15 % Allowed : 10.87 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.13), residues: 4048 helix: 2.59 (0.11), residues: 2032 sheet: -0.02 (0.21), residues: 644 loop : -0.20 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 97 HIS 0.010 0.001 HIS O 151 PHE 0.018 0.001 PHE M 24 TYR 0.029 0.001 TYR A 121 ARG 0.003 0.000 ARG J 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5356.17 seconds wall clock time: 99 minutes 48.06 seconds (5988.06 seconds total)