Starting phenix.real_space_refine on Mon Mar 25 16:32:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ueg_26474/03_2024/7ueg_26474.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ueg_26474/03_2024/7ueg_26474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ueg_26474/03_2024/7ueg_26474.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ueg_26474/03_2024/7ueg_26474.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ueg_26474/03_2024/7ueg_26474.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ueg_26474/03_2024/7ueg_26474.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 32040 2.51 5 N 7848 2.21 5 O 9972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ASP 50": "OD1" <-> "OD2" Residue "G ASP 57": "OD1" <-> "OD2" Residue "G PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 186": "OD1" <-> "OD2" Residue "I PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 186": "OD1" <-> "OD2" Residue "M ASP 50": "OD1" <-> "OD2" Residue "M ASP 57": "OD1" <-> "OD2" Residue "M PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 186": "OD1" <-> "OD2" Residue "O PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 186": "OD1" <-> "OD2" Residue "S ASP 50": "OD1" <-> "OD2" Residue "S ASP 57": "OD1" <-> "OD2" Residue "S PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 186": "OD1" <-> "OD2" Residue "U PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 186": "OD1" <-> "OD2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 186": "OD1" <-> "OD2" Residue "Y ASP 50": "OD1" <-> "OD2" Residue "Y ASP 57": "OD1" <-> "OD2" Residue "Y PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 186": "OD1" <-> "OD2" Residue "0 PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 186": "OD1" <-> "OD2" Residue "4 ASP 50": "OD1" <-> "OD2" Residue "4 ASP 57": "OD1" <-> "OD2" Residue "4 PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 186": "OD1" <-> "OD2" Residue "6 PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 186": "OD1" <-> "OD2" 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: 49968 Number of models: 1 Model: "" Number of chains: 36 Chain: "G" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "H" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "I" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "J" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "K" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "L" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "M" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "N" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "O" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "P" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "Q" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "R" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "S" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "T" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "U" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "V" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "W" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "X" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "A" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "E" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "B" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "C" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "D" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "F" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "Y" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "Z" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "0" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "1" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "2" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "3" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "4" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "5" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "6" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "7" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "8" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "9" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Time building chain proxies: 24.26, per 1000 atoms: 0.49 Number of scatterers: 49968 At special positions: 0 Unit cell: (168.48, 169.56, 322.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 9972 8.00 N 7848 7.00 C 32040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS G 101 " - pdb=" SG CYS G 167 " distance=2.04 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 167 " distance=2.03 Simple disulfide: pdb=" SG CYS I 101 " - pdb=" SG CYS I 167 " distance=2.03 Simple disulfide: pdb=" SG CYS J 101 " - pdb=" SG CYS J 167 " distance=2.04 Simple disulfide: pdb=" SG CYS K 101 " - pdb=" SG CYS K 167 " distance=2.04 Simple disulfide: pdb=" SG CYS L 101 " - pdb=" SG CYS L 167 " distance=2.03 Simple disulfide: pdb=" SG CYS M 101 " - pdb=" SG CYS M 167 " distance=2.04 Simple disulfide: pdb=" SG CYS N 101 " - pdb=" SG CYS N 167 " distance=2.03 Simple disulfide: pdb=" SG CYS O 101 " - pdb=" SG CYS O 167 " distance=2.03 Simple disulfide: pdb=" SG CYS P 101 " - pdb=" SG CYS P 167 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 167 " distance=2.04 Simple disulfide: pdb=" SG CYS R 101 " - pdb=" SG CYS R 167 " distance=2.03 Simple disulfide: pdb=" SG CYS S 101 " - pdb=" SG CYS S 167 " distance=2.04 Simple disulfide: pdb=" SG CYS T 101 " - pdb=" SG CYS T 167 " distance=2.03 Simple disulfide: pdb=" SG CYS U 101 " - pdb=" SG CYS U 167 " distance=2.03 Simple disulfide: pdb=" SG CYS V 101 " - pdb=" SG CYS V 167 " distance=2.04 Simple disulfide: pdb=" SG CYS W 101 " - pdb=" SG CYS W 167 " distance=2.04 Simple disulfide: pdb=" SG CYS X 101 " - pdb=" SG CYS X 167 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 167 " distance=2.04 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 167 " distance=2.03 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 167 " distance=2.04 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 167 " distance=2.04 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 167 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 101 " - pdb=" SG CYS Y 167 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 101 " - pdb=" SG CYS Z 167 " distance=2.03 Simple disulfide: pdb=" SG CYS 0 101 " - pdb=" SG CYS 0 167 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 101 " - pdb=" SG CYS 1 167 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 101 " - pdb=" SG CYS 2 167 " distance=2.04 Simple disulfide: pdb=" SG CYS 3 101 " - pdb=" SG CYS 3 167 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 101 " - pdb=" SG CYS 4 167 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 101 " - pdb=" SG CYS 5 167 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 101 " - pdb=" SG CYS 6 167 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 101 " - pdb=" SG CYS 7 167 " distance=2.04 Simple disulfide: pdb=" SG CYS 8 101 " - pdb=" SG CYS 8 167 " distance=2.04 Simple disulfide: pdb=" SG CYS 9 101 " - pdb=" SG CYS 9 167 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.11 Conformation dependent library (CDL) restraints added in 9.0 seconds 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11952 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 132 sheets defined 8.1% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.95 Creating SS restraints... Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'E' and resid 49 through 53 removed outlier: 3.761A pdb=" N ILE E 53 " --> pdb=" O ASP E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 181 through 185 Processing helix chain 'B' and resid 49 through 53 removed outlier: 4.028A pdb=" N ILE B 53 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'C' and resid 49 through 54 removed outlier: 4.492A pdb=" N THR C 54 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 181 through 185 Processing helix chain 'D' and resid 49 through 53 Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 181 through 187 removed outlier: 4.319A pdb=" N ASP D 186 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 187 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 removed outlier: 3.780A pdb=" N THR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE F 53 " --> pdb=" O ASP F 50 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR F 54 " --> pdb=" O THR F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 126 No H-bonds generated for 'chain 'F' and resid 124 through 126' Processing helix chain 'F' and resid 181 through 187 removed outlier: 3.936A pdb=" N ASP F 186 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY F 187 " --> pdb=" O ALA F 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 53 Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 181 through 185 Processing helix chain 'H' and resid 49 through 53 removed outlier: 3.761A pdb=" N ILE H 53 " --> pdb=" O ASP H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 126 No H-bonds generated for 'chain 'H' and resid 124 through 126' Processing helix chain 'H' and resid 181 through 185 Processing helix chain 'I' and resid 49 through 53 removed outlier: 4.028A pdb=" N ILE I 53 " --> pdb=" O ASP I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 126 No H-bonds generated for 'chain 'I' and resid 124 through 126' Processing helix chain 'I' and resid 181 through 185 Processing helix chain 'J' and resid 49 through 54 removed outlier: 4.492A pdb=" N THR J 54 " --> pdb=" O THR J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 128 Processing helix chain 'J' and resid 181 through 185 Processing helix chain 'K' and resid 49 through 53 Processing helix chain 'K' and resid 124 through 126 No H-bonds generated for 'chain 'K' and resid 124 through 126' Processing helix chain 'K' and resid 181 through 187 removed outlier: 4.319A pdb=" N ASP K 186 " --> pdb=" O SER K 183 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY K 187 " --> pdb=" O ALA K 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 54 removed outlier: 3.780A pdb=" N THR L 51 " --> pdb=" O GLY L 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE L 53 " --> pdb=" O ASP L 50 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR L 54 " --> pdb=" O THR L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 126 No H-bonds generated for 'chain 'L' and resid 124 through 126' Processing helix chain 'L' and resid 181 through 187 removed outlier: 3.936A pdb=" N ASP L 186 " --> pdb=" O SER L 183 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY L 187 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 53 Processing helix chain 'M' and resid 124 through 126 No H-bonds generated for 'chain 'M' and resid 124 through 126' Processing helix chain 'M' and resid 181 through 185 Processing helix chain 'N' and resid 49 through 53 removed outlier: 3.761A pdb=" N ILE N 53 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 126 No H-bonds generated for 'chain 'N' and resid 124 through 126' Processing helix chain 'N' and resid 181 through 185 Processing helix chain 'O' and resid 49 through 53 removed outlier: 4.029A pdb=" N ILE O 53 " --> pdb=" O ASP O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 126 No H-bonds generated for 'chain 'O' and resid 124 through 126' Processing helix chain 'O' and resid 181 through 185 Processing helix chain 'P' and resid 49 through 54 removed outlier: 4.492A pdb=" N THR P 54 " --> pdb=" O THR P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 128 Processing helix chain 'P' and resid 181 through 185 Processing helix chain 'Q' and resid 49 through 53 Processing helix chain 'Q' and resid 124 through 126 No H-bonds generated for 'chain 'Q' and resid 124 through 126' Processing helix chain 'Q' and resid 181 through 187 removed outlier: 4.320A pdb=" N ASP Q 186 " --> pdb=" O SER Q 183 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY Q 187 " --> pdb=" O ALA Q 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 54 removed outlier: 3.780A pdb=" N THR R 51 " --> pdb=" O GLY R 48 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE R 53 " --> pdb=" O ASP R 50 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR R 54 " --> pdb=" O THR R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 126 No H-bonds generated for 'chain 'R' and resid 124 through 126' Processing helix chain 'R' and resid 181 through 187 removed outlier: 3.936A pdb=" N ASP R 186 " --> pdb=" O SER R 183 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY R 187 " --> pdb=" O ALA R 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 53 Processing helix chain 'S' and resid 124 through 126 No H-bonds generated for 'chain 'S' and resid 124 through 126' Processing helix chain 'S' and resid 181 through 185 Processing helix chain 'T' and resid 49 through 53 removed outlier: 3.761A pdb=" N ILE T 53 " --> pdb=" O ASP T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 126 No H-bonds generated for 'chain 'T' and resid 124 through 126' Processing helix chain 'T' and resid 181 through 185 Processing helix chain 'U' and resid 49 through 53 removed outlier: 4.028A pdb=" N ILE U 53 " --> pdb=" O ASP U 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 126 No H-bonds generated for 'chain 'U' and resid 124 through 126' Processing helix chain 'U' and resid 181 through 185 Processing helix chain 'V' and resid 49 through 54 removed outlier: 4.492A pdb=" N THR V 54 " --> pdb=" O THR V 51 " (cutoff:3.500A) Processing helix chain 'V' and resid 124 through 128 Processing helix chain 'V' and resid 181 through 185 Processing helix chain 'W' and resid 49 through 53 Processing helix chain 'W' and resid 124 through 126 No H-bonds generated for 'chain 'W' and resid 124 through 126' Processing helix chain 'W' and resid 181 through 187 removed outlier: 4.320A pdb=" N ASP W 186 " --> pdb=" O SER W 183 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY W 187 " --> pdb=" O ALA W 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 54 removed outlier: 3.780A pdb=" N THR X 51 " --> pdb=" O GLY X 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE X 53 " --> pdb=" O ASP X 50 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR X 54 " --> pdb=" O THR X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 124 through 126 No H-bonds generated for 'chain 'X' and resid 124 through 126' Processing helix chain 'X' and resid 181 through 187 removed outlier: 3.936A pdb=" N ASP X 186 " --> pdb=" O SER X 183 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY X 187 " --> pdb=" O ALA X 184 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 53 Processing helix chain 'Y' and resid 124 through 126 No H-bonds generated for 'chain 'Y' and resid 124 through 126' Processing helix chain 'Y' and resid 181 through 185 Processing helix chain 'Z' and resid 49 through 53 removed outlier: 3.761A pdb=" N ILE Z 53 " --> pdb=" O ASP Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 124 through 126 No H-bonds generated for 'chain 'Z' and resid 124 through 126' Processing helix chain 'Z' and resid 181 through 185 Processing helix chain '0' and resid 49 through 53 removed outlier: 4.028A pdb=" N ILE 0 53 " --> pdb=" O ASP 0 50 " (cutoff:3.500A) Processing helix chain '0' and resid 124 through 126 No H-bonds generated for 'chain '0' and resid 124 through 126' Processing helix chain '0' and resid 181 through 185 Processing helix chain '1' and resid 49 through 54 removed outlier: 4.492A pdb=" N THR 1 54 " --> pdb=" O THR 1 51 " (cutoff:3.500A) Processing helix chain '1' and resid 124 through 128 Processing helix chain '1' and resid 181 through 185 Processing helix chain '2' and resid 49 through 53 Processing helix chain '2' and resid 124 through 126 No H-bonds generated for 'chain '2' and resid 124 through 126' Processing helix chain '2' and resid 181 through 187 removed outlier: 4.319A pdb=" N ASP 2 186 " --> pdb=" O SER 2 183 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY 2 187 " --> pdb=" O ALA 2 184 " (cutoff:3.500A) Processing helix chain '3' and resid 48 through 54 removed outlier: 3.780A pdb=" N THR 3 51 " --> pdb=" O GLY 3 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE 3 53 " --> pdb=" O ASP 3 50 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR 3 54 " --> pdb=" O THR 3 51 " (cutoff:3.500A) Processing helix chain '3' and resid 124 through 126 No H-bonds generated for 'chain '3' and resid 124 through 126' Processing helix chain '3' and resid 181 through 187 removed outlier: 3.935A pdb=" N ASP 3 186 " --> pdb=" O SER 3 183 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY 3 187 " --> pdb=" O ALA 3 184 " (cutoff:3.500A) Processing helix chain '4' and resid 49 through 53 Processing helix chain '4' and resid 124 through 126 No H-bonds generated for 'chain '4' and resid 124 through 126' Processing helix chain '4' and resid 181 through 185 Processing helix chain '5' and resid 49 through 53 removed outlier: 3.762A pdb=" N ILE 5 53 " --> pdb=" O ASP 5 50 " (cutoff:3.500A) Processing helix chain '5' and resid 124 through 126 No H-bonds generated for 'chain '5' and resid 124 through 126' Processing helix chain '5' and resid 181 through 185 Processing helix chain '6' and resid 49 through 53 removed outlier: 4.028A pdb=" N ILE 6 53 " --> pdb=" O ASP 6 50 " (cutoff:3.500A) Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 181 through 185 Processing helix chain '7' and resid 49 through 54 removed outlier: 4.492A pdb=" N THR 7 54 " --> pdb=" O THR 7 51 " (cutoff:3.500A) Processing helix chain '7' and resid 124 through 128 Processing helix chain '7' and resid 181 through 185 Processing helix chain '8' and resid 49 through 53 Processing helix chain '8' and resid 124 through 126 No H-bonds generated for 'chain '8' and resid 124 through 126' Processing helix chain '8' and resid 181 through 187 removed outlier: 4.319A pdb=" N ASP 8 186 " --> pdb=" O SER 8 183 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY 8 187 " --> pdb=" O ALA 8 184 " (cutoff:3.500A) Processing helix chain '9' and resid 48 through 54 removed outlier: 3.780A pdb=" N THR 9 51 " --> pdb=" O GLY 9 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE 9 53 " --> pdb=" O ASP 9 50 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR 9 54 " --> pdb=" O THR 9 51 " (cutoff:3.500A) Processing helix chain '9' and resid 124 through 126 No H-bonds generated for 'chain '9' and resid 124 through 126' Processing helix chain '9' and resid 181 through 187 removed outlier: 3.936A pdb=" N ASP 9 186 " --> pdb=" O SER 9 183 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY 9 187 " --> pdb=" O ALA 9 184 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 65 through 71 removed outlier: 3.955A pdb=" N VAL A 79 " --> pdb=" O TYR A 70 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 92 through 100 removed outlier: 8.494A pdb=" N THR A 92 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL A 176 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TYR A 94 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL A 174 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASN A 96 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA A 172 " --> pdb=" O ASN A 96 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 130 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLN A 146 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 160 through 162 removed outlier: 5.739A pdb=" N ALA A 111 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER A 201 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU A 113 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL A 199 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA A 115 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN A 197 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY A 117 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'E' and resid 65 through 67 Processing sheet with id= 5, first strand: chain 'E' and resid 70 through 71 removed outlier: 3.767A pdb=" N VAL E 79 " --> pdb=" O TYR E 70 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 92 through 93 removed outlier: 3.855A pdb=" N ASP E 130 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 131 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 98 through 100 Processing sheet with id= 8, first strand: chain 'E' and resid 160 through 162 removed outlier: 3.700A pdb=" N ILE E 162 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN E 195 " --> pdb=" O VAL E 116 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 65 through 71 Processing sheet with id= 10, first strand: chain 'B' and resid 92 through 100 removed outlier: 8.397A pdb=" N THR B 92 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL B 176 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR B 94 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL B 174 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN B 96 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA B 172 " --> pdb=" O ASN B 96 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP B 130 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 131 " --> pdb=" O PHE B 147 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 160 through 162 removed outlier: 6.928A pdb=" N GLN B 195 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 65 through 71 Processing sheet with id= 13, first strand: chain 'C' and resid 92 through 93 removed outlier: 3.625A pdb=" N LEU C 98 " --> pdb=" O VAL C 170 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 92 through 93 removed outlier: 3.742A pdb=" N ASP C 130 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C 131 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.656A pdb=" N VAL C 116 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLN C 195 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 65 through 71 removed outlier: 3.584A pdb=" N VAL D 79 " --> pdb=" O TYR D 70 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 92 through 93 Processing sheet with id= 18, first strand: chain 'D' and resid 92 through 93 removed outlier: 3.652A pdb=" N TYR D 134 " --> pdb=" O GLY D 171 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D 133 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'D' and resid 160 through 162 removed outlier: 6.754A pdb=" N GLN D 195 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.743A pdb=" N TYR F 46 " --> pdb=" O GLN F 99 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN F 99 " --> pdb=" O TYR F 46 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN F 96 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL F 170 " --> pdb=" O ASN F 96 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU F 98 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA F 168 " --> pdb=" O LEU F 98 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP F 130 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL F 145 " --> pdb=" O VAL F 133 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'F' and resid 68 through 72 Processing sheet with id= 22, first strand: chain 'F' and resid 160 through 162 removed outlier: 6.816A pdb=" N GLN F 195 " --> pdb=" O VAL F 116 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'G' and resid 65 through 71 removed outlier: 3.954A pdb=" N VAL G 79 " --> pdb=" O TYR G 70 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'G' and resid 92 through 100 removed outlier: 8.494A pdb=" N THR G 92 " --> pdb=" O VAL G 176 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL G 176 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TYR G 94 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL G 174 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASN G 96 " --> pdb=" O ALA G 172 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ALA G 172 " --> pdb=" O ASN G 96 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP G 130 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLN G 146 " --> pdb=" O THR G 153 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'G' and resid 160 through 162 removed outlier: 5.739A pdb=" N ALA G 111 " --> pdb=" O SER G 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER G 201 " --> pdb=" O ALA G 111 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU G 113 " --> pdb=" O VAL G 199 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL G 199 " --> pdb=" O LEU G 113 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA G 115 " --> pdb=" O ASN G 197 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN G 197 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY G 117 " --> pdb=" O GLN G 195 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'H' and resid 65 through 67 Processing sheet with id= 27, first strand: chain 'H' and resid 70 through 71 removed outlier: 3.767A pdb=" N VAL H 79 " --> pdb=" O TYR H 70 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'H' and resid 92 through 93 removed outlier: 3.855A pdb=" N ASP H 130 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE H 131 " --> pdb=" O PHE H 147 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'H' and resid 98 through 100 Processing sheet with id= 30, first strand: chain 'H' and resid 160 through 162 removed outlier: 3.701A pdb=" N ILE H 162 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN H 195 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'I' and resid 65 through 71 Processing sheet with id= 32, first strand: chain 'I' and resid 92 through 100 removed outlier: 8.397A pdb=" N THR I 92 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL I 176 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR I 94 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL I 174 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN I 96 " --> pdb=" O ALA I 172 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA I 172 " --> pdb=" O ASN I 96 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP I 130 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE I 131 " --> pdb=" O PHE I 147 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'I' and resid 160 through 162 removed outlier: 6.928A pdb=" N GLN I 195 " --> pdb=" O VAL I 116 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'J' and resid 65 through 71 Processing sheet with id= 35, first strand: chain 'J' and resid 92 through 93 removed outlier: 3.625A pdb=" N LEU J 98 " --> pdb=" O VAL J 170 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'J' and resid 92 through 93 removed outlier: 3.742A pdb=" N ASP J 130 " --> pdb=" O LEU J 175 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE J 131 " --> pdb=" O PHE J 147 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'J' and resid 161 through 162 removed outlier: 3.656A pdb=" N VAL J 116 " --> pdb=" O GLN J 195 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLN J 195 " --> pdb=" O VAL J 116 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'K' and resid 65 through 71 removed outlier: 3.584A pdb=" N VAL K 79 " --> pdb=" O TYR K 70 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'K' and resid 92 through 93 Processing sheet with id= 40, first strand: chain 'K' and resid 92 through 93 removed outlier: 3.652A pdb=" N TYR K 134 " --> pdb=" O GLY K 171 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL K 133 " --> pdb=" O VAL K 145 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'K' and resid 160 through 162 removed outlier: 6.755A pdb=" N GLN K 195 " --> pdb=" O VAL K 116 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.743A pdb=" N TYR L 46 " --> pdb=" O GLN L 99 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN L 99 " --> pdb=" O TYR L 46 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN L 96 " --> pdb=" O VAL L 170 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL L 170 " --> pdb=" O ASN L 96 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU L 98 " --> pdb=" O ALA L 168 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA L 168 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP L 130 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL L 145 " --> pdb=" O VAL L 133 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'L' and resid 68 through 72 Processing sheet with id= 44, first strand: chain 'L' and resid 160 through 162 removed outlier: 6.816A pdb=" N GLN L 195 " --> pdb=" O VAL L 116 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'M' and resid 65 through 71 removed outlier: 3.954A pdb=" N VAL M 79 " --> pdb=" O TYR M 70 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'M' and resid 92 through 100 removed outlier: 8.494A pdb=" N THR M 92 " --> pdb=" O VAL M 176 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL M 176 " --> pdb=" O THR M 92 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TYR M 94 " --> pdb=" O VAL M 174 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL M 174 " --> pdb=" O TYR M 94 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASN M 96 " --> pdb=" O ALA M 172 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA M 172 " --> pdb=" O ASN M 96 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP M 130 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLN M 146 " --> pdb=" O THR M 153 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'M' and resid 160 through 162 removed outlier: 5.740A pdb=" N ALA M 111 " --> pdb=" O SER M 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER M 201 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU M 113 " --> pdb=" O VAL M 199 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL M 199 " --> pdb=" O LEU M 113 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA M 115 " --> pdb=" O ASN M 197 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN M 197 " --> pdb=" O ALA M 115 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY M 117 " --> pdb=" O GLN M 195 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'N' and resid 65 through 67 Processing sheet with id= 49, first strand: chain 'N' and resid 70 through 71 removed outlier: 3.766A pdb=" N VAL N 79 " --> pdb=" O TYR N 70 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'N' and resid 92 through 93 removed outlier: 3.855A pdb=" N ASP N 130 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE N 131 " --> pdb=" O PHE N 147 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'N' and resid 98 through 100 Processing sheet with id= 52, first strand: chain 'N' and resid 160 through 162 removed outlier: 3.700A pdb=" N ILE N 162 " --> pdb=" O LEU N 109 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN N 195 " --> pdb=" O VAL N 116 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'O' and resid 65 through 71 Processing sheet with id= 54, first strand: chain 'O' and resid 92 through 100 removed outlier: 8.397A pdb=" N THR O 92 " --> pdb=" O VAL O 176 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL O 176 " --> pdb=" O THR O 92 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR O 94 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL O 174 " --> pdb=" O TYR O 94 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN O 96 " --> pdb=" O ALA O 172 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA O 172 " --> pdb=" O ASN O 96 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP O 130 " --> pdb=" O LEU O 175 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE O 131 " --> pdb=" O PHE O 147 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'O' and resid 160 through 162 removed outlier: 6.928A pdb=" N GLN O 195 " --> pdb=" O VAL O 116 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'P' and resid 65 through 71 Processing sheet with id= 57, first strand: chain 'P' and resid 92 through 93 removed outlier: 3.625A pdb=" N LEU P 98 " --> pdb=" O VAL P 170 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'P' and resid 92 through 93 removed outlier: 3.742A pdb=" N ASP P 130 " --> pdb=" O LEU P 175 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE P 131 " --> pdb=" O PHE P 147 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'P' and resid 161 through 162 removed outlier: 3.655A pdb=" N VAL P 116 " --> pdb=" O GLN P 195 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLN P 195 " --> pdb=" O VAL P 116 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Q' and resid 65 through 71 removed outlier: 3.584A pdb=" N VAL Q 79 " --> pdb=" O TYR Q 70 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Q' and resid 92 through 93 Processing sheet with id= 62, first strand: chain 'Q' and resid 92 through 93 removed outlier: 3.653A pdb=" N TYR Q 134 " --> pdb=" O GLY Q 171 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL Q 133 " --> pdb=" O VAL Q 145 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Q' and resid 160 through 162 removed outlier: 6.755A pdb=" N GLN Q 195 " --> pdb=" O VAL Q 116 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'R' and resid 45 through 46 removed outlier: 3.744A pdb=" N TYR R 46 " --> pdb=" O GLN R 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN R 99 " --> pdb=" O TYR R 46 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN R 96 " --> pdb=" O VAL R 170 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL R 170 " --> pdb=" O ASN R 96 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU R 98 " --> pdb=" O ALA R 168 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA R 168 " --> pdb=" O LEU R 98 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP R 130 " --> pdb=" O LEU R 175 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL R 145 " --> pdb=" O VAL R 133 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'R' and resid 68 through 72 Processing sheet with id= 66, first strand: chain 'R' and resid 160 through 162 removed outlier: 6.816A pdb=" N GLN R 195 " --> pdb=" O VAL R 116 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'S' and resid 65 through 71 removed outlier: 3.955A pdb=" N VAL S 79 " --> pdb=" O TYR S 70 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'S' and resid 92 through 100 removed outlier: 8.495A pdb=" N THR S 92 " --> pdb=" O VAL S 176 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N VAL S 176 " --> pdb=" O THR S 92 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TYR S 94 " --> pdb=" O VAL S 174 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL S 174 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASN S 96 " --> pdb=" O ALA S 172 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA S 172 " --> pdb=" O ASN S 96 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP S 130 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLN S 146 " --> pdb=" O THR S 153 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'S' and resid 160 through 162 removed outlier: 5.740A pdb=" N ALA S 111 " --> pdb=" O SER S 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER S 201 " --> pdb=" O ALA S 111 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU S 113 " --> pdb=" O VAL S 199 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL S 199 " --> pdb=" O LEU S 113 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA S 115 " --> pdb=" O ASN S 197 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN S 197 " --> pdb=" O ALA S 115 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY S 117 " --> pdb=" O GLN S 195 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'T' and resid 65 through 67 Processing sheet with id= 71, first strand: chain 'T' and resid 70 through 71 removed outlier: 3.766A pdb=" N VAL T 79 " --> pdb=" O TYR T 70 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'T' and resid 92 through 93 removed outlier: 3.855A pdb=" N ASP T 130 " --> pdb=" O LEU T 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE T 131 " --> pdb=" O PHE T 147 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'T' and resid 98 through 100 Processing sheet with id= 74, first strand: chain 'T' and resid 160 through 162 removed outlier: 3.701A pdb=" N ILE T 162 " --> pdb=" O LEU T 109 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN T 195 " --> pdb=" O VAL T 116 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'U' and resid 65 through 71 Processing sheet with id= 76, first strand: chain 'U' and resid 92 through 100 removed outlier: 8.396A pdb=" N THR U 92 " --> pdb=" O VAL U 176 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL U 176 " --> pdb=" O THR U 92 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N TYR U 94 " --> pdb=" O VAL U 174 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL U 174 " --> pdb=" O TYR U 94 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN U 96 " --> pdb=" O ALA U 172 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA U 172 " --> pdb=" O ASN U 96 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP U 130 " --> pdb=" O LEU U 175 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE U 131 " --> pdb=" O PHE U 147 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'U' and resid 160 through 162 removed outlier: 6.928A pdb=" N GLN U 195 " --> pdb=" O VAL U 116 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'V' and resid 65 through 71 Processing sheet with id= 79, first strand: chain 'V' and resid 92 through 93 removed outlier: 3.625A pdb=" N LEU V 98 " --> pdb=" O VAL V 170 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'V' and resid 92 through 93 removed outlier: 3.742A pdb=" N ASP V 130 " --> pdb=" O LEU V 175 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE V 131 " --> pdb=" O PHE V 147 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'V' and resid 161 through 162 removed outlier: 3.656A pdb=" N VAL V 116 " --> pdb=" O GLN V 195 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLN V 195 " --> pdb=" O VAL V 116 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'W' and resid 65 through 71 removed outlier: 3.584A pdb=" N VAL W 79 " --> pdb=" O TYR W 70 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'W' and resid 92 through 93 Processing sheet with id= 84, first strand: chain 'W' and resid 92 through 93 removed outlier: 3.653A pdb=" N TYR W 134 " --> pdb=" O GLY W 171 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL W 133 " --> pdb=" O VAL W 145 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'W' and resid 160 through 162 removed outlier: 6.755A pdb=" N GLN W 195 " --> pdb=" O VAL W 116 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'X' and resid 45 through 46 removed outlier: 3.743A pdb=" N TYR X 46 " --> pdb=" O GLN X 99 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN X 99 " --> pdb=" O TYR X 46 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN X 96 " --> pdb=" O VAL X 170 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL X 170 " --> pdb=" O ASN X 96 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU X 98 " --> pdb=" O ALA X 168 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA X 168 " --> pdb=" O LEU X 98 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP X 130 " --> pdb=" O LEU X 175 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL X 145 " --> pdb=" O VAL X 133 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'X' and resid 68 through 72 Processing sheet with id= 88, first strand: chain 'X' and resid 160 through 162 removed outlier: 6.817A pdb=" N GLN X 195 " --> pdb=" O VAL X 116 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'Y' and resid 65 through 71 removed outlier: 3.955A pdb=" N VAL Y 79 " --> pdb=" O TYR Y 70 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'Y' and resid 92 through 100 removed outlier: 8.494A pdb=" N THR Y 92 " --> pdb=" O VAL Y 176 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL Y 176 " --> pdb=" O THR Y 92 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TYR Y 94 " --> pdb=" O VAL Y 174 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL Y 174 " --> pdb=" O TYR Y 94 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ASN Y 96 " --> pdb=" O ALA Y 172 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ALA Y 172 " --> pdb=" O ASN Y 96 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP Y 130 " --> pdb=" O LEU Y 175 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLN Y 146 " --> pdb=" O THR Y 153 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'Y' and resid 160 through 162 removed outlier: 5.740A pdb=" N ALA Y 111 " --> pdb=" O SER Y 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER Y 201 " --> pdb=" O ALA Y 111 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU Y 113 " --> pdb=" O VAL Y 199 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL Y 199 " --> pdb=" O LEU Y 113 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA Y 115 " --> pdb=" O ASN Y 197 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN Y 197 " --> pdb=" O ALA Y 115 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY Y 117 " --> pdb=" O GLN Y 195 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'Z' and resid 65 through 67 Processing sheet with id= 93, first strand: chain 'Z' and resid 70 through 71 removed outlier: 3.766A pdb=" N VAL Z 79 " --> pdb=" O TYR Z 70 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'Z' and resid 92 through 93 removed outlier: 3.855A pdb=" N ASP Z 130 " --> pdb=" O LEU Z 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE Z 131 " --> pdb=" O PHE Z 147 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'Z' and resid 98 through 100 Processing sheet with id= 96, first strand: chain 'Z' and resid 160 through 162 removed outlier: 3.701A pdb=" N ILE Z 162 " --> pdb=" O LEU Z 109 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN Z 195 " --> pdb=" O VAL Z 116 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain '0' and resid 65 through 71 Processing sheet with id= 98, first strand: chain '0' and resid 92 through 100 removed outlier: 8.397A pdb=" N THR 0 92 " --> pdb=" O VAL 0 176 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL 0 176 " --> pdb=" O THR 0 92 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N TYR 0 94 " --> pdb=" O VAL 0 174 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL 0 174 " --> pdb=" O TYR 0 94 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN 0 96 " --> pdb=" O ALA 0 172 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA 0 172 " --> pdb=" O ASN 0 96 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP 0 130 " --> pdb=" O LEU 0 175 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE 0 131 " --> pdb=" O PHE 0 147 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain '0' and resid 160 through 162 removed outlier: 6.928A pdb=" N GLN 0 195 " --> pdb=" O VAL 0 116 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain '1' and resid 65 through 71 Processing sheet with id=101, first strand: chain '1' and resid 92 through 93 removed outlier: 3.625A pdb=" N LEU 1 98 " --> pdb=" O VAL 1 170 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain '1' and resid 92 through 93 removed outlier: 3.742A pdb=" N ASP 1 130 " --> pdb=" O LEU 1 175 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE 1 131 " --> pdb=" O PHE 1 147 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain '1' and resid 161 through 162 removed outlier: 3.655A pdb=" N VAL 1 116 " --> pdb=" O GLN 1 195 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLN 1 195 " --> pdb=" O VAL 1 116 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain '2' and resid 65 through 71 removed outlier: 3.585A pdb=" N VAL 2 79 " --> pdb=" O TYR 2 70 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain '2' and resid 92 through 93 Processing sheet with id=106, first strand: chain '2' and resid 92 through 93 removed outlier: 3.653A pdb=" N TYR 2 134 " --> pdb=" O GLY 2 171 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL 2 133 " --> pdb=" O VAL 2 145 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain '2' and resid 160 through 162 removed outlier: 6.755A pdb=" N GLN 2 195 " --> pdb=" O VAL 2 116 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain '3' and resid 45 through 46 removed outlier: 3.743A pdb=" N TYR 3 46 " --> pdb=" O GLN 3 99 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN 3 99 " --> pdb=" O TYR 3 46 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN 3 96 " --> pdb=" O VAL 3 170 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL 3 170 " --> pdb=" O ASN 3 96 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU 3 98 " --> pdb=" O ALA 3 168 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA 3 168 " --> pdb=" O LEU 3 98 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP 3 130 " --> pdb=" O LEU 3 175 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL 3 145 " --> pdb=" O VAL 3 133 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain '3' and resid 68 through 72 Processing sheet with id=110, first strand: chain '3' and resid 160 through 162 removed outlier: 6.816A pdb=" N GLN 3 195 " --> pdb=" O VAL 3 116 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain '4' and resid 65 through 71 removed outlier: 3.954A pdb=" N VAL 4 79 " --> pdb=" O TYR 4 70 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain '4' and resid 92 through 100 removed outlier: 8.494A pdb=" N THR 4 92 " --> pdb=" O VAL 4 176 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL 4 176 " --> pdb=" O THR 4 92 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TYR 4 94 " --> pdb=" O VAL 4 174 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL 4 174 " --> pdb=" O TYR 4 94 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASN 4 96 " --> pdb=" O ALA 4 172 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA 4 172 " --> pdb=" O ASN 4 96 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP 4 130 " --> pdb=" O LEU 4 175 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLN 4 146 " --> pdb=" O THR 4 153 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain '4' and resid 160 through 162 removed outlier: 5.740A pdb=" N ALA 4 111 " --> pdb=" O SER 4 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER 4 201 " --> pdb=" O ALA 4 111 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU 4 113 " --> pdb=" O VAL 4 199 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL 4 199 " --> pdb=" O LEU 4 113 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA 4 115 " --> pdb=" O ASN 4 197 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN 4 197 " --> pdb=" O ALA 4 115 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY 4 117 " --> pdb=" O GLN 4 195 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain '5' and resid 65 through 67 Processing sheet with id=115, first strand: chain '5' and resid 70 through 71 removed outlier: 3.767A pdb=" N VAL 5 79 " --> pdb=" O TYR 5 70 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain '5' and resid 92 through 93 removed outlier: 3.855A pdb=" N ASP 5 130 " --> pdb=" O LEU 5 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE 5 131 " --> pdb=" O PHE 5 147 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain '5' and resid 98 through 100 Processing sheet with id=118, first strand: chain '5' and resid 160 through 162 removed outlier: 3.701A pdb=" N ILE 5 162 " --> pdb=" O LEU 5 109 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN 5 195 " --> pdb=" O VAL 5 116 " (cutoff:3.500A) Processing sheet with id=119, first strand: chain '6' and resid 65 through 71 Processing sheet with id=120, first strand: chain '6' and resid 92 through 100 removed outlier: 8.397A pdb=" N THR 6 92 " --> pdb=" O VAL 6 176 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL 6 176 " --> pdb=" O THR 6 92 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N TYR 6 94 " --> pdb=" O VAL 6 174 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL 6 174 " --> pdb=" O TYR 6 94 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN 6 96 " --> pdb=" O ALA 6 172 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA 6 172 " --> pdb=" O ASN 6 96 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP 6 130 " --> pdb=" O LEU 6 175 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE 6 131 " --> pdb=" O PHE 6 147 " (cutoff:3.500A) Processing sheet with id=121, first strand: chain '6' and resid 160 through 162 removed outlier: 6.928A pdb=" N GLN 6 195 " --> pdb=" O VAL 6 116 " (cutoff:3.500A) Processing sheet with id=122, first strand: chain '7' and resid 65 through 71 Processing sheet with id=123, first strand: chain '7' and resid 92 through 93 removed outlier: 3.625A pdb=" N LEU 7 98 " --> pdb=" O VAL 7 170 " (cutoff:3.500A) Processing sheet with id=124, first strand: chain '7' and resid 92 through 93 removed outlier: 3.741A pdb=" N ASP 7 130 " --> pdb=" O LEU 7 175 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE 7 131 " --> pdb=" O PHE 7 147 " (cutoff:3.500A) Processing sheet with id=125, first strand: chain '7' and resid 161 through 162 removed outlier: 3.655A pdb=" N VAL 7 116 " --> pdb=" O GLN 7 195 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLN 7 195 " --> pdb=" O VAL 7 116 " (cutoff:3.500A) Processing sheet with id=126, first strand: chain '8' and resid 65 through 71 removed outlier: 3.584A pdb=" N VAL 8 79 " --> pdb=" O TYR 8 70 " (cutoff:3.500A) Processing sheet with id=127, first strand: chain '8' and resid 92 through 93 Processing sheet with id=128, first strand: chain '8' and resid 92 through 93 removed outlier: 3.652A pdb=" N TYR 8 134 " --> pdb=" O GLY 8 171 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL 8 133 " --> pdb=" O VAL 8 145 " (cutoff:3.500A) Processing sheet with id=129, first strand: chain '8' and resid 160 through 162 removed outlier: 6.754A pdb=" N GLN 8 195 " --> pdb=" O VAL 8 116 " (cutoff:3.500A) Processing sheet with id=130, first strand: chain '9' and resid 45 through 46 removed outlier: 3.744A pdb=" N TYR 9 46 " --> pdb=" O GLN 9 99 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN 9 99 " --> pdb=" O TYR 9 46 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN 9 96 " --> pdb=" O VAL 9 170 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL 9 170 " --> pdb=" O ASN 9 96 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU 9 98 " --> pdb=" O ALA 9 168 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA 9 168 " --> pdb=" O LEU 9 98 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP 9 130 " --> pdb=" O LEU 9 175 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL 9 145 " --> pdb=" O VAL 9 133 " (cutoff:3.500A) Processing sheet with id=131, first strand: chain '9' and resid 68 through 72 Processing sheet with id=132, first strand: chain '9' and resid 160 through 162 removed outlier: 6.816A pdb=" N GLN 9 195 " --> pdb=" O VAL 9 116 " (cutoff:3.500A) 1182 hydrogen bonds defined for protein. 2448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.06 Time building geometry restraints manager: 19.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.51: 31657 1.51 - 1.79: 19428 1.79 - 2.07: 155 2.07 - 2.35: 48 2.35 - 2.63: 12 Bond restraints: 51300 Sorted by residual: bond pdb=" CA PHE 5 28 " pdb=" CB PHE 5 28 " ideal model delta sigma weight residual 1.530 2.251 -0.721 1.43e-02 4.89e+03 2.55e+03 bond pdb=" CA PHE E 28 " pdb=" CB PHE E 28 " ideal model delta sigma weight residual 1.530 2.251 -0.721 1.43e-02 4.89e+03 2.54e+03 bond pdb=" CA PHE Z 28 " pdb=" CB PHE Z 28 " ideal model delta sigma weight residual 1.530 2.251 -0.721 1.43e-02 4.89e+03 2.54e+03 bond pdb=" CA PHE H 28 " pdb=" CB PHE H 28 " ideal model delta sigma weight residual 1.530 2.251 -0.721 1.43e-02 4.89e+03 2.54e+03 bond pdb=" CA PHE N 28 " pdb=" CB PHE N 28 " ideal model delta sigma weight residual 1.530 2.251 -0.721 1.43e-02 4.89e+03 2.54e+03 ... (remaining 51295 not shown) Histogram of bond angle deviations from ideal: 96.87 - 104.30: 1021 104.30 - 111.73: 24226 111.73 - 119.16: 15822 119.16 - 126.59: 29002 126.59 - 134.02: 525 Bond angle restraints: 70596 Sorted by residual: angle pdb=" CA PHE T 28 " pdb=" CB PHE T 28 " pdb=" CG PHE T 28 " ideal model delta sigma weight residual 113.80 129.12 -15.32 1.00e+00 1.00e+00 2.35e+02 angle pdb=" CA PHE H 28 " pdb=" CB PHE H 28 " pdb=" CG PHE H 28 " ideal model delta sigma weight residual 113.80 129.11 -15.31 1.00e+00 1.00e+00 2.35e+02 angle pdb=" CA PHE N 28 " pdb=" CB PHE N 28 " pdb=" CG PHE N 28 " ideal model delta sigma weight residual 113.80 129.10 -15.30 1.00e+00 1.00e+00 2.34e+02 angle pdb=" CA PHE Z 28 " pdb=" CB PHE Z 28 " pdb=" CG PHE Z 28 " ideal model delta sigma weight residual 113.80 129.10 -15.30 1.00e+00 1.00e+00 2.34e+02 angle pdb=" CA PHE E 28 " pdb=" CB PHE E 28 " pdb=" CG PHE E 28 " ideal model delta sigma weight residual 113.80 129.10 -15.30 1.00e+00 1.00e+00 2.34e+02 ... (remaining 70591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.73: 26671 14.73 - 29.46: 2290 29.46 - 44.19: 577 44.19 - 58.92: 78 58.92 - 73.65: 48 Dihedral angle restraints: 29664 sinusoidal: 10584 harmonic: 19080 Sorted by residual: dihedral pdb=" CA THR Y 141 " pdb=" C THR Y 141 " pdb=" N PRO Y 142 " pdb=" CA PRO Y 142 " ideal model delta harmonic sigma weight residual -180.00 -130.92 -49.08 0 5.00e+00 4.00e-02 9.63e+01 dihedral pdb=" CA THR 4 141 " pdb=" C THR 4 141 " pdb=" N PRO 4 142 " pdb=" CA PRO 4 142 " ideal model delta harmonic sigma weight residual 180.00 -130.94 -49.06 0 5.00e+00 4.00e-02 9.63e+01 dihedral pdb=" CA THR M 141 " pdb=" C THR M 141 " pdb=" N PRO M 142 " pdb=" CA PRO M 142 " ideal model delta harmonic sigma weight residual -180.00 -130.96 -49.04 0 5.00e+00 4.00e-02 9.62e+01 ... (remaining 29661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 8224 0.121 - 0.242: 122 0.242 - 0.363: 0 0.363 - 0.484: 0 0.484 - 0.605: 6 Chirality restraints: 8352 Sorted by residual: chirality pdb=" CA PHE E 28 " pdb=" N PHE E 28 " pdb=" C PHE E 28 " pdb=" CB PHE E 28 " both_signs ideal model delta sigma weight residual False 2.51 3.12 -0.61 2.00e-01 2.50e+01 9.15e+00 chirality pdb=" CA PHE N 28 " pdb=" N PHE N 28 " pdb=" C PHE N 28 " pdb=" CB PHE N 28 " both_signs ideal model delta sigma weight residual False 2.51 3.12 -0.60 2.00e-01 2.50e+01 9.15e+00 chirality pdb=" CA PHE H 28 " pdb=" N PHE H 28 " pdb=" C PHE H 28 " pdb=" CB PHE H 28 " both_signs ideal model delta sigma weight residual False 2.51 3.11 -0.60 2.00e-01 2.50e+01 9.14e+00 ... (remaining 8349 not shown) Planarity restraints: 8856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP 3 34 " 0.007 2.00e-02 2.50e+03 3.03e-02 2.30e+01 pdb=" CG TRP 3 34 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP 3 34 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TRP 3 34 " 0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP 3 34 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP 3 34 " 0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP 3 34 " -0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP 3 34 " -0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP 3 34 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP 3 34 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 34 " -0.007 2.00e-02 2.50e+03 3.03e-02 2.30e+01 pdb=" CG TRP L 34 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP L 34 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 TRP L 34 " -0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP L 34 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP L 34 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP L 34 " 0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 34 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 34 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP L 34 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP X 34 " -0.007 2.00e-02 2.50e+03 3.03e-02 2.30e+01 pdb=" CG TRP X 34 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP X 34 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 TRP X 34 " -0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP X 34 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP X 34 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP X 34 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 34 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 34 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP X 34 " -0.023 2.00e-02 2.50e+03 ... (remaining 8853 not shown) Histogram of nonbonded interaction distances: 0.44 - 1.33: 44 1.33 - 2.22: 270 2.22 - 3.11: 40911 3.11 - 4.01: 124146 4.01 - 4.90: 224206 Warning: very small nonbonded interaction distances. Nonbonded interactions: 389577 Sorted by model distance: nonbonded pdb=" CZ2 TRP R 34 " pdb=" O THR C 193 " model vdw 0.436 3.340 nonbonded pdb=" CZ2 TRP F 34 " pdb=" O THR 7 193 " model vdw 0.436 3.340 nonbonded pdb=" CZ2 TRP L 34 " pdb=" O THR V 193 " model vdw 0.437 3.340 nonbonded pdb=" CZ2 TRP X 34 " pdb=" O THR 1 193 " model vdw 0.437 3.340 nonbonded pdb=" NH2 ARG R 55 " pdb=" OH TYR U 105 " model vdw 0.782 2.520 ... (remaining 389572 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 20.800 Check model and map are aligned: 0.810 Set scattering table: 0.390 Process input model: 120.930 Find NCS groups from input model: 3.490 Set up NCS constraints: 0.570 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.034 1.132 51300 Z= 2.253 Angle : 0.786 15.397 70596 Z= 0.487 Chirality : 0.050 0.605 8352 Planarity : 0.007 0.078 8856 Dihedral : 12.164 73.655 17604 Min Nonbonded Distance : 0.436 Molprobity Statistics. All-atom Clashscore : 24.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.94 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.10), residues: 6408 helix: -4.50 (0.08), residues: 438 sheet: -0.81 (0.11), residues: 2346 loop : -2.27 (0.10), residues: 3624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.005 TRP R 34 PHE 0.033 0.003 PHE W 28 TYR 0.023 0.001 TYR 5 105 ARG 0.008 0.001 ARG X 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 482 time to evaluate : 6.302 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: H 185 ARG cc_start: 0.6863 (tpp-160) cc_final: 0.6125 (tpt90) REVERT: H 186 ASP cc_start: 0.9045 (p0) cc_final: 0.8585 (p0) REVERT: I 191 ILE cc_start: 0.8987 (pt) cc_final: 0.8716 (tt) REVERT: L 57 ASP cc_start: 0.7580 (p0) cc_final: 0.7370 (p0) REVERT: N 44 MET cc_start: 0.5900 (mtp) cc_final: 0.5313 (mtp) REVERT: O 57 ASP cc_start: 0.8128 (p0) cc_final: 0.7732 (p0) REVERT: U 84 ILE cc_start: 0.8934 (mm) cc_final: 0.8705 (mt) REVERT: W 185 ARG cc_start: 0.7784 (mmm160) cc_final: 0.7437 (mmm160) REVERT: X 57 ASP cc_start: 0.7167 (p0) cc_final: 0.6557 (p0) REVERT: E 186 ASP cc_start: 0.9284 (p0) cc_final: 0.8790 (p0) REVERT: B 35 LEU cc_start: 0.8950 (mp) cc_final: 0.8660 (pp) REVERT: Z 44 MET cc_start: 0.6739 (mtp) cc_final: 0.6400 (mtp) REVERT: 0 44 MET cc_start: 0.2764 (tpt) cc_final: 0.2422 (tpt) REVERT: 0 186 ASP cc_start: 0.8615 (p0) cc_final: 0.8257 (p0) REVERT: 6 57 ASP cc_start: 0.8141 (p0) cc_final: 0.7917 (p0) REVERT: 9 57 ASP cc_start: 0.7435 (p0) cc_final: 0.6562 (m-30) outliers start: 0 outliers final: 0 residues processed: 482 average time/residue: 0.6151 time to fit residues: 498.3039 Evaluate side-chains 237 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 5.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 547 optimal weight: 3.9990 chunk 491 optimal weight: 20.0000 chunk 272 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 chunk 331 optimal weight: 4.9990 chunk 262 optimal weight: 5.9990 chunk 507 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 308 optimal weight: 7.9990 chunk 378 optimal weight: 10.0000 chunk 588 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 102 ASN I 30 ASN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN L 143 ASN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 123 ASN O 195 GLN ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 195 GLN ** R 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 ASN ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 143 ASN ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 GLN U 30 ASN U 195 GLN ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 93 ASN ** X 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 143 ASN ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 ASN ** Y 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 102 ASN ** 3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 143 ASN ** 4 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 30 ASN 6 195 GLN 7 30 ASN ** 9 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 143 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.157 51300 Z= 2.143 Angle : 0.869 39.164 70596 Z= 0.501 Chirality : 0.051 0.352 8352 Planarity : 0.007 0.087 8856 Dihedral : 5.989 51.658 7308 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.52 % Favored : 89.20 % Rotamer: Outliers : 0.46 % Allowed : 7.91 % Favored : 91.63 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.10), residues: 6408 helix: -4.58 (0.08), residues: 396 sheet: -0.79 (0.11), residues: 2346 loop : -2.52 (0.10), residues: 3666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP R 34 PHE 0.101 0.004 PHE U 200 TYR 0.032 0.001 TYR S 105 ARG 0.008 0.001 ARG 7 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 265 time to evaluate : 5.764 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: G 26 LEU cc_start: 0.8652 (tp) cc_final: 0.8218 (tt) REVERT: H 186 ASP cc_start: 0.9082 (p0) cc_final: 0.8816 (p0) REVERT: I 191 ILE cc_start: 0.9095 (pt) cc_final: 0.8802 (tt) REVERT: N 44 MET cc_start: 0.5869 (mtp) cc_final: 0.5319 (mtp) REVERT: O 57 ASP cc_start: 0.8071 (p0) cc_final: 0.7588 (p0) REVERT: P 90 ASP cc_start: 0.7593 (t0) cc_final: 0.7352 (t0) REVERT: R 55 ARG cc_start: 0.6211 (ptt180) cc_final: 0.5954 (ptt-90) REVERT: R 129 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8734 (mmmm) REVERT: R 177 ASP cc_start: 0.9169 (t0) cc_final: 0.8949 (t0) REVERT: T 55 ARG cc_start: 0.6875 (ptm160) cc_final: 0.6037 (mtm180) REVERT: U 84 ILE cc_start: 0.9064 (mm) cc_final: 0.8856 (mt) REVERT: X 57 ASP cc_start: 0.7472 (p0) cc_final: 0.6882 (p0) REVERT: E 55 ARG cc_start: 0.6504 (ptm160) cc_final: 0.5641 (mtm180) REVERT: B 35 LEU cc_start: 0.9192 (mp) cc_final: 0.8667 (pp) REVERT: Z 44 MET cc_start: 0.6829 (mtp) cc_final: 0.6470 (mtp) REVERT: 0 35 LEU cc_start: 0.9204 (mp) cc_final: 0.8826 (pp) REVERT: 0 186 ASP cc_start: 0.8747 (p0) cc_final: 0.8381 (p0) REVERT: 5 55 ARG cc_start: 0.6652 (ptm160) cc_final: 0.6350 (mtm110) REVERT: 6 57 ASP cc_start: 0.8157 (p0) cc_final: 0.7954 (p0) REVERT: 8 90 ASP cc_start: 0.7316 (t0) cc_final: 0.6786 (t0) REVERT: 8 175 LEU cc_start: 0.9357 (tt) cc_final: 0.9116 (tp) REVERT: 9 57 ASP cc_start: 0.7467 (p0) cc_final: 0.6729 (m-30) outliers start: 26 outliers final: 17 residues processed: 286 average time/residue: 0.6060 time to fit residues: 294.8495 Evaluate side-chains 234 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 217 time to evaluate : 5.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 191 ILE Chi-restraints excluded: chain I residue 112 LYS Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain W residue 50 ASP Chi-restraints excluded: chain W residue 100 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain 2 residue 99 GLN Chi-restraints excluded: chain 3 residue 123 ASN Chi-restraints excluded: chain 6 residue 36 ILE Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 9 residue 84 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 327 optimal weight: 6.9990 chunk 182 optimal weight: 0.0570 chunk 489 optimal weight: 20.0000 chunk 400 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 589 optimal weight: 10.0000 chunk 636 optimal weight: 20.0000 chunk 525 optimal weight: 4.9990 chunk 584 optimal weight: 5.9990 chunk 200 optimal weight: 20.0000 chunk 472 optimal weight: 3.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 195 GLN H 30 ASN ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 GLN ** N 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 ASN V 37 ASN W 195 GLN ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 93 ASN ** 3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 30 ASN ** 9 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.133 51300 Z= 2.132 Angle : 0.858 40.104 70596 Z= 0.487 Chirality : 0.050 0.365 8352 Planarity : 0.006 0.117 8856 Dihedral : 6.050 53.385 7308 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.66 % Favored : 89.06 % Rotamer: Outliers : 1.43 % Allowed : 11.85 % Favored : 86.71 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.10), residues: 6408 helix: -4.60 (0.07), residues: 432 sheet: -0.89 (0.11), residues: 2382 loop : -2.54 (0.10), residues: 3594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP L 34 PHE 0.071 0.004 PHE U 200 TYR 0.033 0.002 TYR Y 105 ARG 0.018 0.001 ARG N 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 250 time to evaluate : 5.166 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: G 26 LEU cc_start: 0.8380 (tp) cc_final: 0.7886 (tt) REVERT: G 40 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8933 (mp) REVERT: H 55 ARG cc_start: 0.2779 (ttt180) cc_final: 0.2134 (ttt-90) REVERT: N 44 MET cc_start: 0.6574 (mtp) cc_final: 0.6064 (mtp) REVERT: O 35 LEU cc_start: 0.9166 (mp) cc_final: 0.8860 (mt) REVERT: O 57 ASP cc_start: 0.8135 (p0) cc_final: 0.7605 (p0) REVERT: P 90 ASP cc_start: 0.7608 (t0) cc_final: 0.7346 (t0) REVERT: R 55 ARG cc_start: 0.6027 (ptt180) cc_final: 0.5576 (ttp-170) REVERT: R 177 ASP cc_start: 0.9118 (t0) cc_final: 0.8831 (t0) REVERT: U 90 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.7023 (m-30) REVERT: X 57 ASP cc_start: 0.7606 (p0) cc_final: 0.7041 (p0) REVERT: E 55 ARG cc_start: 0.6900 (ptm160) cc_final: 0.6615 (mtm110) REVERT: B 35 LEU cc_start: 0.9285 (mp) cc_final: 0.8770 (pp) REVERT: D 175 LEU cc_start: 0.8753 (tt) cc_final: 0.8277 (tp) REVERT: Y 195 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.7948 (tp40) REVERT: Z 44 MET cc_start: 0.6866 (mtp) cc_final: 0.6509 (mtp) REVERT: 0 35 LEU cc_start: 0.9238 (mp) cc_final: 0.8879 (pp) REVERT: 2 175 LEU cc_start: 0.9189 (tt) cc_final: 0.8757 (tp) REVERT: 6 57 ASP cc_start: 0.8094 (p0) cc_final: 0.7868 (p0) REVERT: 7 50 ASP cc_start: 0.7639 (m-30) cc_final: 0.7416 (m-30) REVERT: 8 90 ASP cc_start: 0.7761 (t0) cc_final: 0.7312 (t0) REVERT: 8 175 LEU cc_start: 0.9314 (tt) cc_final: 0.9073 (tp) REVERT: 9 57 ASP cc_start: 0.7719 (p0) cc_final: 0.6941 (m-30) outliers start: 81 outliers final: 37 residues processed: 321 average time/residue: 0.5547 time to fit residues: 306.8003 Evaluate side-chains 253 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 213 time to evaluate : 5.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain I residue 112 LYS Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain L residue 123 ASN Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain T residue 198 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 100 LEU Chi-restraints excluded: chain X residue 137 ASN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 157 THR Chi-restraints excluded: chain Y residue 195 GLN Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain 2 residue 99 GLN Chi-restraints excluded: chain 3 residue 123 ASN Chi-restraints excluded: chain 3 residue 137 ASN Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 4 residue 80 THR Chi-restraints excluded: chain 4 residue 88 THR Chi-restraints excluded: chain 4 residue 95 THR Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 6 residue 35 LEU Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 145 VAL Chi-restraints excluded: chain 9 residue 137 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 582 optimal weight: 5.9990 chunk 443 optimal weight: 4.9990 chunk 305 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 chunk 281 optimal weight: 0.0170 chunk 395 optimal weight: 9.9990 chunk 591 optimal weight: 0.9980 chunk 626 optimal weight: 20.0000 chunk 309 optimal weight: 0.0030 chunk 560 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 overall best weight: 0.8830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 102 ASN J 30 ASN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 195 GLN 1 30 ASN 3 93 ASN ** 3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 143 ASN ** 9 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 1.144 51300 Z= 2.108 Angle : 0.795 40.546 70596 Z= 0.454 Chirality : 0.049 0.357 8352 Planarity : 0.006 0.127 8856 Dihedral : 5.647 51.271 7308 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.38 % Favored : 90.36 % Rotamer: Outliers : 0.97 % Allowed : 13.82 % Favored : 85.21 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.10), residues: 6408 helix: -4.53 (0.08), residues: 396 sheet: -0.62 (0.11), residues: 2352 loop : -2.36 (0.10), residues: 3660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 34 PHE 0.056 0.003 PHE U 200 TYR 0.031 0.001 TYR S 105 ARG 0.012 0.000 ARG N 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 257 time to evaluate : 5.551 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: G 26 LEU cc_start: 0.8186 (tp) cc_final: 0.7685 (tt) REVERT: H 55 ARG cc_start: 0.3126 (ttt180) cc_final: 0.2612 (ttt-90) REVERT: I 191 ILE cc_start: 0.9098 (mp) cc_final: 0.8735 (mp) REVERT: J 130 ASP cc_start: 0.8422 (m-30) cc_final: 0.7621 (t0) REVERT: N 44 MET cc_start: 0.7085 (mtp) cc_final: 0.6568 (mtp) REVERT: O 35 LEU cc_start: 0.9177 (mp) cc_final: 0.8890 (mt) REVERT: O 57 ASP cc_start: 0.8123 (p0) cc_final: 0.7565 (p0) REVERT: P 90 ASP cc_start: 0.7755 (t0) cc_final: 0.7530 (t0) REVERT: P 130 ASP cc_start: 0.8738 (m-30) cc_final: 0.7735 (t0) REVERT: R 55 ARG cc_start: 0.6272 (ptt180) cc_final: 0.5141 (ttp-110) REVERT: R 177 ASP cc_start: 0.9073 (t0) cc_final: 0.8726 (t0) REVERT: W 31 LEU cc_start: 0.9062 (tp) cc_final: 0.8811 (tp) REVERT: X 57 ASP cc_start: 0.7494 (p0) cc_final: 0.7037 (p0) REVERT: B 35 LEU cc_start: 0.9267 (mp) cc_final: 0.8724 (pp) REVERT: D 90 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7647 (t70) REVERT: D 175 LEU cc_start: 0.8710 (tt) cc_final: 0.8352 (tp) REVERT: Z 44 MET cc_start: 0.6779 (mtp) cc_final: 0.6552 (mtp) REVERT: 0 35 LEU cc_start: 0.9247 (mp) cc_final: 0.8904 (pp) REVERT: 0 109 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8180 (mm) REVERT: 6 57 ASP cc_start: 0.8098 (p0) cc_final: 0.7891 (p0) REVERT: 7 50 ASP cc_start: 0.7747 (m-30) cc_final: 0.7503 (m-30) REVERT: 8 90 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.6977 (t0) REVERT: 8 175 LEU cc_start: 0.9279 (tt) cc_final: 0.9004 (tp) REVERT: 9 57 ASP cc_start: 0.7479 (p0) cc_final: 0.6870 (m-30) outliers start: 55 outliers final: 20 residues processed: 304 average time/residue: 0.5777 time to fit residues: 301.6622 Evaluate side-chains 247 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 224 time to evaluate : 6.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain M residue 101 CYS Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain 0 residue 109 LEU Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 2 residue 113 LEU Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 6 residue 35 LEU Chi-restraints excluded: chain 6 residue 36 ILE Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 88 THR Chi-restraints excluded: chain 8 residue 90 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 521 optimal weight: 7.9990 chunk 355 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 466 optimal weight: 3.9990 chunk 258 optimal weight: 6.9990 chunk 534 optimal weight: 6.9990 chunk 432 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 319 optimal weight: 0.7980 chunk 562 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 ASN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN ** R 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 ASN ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 ASN ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN C 30 ASN F 37 ASN F 93 ASN ** Z 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 30 ASN 1 37 ASN 3 93 ASN ** 3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 143 ASN ** 4 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.127 51300 Z= 2.130 Angle : 0.840 40.497 70596 Z= 0.476 Chirality : 0.049 0.350 8352 Planarity : 0.006 0.139 8856 Dihedral : 5.769 52.838 7308 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.05 % Favored : 88.67 % Rotamer: Outliers : 1.66 % Allowed : 15.06 % Favored : 83.28 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.10), residues: 6408 helix: -4.58 (0.07), residues: 432 sheet: -0.90 (0.10), residues: 2454 loop : -2.41 (0.10), residues: 3522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP L 34 PHE 0.054 0.004 PHE U 200 TYR 0.021 0.001 TYR F 124 ARG 0.011 0.001 ARG 5 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 224 time to evaluate : 5.696 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: G 26 LEU cc_start: 0.8169 (tp) cc_final: 0.7683 (tt) REVERT: H 55 ARG cc_start: 0.3070 (ttt180) cc_final: 0.2593 (ttt-90) REVERT: H 145 VAL cc_start: 0.9392 (OUTLIER) cc_final: 0.9031 (p) REVERT: J 130 ASP cc_start: 0.8369 (m-30) cc_final: 0.7559 (t0) REVERT: N 44 MET cc_start: 0.7221 (mtp) cc_final: 0.6646 (mtp) REVERT: O 35 LEU cc_start: 0.9162 (mp) cc_final: 0.8891 (mt) REVERT: O 57 ASP cc_start: 0.8068 (p0) cc_final: 0.7536 (p0) REVERT: P 90 ASP cc_start: 0.7872 (t0) cc_final: 0.7627 (t0) REVERT: P 130 ASP cc_start: 0.8740 (m-30) cc_final: 0.7757 (t0) REVERT: R 55 ARG cc_start: 0.6306 (ptt180) cc_final: 0.5361 (ttm110) REVERT: R 177 ASP cc_start: 0.9064 (t0) cc_final: 0.8688 (t0) REVERT: S 44 MET cc_start: 0.6312 (mmm) cc_final: 0.5605 (tpt) REVERT: T 95 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8191 (t) REVERT: X 57 ASP cc_start: 0.7765 (p0) cc_final: 0.7272 (p0) REVERT: B 35 LEU cc_start: 0.9295 (mp) cc_final: 0.8769 (pp) REVERT: D 175 LEU cc_start: 0.8765 (tt) cc_final: 0.8390 (tp) REVERT: F 46 TYR cc_start: 0.6519 (m-10) cc_final: 0.6311 (m-10) REVERT: Y 195 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8245 (tp40) REVERT: 0 35 LEU cc_start: 0.9198 (mp) cc_final: 0.8947 (pp) REVERT: 6 57 ASP cc_start: 0.7971 (p0) cc_final: 0.7758 (p0) REVERT: 7 50 ASP cc_start: 0.7713 (m-30) cc_final: 0.7460 (m-30) REVERT: 8 90 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.6945 (t0) REVERT: 8 175 LEU cc_start: 0.9294 (tt) cc_final: 0.9008 (tp) REVERT: 9 57 ASP cc_start: 0.7722 (p0) cc_final: 0.7058 (m-30) REVERT: 9 98 LEU cc_start: 0.9096 (mm) cc_final: 0.8689 (tp) outliers start: 94 outliers final: 52 residues processed: 307 average time/residue: 0.5600 time to fit residues: 296.6537 Evaluate side-chains 266 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 210 time to evaluate : 5.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 112 LYS Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 191 ILE Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 123 ASN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain M residue 101 CYS Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain T residue 95 THR Chi-restraints excluded: chain T residue 198 VAL Chi-restraints excluded: chain U residue 191 ILE Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain X residue 137 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain Y residue 80 THR Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 195 GLN Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 30 ASN Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 2 residue 99 GLN Chi-restraints excluded: chain 2 residue 113 LEU Chi-restraints excluded: chain 3 residue 137 ASN Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 4 residue 95 THR Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 6 residue 35 LEU Chi-restraints excluded: chain 6 residue 36 ILE Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 88 THR Chi-restraints excluded: chain 7 residue 145 VAL Chi-restraints excluded: chain 8 residue 90 ASP Chi-restraints excluded: chain 9 residue 137 ASN Chi-restraints excluded: chain 9 residue 175 LEU Chi-restraints excluded: chain 9 residue 198 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 210 optimal weight: 9.9990 chunk 564 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 367 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 626 optimal weight: 2.9990 chunk 520 optimal weight: 20.0000 chunk 290 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 207 optimal weight: 30.0000 chunk 329 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 30 ASN ** R 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 30 ASN 2 148 GLN 3 93 ASN ** 3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 143 ASN ** 9 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 1.138 51300 Z= 2.108 Angle : 0.791 40.694 70596 Z= 0.451 Chirality : 0.048 0.356 8352 Planarity : 0.006 0.087 8856 Dihedral : 5.573 51.357 7308 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.49 % Favored : 90.23 % Rotamer: Outliers : 1.15 % Allowed : 16.22 % Favored : 82.63 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.10), residues: 6408 helix: -4.53 (0.07), residues: 432 sheet: -0.62 (0.11), residues: 2364 loop : -2.34 (0.10), residues: 3612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 34 PHE 0.053 0.003 PHE T 200 TYR 0.021 0.001 TYR Y 105 ARG 0.018 0.000 ARG 5 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 236 time to evaluate : 5.502 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: G 26 LEU cc_start: 0.8120 (tp) cc_final: 0.7608 (tt) REVERT: H 55 ARG cc_start: 0.3455 (ttt180) cc_final: 0.3057 (ttt-90) REVERT: J 130 ASP cc_start: 0.8261 (m-30) cc_final: 0.7558 (t0) REVERT: K 28 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.6990 (m-80) REVERT: N 44 MET cc_start: 0.7109 (mtp) cc_final: 0.6532 (mtp) REVERT: O 35 LEU cc_start: 0.9194 (mp) cc_final: 0.8959 (mt) REVERT: O 57 ASP cc_start: 0.8132 (p0) cc_final: 0.7583 (p0) REVERT: P 90 ASP cc_start: 0.7926 (t0) cc_final: 0.7712 (t0) REVERT: P 130 ASP cc_start: 0.8691 (m-30) cc_final: 0.7847 (t0) REVERT: R 177 ASP cc_start: 0.9033 (t0) cc_final: 0.8641 (t0) REVERT: X 46 TYR cc_start: 0.6560 (m-10) cc_final: 0.6202 (m-80) REVERT: X 57 ASP cc_start: 0.7746 (p0) cc_final: 0.7347 (p0) REVERT: E 44 MET cc_start: 0.6668 (mtp) cc_final: 0.6213 (mtp) REVERT: B 35 LEU cc_start: 0.9295 (mp) cc_final: 0.8803 (pp) REVERT: D 90 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7630 (t70) REVERT: D 175 LEU cc_start: 0.8729 (tt) cc_final: 0.8262 (tp) REVERT: 0 35 LEU cc_start: 0.9188 (mp) cc_final: 0.8941 (pp) REVERT: 0 109 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8270 (mm) REVERT: 1 44 MET cc_start: 0.2401 (tpt) cc_final: 0.1307 (tpt) REVERT: 2 90 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7662 (t70) REVERT: 2 175 LEU cc_start: 0.9208 (tt) cc_final: 0.8730 (tp) REVERT: 7 50 ASP cc_start: 0.7758 (m-30) cc_final: 0.7488 (m-30) REVERT: 8 90 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7011 (t0) REVERT: 8 175 LEU cc_start: 0.9260 (tt) cc_final: 0.9015 (tp) REVERT: 9 57 ASP cc_start: 0.7552 (p0) cc_final: 0.6983 (m-30) REVERT: 9 98 LEU cc_start: 0.9145 (mm) cc_final: 0.8793 (tp) outliers start: 65 outliers final: 40 residues processed: 297 average time/residue: 0.5505 time to fit residues: 283.7164 Evaluate side-chains 259 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 214 time to evaluate : 6.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 112 LYS Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 101 CYS Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain 0 residue 109 LEU Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 2 residue 28 PHE Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 2 residue 90 ASP Chi-restraints excluded: chain 2 residue 113 LEU Chi-restraints excluded: chain 3 residue 93 ASN Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 5 residue 145 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 6 residue 35 LEU Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 145 VAL Chi-restraints excluded: chain 8 residue 90 ASP Chi-restraints excluded: chain 9 residue 198 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 604 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 357 optimal weight: 0.8980 chunk 457 optimal weight: 4.9990 chunk 354 optimal weight: 1.9990 chunk 527 optimal weight: 9.9990 chunk 350 optimal weight: 10.0000 chunk 624 optimal weight: 3.9990 chunk 390 optimal weight: 2.9990 chunk 380 optimal weight: 20.0000 chunk 288 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN F 93 ASN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 30 ASN ** 3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 143 ASN ** 9 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 1.131 51300 Z= 2.116 Angle : 0.809 40.642 70596 Z= 0.459 Chirality : 0.049 0.359 8352 Planarity : 0.006 0.151 8856 Dihedral : 5.553 51.691 7308 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.55 % Favored : 89.17 % Rotamer: Outliers : 1.56 % Allowed : 16.83 % Favored : 81.62 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.10), residues: 6408 helix: -4.53 (0.07), residues: 432 sheet: -0.69 (0.11), residues: 2388 loop : -2.36 (0.10), residues: 3588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 34 PHE 0.059 0.003 PHE T 200 TYR 0.029 0.001 TYR S 105 ARG 0.008 0.001 ARG E 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 221 time to evaluate : 5.647 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: G 26 LEU cc_start: 0.8127 (tp) cc_final: 0.7632 (tt) REVERT: H 55 ARG cc_start: 0.3788 (ttt180) cc_final: 0.3360 (ttt-90) REVERT: H 145 VAL cc_start: 0.9388 (OUTLIER) cc_final: 0.9041 (p) REVERT: J 130 ASP cc_start: 0.8309 (m-30) cc_final: 0.7635 (t0) REVERT: K 28 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7092 (m-80) REVERT: N 44 MET cc_start: 0.7197 (mtp) cc_final: 0.6578 (mtp) REVERT: O 35 LEU cc_start: 0.9165 (mp) cc_final: 0.8938 (mt) REVERT: O 57 ASP cc_start: 0.8087 (p0) cc_final: 0.7559 (p0) REVERT: P 90 ASP cc_start: 0.7931 (t0) cc_final: 0.7700 (t0) REVERT: P 130 ASP cc_start: 0.8672 (m-30) cc_final: 0.7840 (t0) REVERT: R 177 ASP cc_start: 0.9046 (t0) cc_final: 0.8670 (t0) REVERT: X 46 TYR cc_start: 0.6773 (m-10) cc_final: 0.6351 (m-80) REVERT: X 57 ASP cc_start: 0.7828 (p0) cc_final: 0.7406 (p0) REVERT: E 44 MET cc_start: 0.6641 (mtp) cc_final: 0.6169 (mtp) REVERT: B 35 LEU cc_start: 0.9292 (mp) cc_final: 0.8802 (pp) REVERT: C 44 MET cc_start: 0.2707 (tpt) cc_final: 0.1749 (tpt) REVERT: D 90 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7735 (t70) REVERT: D 175 LEU cc_start: 0.8764 (tt) cc_final: 0.8296 (tp) REVERT: F 65 VAL cc_start: 0.7898 (OUTLIER) cc_final: 0.7470 (p) REVERT: 0 35 LEU cc_start: 0.9183 (mp) cc_final: 0.8955 (pp) REVERT: 0 109 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8223 (mm) REVERT: 1 44 MET cc_start: 0.2307 (tpt) cc_final: 0.1280 (tpt) REVERT: 2 90 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7711 (t70) REVERT: 2 175 LEU cc_start: 0.9217 (tt) cc_final: 0.8874 (tp) REVERT: 7 50 ASP cc_start: 0.7726 (m-30) cc_final: 0.7445 (m-30) REVERT: 8 90 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7059 (t0) REVERT: 8 175 LEU cc_start: 0.9260 (tt) cc_final: 0.8997 (tp) REVERT: 9 57 ASP cc_start: 0.7715 (p0) cc_final: 0.7093 (m-30) REVERT: 9 98 LEU cc_start: 0.9156 (mm) cc_final: 0.8810 (tp) outliers start: 88 outliers final: 65 residues processed: 296 average time/residue: 0.5496 time to fit residues: 282.2117 Evaluate side-chains 281 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 209 time to evaluate : 5.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 191 ILE Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 112 LYS Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 101 CYS Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain N residue 197 ASN Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain Q residue 82 ILE Chi-restraints excluded: chain R residue 37 ASN Chi-restraints excluded: chain T residue 123 ASN Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 198 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 105 TYR Chi-restraints excluded: chain Y residue 157 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 180 LEU Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain 0 residue 109 LEU Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 2 residue 28 PHE Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 2 residue 90 ASP Chi-restraints excluded: chain 2 residue 113 LEU Chi-restraints excluded: chain 2 residue 198 VAL Chi-restraints excluded: chain 3 residue 162 ILE Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 5 residue 101 CYS Chi-restraints excluded: chain 5 residue 145 VAL Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 6 residue 35 LEU Chi-restraints excluded: chain 6 residue 36 ILE Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 145 VAL Chi-restraints excluded: chain 8 residue 90 ASP Chi-restraints excluded: chain 9 residue 137 ASN Chi-restraints excluded: chain 9 residue 175 LEU Chi-restraints excluded: chain 9 residue 198 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 386 optimal weight: 20.0000 chunk 249 optimal weight: 0.9990 chunk 373 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 397 optimal weight: 0.8980 chunk 425 optimal weight: 2.9990 chunk 308 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 490 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 30 ASN ** R 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN F 93 ASN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 102 ASN 1 30 ASN ** 3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 1.133 51300 Z= 2.113 Angle : 0.802 40.654 70596 Z= 0.455 Chirality : 0.049 0.367 8352 Planarity : 0.006 0.092 8856 Dihedral : 5.539 51.488 7308 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.22 % Favored : 89.51 % Rotamer: Outliers : 1.70 % Allowed : 17.25 % Favored : 81.05 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.10), residues: 6408 helix: -4.50 (0.07), residues: 432 sheet: -0.66 (0.11), residues: 2388 loop : -2.34 (0.10), residues: 3588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 34 PHE 0.060 0.003 PHE T 200 TYR 0.028 0.001 TYR Y 105 ARG 0.021 0.001 ARG E 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 218 time to evaluate : 5.604 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: G 26 LEU cc_start: 0.8137 (tp) cc_final: 0.7644 (tt) REVERT: H 55 ARG cc_start: 0.3612 (ttt180) cc_final: 0.3267 (ttt-90) REVERT: H 145 VAL cc_start: 0.9382 (OUTLIER) cc_final: 0.9036 (p) REVERT: J 130 ASP cc_start: 0.8273 (m-30) cc_final: 0.7653 (t0) REVERT: K 28 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.7071 (m-80) REVERT: N 44 MET cc_start: 0.7088 (mtp) cc_final: 0.6492 (mtp) REVERT: O 35 LEU cc_start: 0.9144 (mp) cc_final: 0.8941 (mt) REVERT: O 57 ASP cc_start: 0.8100 (p0) cc_final: 0.7584 (p0) REVERT: P 90 ASP cc_start: 0.7994 (t0) cc_final: 0.7751 (t0) REVERT: P 130 ASP cc_start: 0.8635 (m-30) cc_final: 0.7859 (t0) REVERT: R 65 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8503 (p) REVERT: R 177 ASP cc_start: 0.9132 (t0) cc_final: 0.8736 (t0) REVERT: X 46 TYR cc_start: 0.6855 (m-10) cc_final: 0.6507 (m-80) REVERT: X 57 ASP cc_start: 0.7925 (p0) cc_final: 0.7586 (p0) REVERT: E 44 MET cc_start: 0.6614 (mtp) cc_final: 0.6143 (mtp) REVERT: B 35 LEU cc_start: 0.9300 (mp) cc_final: 0.8830 (pp) REVERT: C 44 MET cc_start: 0.1957 (tpt) cc_final: 0.1301 (tpt) REVERT: D 90 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7724 (t70) REVERT: D 175 LEU cc_start: 0.8779 (tt) cc_final: 0.8329 (tp) REVERT: F 65 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7538 (p) REVERT: 0 35 LEU cc_start: 0.9175 (mp) cc_final: 0.8966 (pp) REVERT: 0 109 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8264 (mm) REVERT: 1 44 MET cc_start: 0.2333 (tpt) cc_final: 0.1349 (tpt) REVERT: 2 90 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7606 (t70) REVERT: 2 175 LEU cc_start: 0.9134 (tt) cc_final: 0.8741 (tp) REVERT: 7 50 ASP cc_start: 0.7809 (m-30) cc_final: 0.7539 (m-30) REVERT: 8 90 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7109 (t0) REVERT: 8 175 LEU cc_start: 0.9237 (tt) cc_final: 0.8958 (tp) REVERT: 9 57 ASP cc_start: 0.7732 (p0) cc_final: 0.7140 (m-30) REVERT: 9 98 LEU cc_start: 0.9175 (mm) cc_final: 0.8830 (tp) outliers start: 96 outliers final: 76 residues processed: 302 average time/residue: 0.5384 time to fit residues: 285.1592 Evaluate side-chains 293 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 209 time to evaluate : 5.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 112 LYS Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 191 ILE Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 101 CYS Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain N residue 197 ASN Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain Q residue 82 ILE Chi-restraints excluded: chain Q residue 101 CYS Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain U residue 101 CYS Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 198 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 105 TYR Chi-restraints excluded: chain Y residue 157 THR Chi-restraints excluded: chain Z residue 180 LEU Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 109 LEU Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 30 ASN Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 2 residue 28 PHE Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 2 residue 90 ASP Chi-restraints excluded: chain 2 residue 99 GLN Chi-restraints excluded: chain 2 residue 113 LEU Chi-restraints excluded: chain 2 residue 198 VAL Chi-restraints excluded: chain 3 residue 162 ILE Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 4 residue 95 THR Chi-restraints excluded: chain 5 residue 101 CYS Chi-restraints excluded: chain 5 residue 145 VAL Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 6 residue 35 LEU Chi-restraints excluded: chain 6 residue 36 ILE Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 88 THR Chi-restraints excluded: chain 7 residue 145 VAL Chi-restraints excluded: chain 8 residue 90 ASP Chi-restraints excluded: chain 9 residue 175 LEU Chi-restraints excluded: chain 9 residue 198 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 568 optimal weight: 8.9990 chunk 598 optimal weight: 10.0000 chunk 545 optimal weight: 1.9990 chunk 582 optimal weight: 6.9990 chunk 350 optimal weight: 6.9990 chunk 253 optimal weight: 0.7980 chunk 457 optimal weight: 1.9990 chunk 178 optimal weight: 20.0000 chunk 525 optimal weight: 10.0000 chunk 550 optimal weight: 2.9990 chunk 579 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 GLN ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 30 ASN ** V 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN 1 30 ASN 3 93 ASN ** 3 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 143 ASN 9 102 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 1.135 51300 Z= 2.109 Angle : 0.789 40.639 70596 Z= 0.448 Chirality : 0.048 0.371 8352 Planarity : 0.005 0.076 8856 Dihedral : 5.436 51.142 7308 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.25 % Favored : 89.48 % Rotamer: Outliers : 1.57 % Allowed : 17.48 % Favored : 80.94 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.10), residues: 6408 helix: -4.48 (0.08), residues: 432 sheet: -0.72 (0.11), residues: 2448 loop : -2.24 (0.10), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 34 PHE 0.059 0.003 PHE T 200 TYR 0.017 0.001 TYR F 94 ARG 0.007 0.000 ARG 5 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 222 time to evaluate : 5.643 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: G 26 LEU cc_start: 0.8106 (tp) cc_final: 0.7637 (tt) REVERT: H 55 ARG cc_start: 0.3746 (ttt180) cc_final: 0.3376 (ttt-90) REVERT: H 145 VAL cc_start: 0.9357 (OUTLIER) cc_final: 0.9003 (p) REVERT: J 130 ASP cc_start: 0.8250 (m-30) cc_final: 0.7661 (t0) REVERT: K 28 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.7142 (m-80) REVERT: M 195 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8661 (tt0) REVERT: N 44 MET cc_start: 0.7059 (mtp) cc_final: 0.6465 (mtp) REVERT: O 57 ASP cc_start: 0.8098 (p0) cc_final: 0.7571 (p0) REVERT: P 90 ASP cc_start: 0.7977 (t0) cc_final: 0.7720 (t0) REVERT: P 130 ASP cc_start: 0.8604 (m-30) cc_final: 0.7814 (t0) REVERT: R 177 ASP cc_start: 0.9117 (t0) cc_final: 0.8730 (t0) REVERT: T 95 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8094 (t) REVERT: X 46 TYR cc_start: 0.6832 (m-10) cc_final: 0.6513 (m-80) REVERT: X 57 ASP cc_start: 0.7906 (p0) cc_final: 0.7596 (p0) REVERT: E 44 MET cc_start: 0.6609 (mtp) cc_final: 0.6136 (mtp) REVERT: B 35 LEU cc_start: 0.9299 (mp) cc_final: 0.8832 (pp) REVERT: D 90 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7764 (t70) REVERT: D 175 LEU cc_start: 0.8761 (tt) cc_final: 0.8318 (tp) REVERT: F 65 VAL cc_start: 0.7928 (OUTLIER) cc_final: 0.7502 (p) REVERT: 0 35 LEU cc_start: 0.9170 (mp) cc_final: 0.8954 (pp) REVERT: 0 109 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8270 (mm) REVERT: 1 44 MET cc_start: 0.2324 (tpt) cc_final: 0.1391 (tpt) REVERT: 2 90 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7614 (t70) REVERT: 2 175 LEU cc_start: 0.9114 (tt) cc_final: 0.8711 (tp) REVERT: 7 50 ASP cc_start: 0.7805 (m-30) cc_final: 0.7539 (m-30) REVERT: 8 90 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7454 (t0) REVERT: 9 57 ASP cc_start: 0.7703 (p0) cc_final: 0.7131 (m-30) REVERT: 9 98 LEU cc_start: 0.9145 (mm) cc_final: 0.8822 (tp) outliers start: 89 outliers final: 71 residues processed: 302 average time/residue: 0.5497 time to fit residues: 290.4152 Evaluate side-chains 293 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 213 time to evaluate : 6.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 112 LYS Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 101 CYS Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 195 GLN Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain N residue 197 ASN Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain Q residue 82 ILE Chi-restraints excluded: chain Q residue 101 CYS Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain T residue 95 THR Chi-restraints excluded: chain U residue 101 CYS Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 198 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain Y residue 80 THR Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 105 TYR Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 109 LEU Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 2 residue 28 PHE Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 2 residue 90 ASP Chi-restraints excluded: chain 2 residue 99 GLN Chi-restraints excluded: chain 2 residue 113 LEU Chi-restraints excluded: chain 2 residue 198 VAL Chi-restraints excluded: chain 3 residue 162 ILE Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 4 residue 95 THR Chi-restraints excluded: chain 5 residue 101 CYS Chi-restraints excluded: chain 5 residue 145 VAL Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 6 residue 35 LEU Chi-restraints excluded: chain 6 residue 36 ILE Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 88 THR Chi-restraints excluded: chain 7 residue 145 VAL Chi-restraints excluded: chain 8 residue 90 ASP Chi-restraints excluded: chain 9 residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 382 optimal weight: 20.0000 chunk 615 optimal weight: 0.6980 chunk 375 optimal weight: 5.9990 chunk 291 optimal weight: 9.9990 chunk 427 optimal weight: 8.9990 chunk 645 optimal weight: 6.9990 chunk 594 optimal weight: 9.9990 chunk 514 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 397 optimal weight: 1.9990 chunk 315 optimal weight: 30.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 102 ASN ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN 1 30 ASN 3 93 ASN ** 3 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 143 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.129 51300 Z= 2.118 Angle : 0.821 40.642 70596 Z= 0.463 Chirality : 0.049 0.371 8352 Planarity : 0.006 0.079 8856 Dihedral : 5.546 51.622 7308 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 22.49 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.69 % Favored : 89.03 % Rotamer: Outliers : 1.54 % Allowed : 17.83 % Favored : 80.63 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.84 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.10), residues: 6408 helix: -4.47 (0.08), residues: 432 sheet: -0.78 (0.11), residues: 2448 loop : -2.25 (0.10), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP R 34 PHE 0.057 0.003 PHE T 200 TYR 0.029 0.001 TYR M 194 ARG 0.024 0.001 ARG N 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 210 time to evaluate : 5.454 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: G 26 LEU cc_start: 0.8128 (tp) cc_final: 0.7635 (tt) REVERT: H 55 ARG cc_start: 0.3703 (ttt180) cc_final: 0.3327 (ttt-90) REVERT: H 145 VAL cc_start: 0.9406 (OUTLIER) cc_final: 0.9058 (p) REVERT: J 130 ASP cc_start: 0.8176 (m-30) cc_final: 0.7636 (t0) REVERT: K 28 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7110 (m-80) REVERT: N 44 MET cc_start: 0.7119 (mtp) cc_final: 0.6465 (mtp) REVERT: O 35 LEU cc_start: 0.9140 (mt) cc_final: 0.8914 (mt) REVERT: O 44 MET cc_start: 0.4459 (tpt) cc_final: 0.4012 (tmm) REVERT: O 57 ASP cc_start: 0.8081 (p0) cc_final: 0.7552 (p0) REVERT: P 44 MET cc_start: 0.2358 (tpt) cc_final: 0.2086 (tpt) REVERT: P 90 ASP cc_start: 0.8008 (t0) cc_final: 0.7733 (t0) REVERT: P 130 ASP cc_start: 0.8591 (m-30) cc_final: 0.7779 (t0) REVERT: R 65 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8575 (p) REVERT: R 177 ASP cc_start: 0.9168 (t0) cc_final: 0.8775 (t0) REVERT: X 57 ASP cc_start: 0.7942 (p0) cc_final: 0.7618 (p0) REVERT: E 44 MET cc_start: 0.6645 (mtp) cc_final: 0.6064 (mtp) REVERT: B 35 LEU cc_start: 0.9301 (mp) cc_final: 0.8843 (pp) REVERT: B 46 TYR cc_start: 0.6521 (m-80) cc_final: 0.5972 (m-10) REVERT: D 90 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7839 (t70) REVERT: D 175 LEU cc_start: 0.8805 (tt) cc_final: 0.8366 (tp) REVERT: F 65 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7737 (p) REVERT: 0 109 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8257 (mm) REVERT: 1 44 MET cc_start: 0.2352 (tpt) cc_final: 0.1343 (tpt) REVERT: 2 90 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7750 (t70) REVERT: 2 175 LEU cc_start: 0.9141 (tt) cc_final: 0.8739 (tp) REVERT: 8 90 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7459 (t0) REVERT: 8 175 LEU cc_start: 0.9243 (tp) cc_final: 0.8995 (mt) REVERT: 9 57 ASP cc_start: 0.7760 (p0) cc_final: 0.7278 (m-30) REVERT: 9 98 LEU cc_start: 0.9267 (mm) cc_final: 0.8910 (tp) outliers start: 87 outliers final: 72 residues processed: 287 average time/residue: 0.5427 time to fit residues: 269.6532 Evaluate side-chains 283 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 203 time to evaluate : 5.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 101 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 191 ILE Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 101 CYS Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain N residue 197 ASN Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain Q residue 82 ILE Chi-restraints excluded: chain Q residue 101 CYS Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain U residue 101 CYS Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 198 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain Y residue 80 THR Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 157 THR Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 109 LEU Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 2 residue 28 PHE Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 2 residue 90 ASP Chi-restraints excluded: chain 2 residue 99 GLN Chi-restraints excluded: chain 2 residue 113 LEU Chi-restraints excluded: chain 2 residue 198 VAL Chi-restraints excluded: chain 3 residue 93 ASN Chi-restraints excluded: chain 3 residue 137 ASN Chi-restraints excluded: chain 3 residue 162 ILE Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 4 residue 95 THR Chi-restraints excluded: chain 5 residue 101 CYS Chi-restraints excluded: chain 5 residue 145 VAL Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 6 residue 36 ILE Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 88 THR Chi-restraints excluded: chain 7 residue 145 VAL Chi-restraints excluded: chain 8 residue 90 ASP Chi-restraints excluded: chain 8 residue 198 VAL Chi-restraints excluded: chain 9 residue 137 ASN Chi-restraints excluded: chain 9 residue 175 LEU Chi-restraints excluded: chain 9 residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 408 optimal weight: 0.6980 chunk 547 optimal weight: 0.6980 chunk 157 optimal weight: 8.9990 chunk 474 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 514 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 528 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 30 ASN ** 3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.076765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.055441 restraints weight = 276010.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.055925 restraints weight = 155186.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.055913 restraints weight = 101946.798| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.130 51300 Z= 2.118 Angle : 0.822 40.653 70596 Z= 0.464 Chirality : 0.049 0.371 8352 Planarity : 0.006 0.108 8856 Dihedral : 5.594 52.072 7308 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.75 % Favored : 88.97 % Rotamer: Outliers : 1.66 % Allowed : 17.76 % Favored : 80.57 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.84 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.10), residues: 6408 helix: -4.46 (0.08), residues: 432 sheet: -0.80 (0.11), residues: 2448 loop : -2.26 (0.10), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP R 34 PHE 0.056 0.003 PHE T 200 TYR 0.036 0.001 TYR 0 105 ARG 0.018 0.001 ARG N 55 =============================================================================== Job complete usr+sys time: 8025.93 seconds wall clock time: 150 minutes 37.29 seconds (9037.29 seconds total)