Starting phenix.real_space_refine on Tue Mar 19 08:14:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb5_23263/03_2024/7lb5_23263.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb5_23263/03_2024/7lb5_23263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb5_23263/03_2024/7lb5_23263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb5_23263/03_2024/7lb5_23263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb5_23263/03_2024/7lb5_23263.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb5_23263/03_2024/7lb5_23263.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.120 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 156 5.16 5 C 14772 2.51 5 N 4236 2.21 5 O 4452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 47": "OE1" <-> "OE2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A ASP 214": "OD1" <-> "OD2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B ASP 214": "OD1" <-> "OD2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 286": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ASP 69": "OD1" <-> "OD2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C ASP 199": "OD1" <-> "OD2" Residue "C ASP 200": "OD1" <-> "OD2" Residue "C ASP 214": "OD1" <-> "OD2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D ASP 69": "OD1" <-> "OD2" Residue "D ASP 132": "OD1" <-> "OD2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D ASP 198": "OD1" <-> "OD2" Residue "D ASP 199": "OD1" <-> "OD2" Residue "D ASP 200": "OD1" <-> "OD2" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 286": "OE1" <-> "OE2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E ASP 69": "OD1" <-> "OD2" Residue "E ASP 132": "OD1" <-> "OD2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E ASP 198": "OD1" <-> "OD2" Residue "E ASP 199": "OD1" <-> "OD2" Residue "E ASP 200": "OD1" <-> "OD2" Residue "E ASP 214": "OD1" <-> "OD2" Residue "E PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 286": "OE1" <-> "OE2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F ASP 69": "OD1" <-> "OD2" Residue "F ASP 132": "OD1" <-> "OD2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F ASP 198": "OD1" <-> "OD2" Residue "F ASP 199": "OD1" <-> "OD2" Residue "F ASP 200": "OD1" <-> "OD2" Residue "F ASP 214": "OD1" <-> "OD2" Residue "F PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 286": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ASP 69": "OD1" <-> "OD2" Residue "G ASP 132": "OD1" <-> "OD2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G ASP 198": "OD1" <-> "OD2" Residue "G ASP 199": "OD1" <-> "OD2" Residue "G ASP 200": "OD1" <-> "OD2" Residue "G ASP 214": "OD1" <-> "OD2" Residue "G PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 286": "OE1" <-> "OE2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H ASP 69": "OD1" <-> "OD2" Residue "H ASP 132": "OD1" <-> "OD2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "H ASP 198": "OD1" <-> "OD2" Residue "H ASP 199": "OD1" <-> "OD2" Residue "H ASP 200": "OD1" <-> "OD2" Residue "H ASP 214": "OD1" <-> "OD2" Residue "H PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 286": "OE1" <-> "OE2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I ASP 69": "OD1" <-> "OD2" Residue "I ASP 132": "OD1" <-> "OD2" Residue "I GLU 190": "OE1" <-> "OE2" Residue "I ASP 198": "OD1" <-> "OD2" Residue "I ASP 199": "OD1" <-> "OD2" Residue "I ASP 200": "OD1" <-> "OD2" Residue "I ASP 214": "OD1" <-> "OD2" Residue "I PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 286": "OE1" <-> "OE2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "J ASP 69": "OD1" <-> "OD2" Residue "J ASP 132": "OD1" <-> "OD2" Residue "J GLU 190": "OE1" <-> "OE2" Residue "J ASP 198": "OD1" <-> "OD2" Residue "J ASP 199": "OD1" <-> "OD2" Residue "J ASP 200": "OD1" <-> "OD2" Residue "J ASP 214": "OD1" <-> "OD2" Residue "J PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 286": "OE1" <-> "OE2" Residue "K GLU 47": "OE1" <-> "OE2" Residue "K ASP 69": "OD1" <-> "OD2" Residue "K ASP 132": "OD1" <-> "OD2" Residue "K GLU 190": "OE1" <-> "OE2" Residue "K ASP 198": "OD1" <-> "OD2" Residue "K ASP 199": "OD1" <-> "OD2" Residue "K ASP 200": "OD1" <-> "OD2" Residue "K ASP 214": "OD1" <-> "OD2" Residue "K PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 286": "OE1" <-> "OE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L ASP 69": "OD1" <-> "OD2" Residue "L ASP 132": "OD1" <-> "OD2" Residue "L GLU 190": "OE1" <-> "OE2" Residue "L ASP 198": "OD1" <-> "OD2" Residue "L ASP 199": "OD1" <-> "OD2" Residue "L ASP 200": "OD1" <-> "OD2" Residue "L ASP 214": "OD1" <-> "OD2" Residue "L PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 286": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23616 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1968 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Chain: "B" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1968 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Chain: "C" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1968 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Chain: "D" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1968 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Chain: "E" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1968 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Chain: "F" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1968 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Chain: "G" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1968 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Chain: "H" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1968 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Chain: "I" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1968 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Chain: "J" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1968 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Chain: "K" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1968 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Chain: "L" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1968 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Residues with excluded nonbonded symmetry interactions: 192 residue: pdb=" N PRO A 29 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO A 29 " occ=0.49 residue: pdb=" N PHE A 30 " occ=0.75 ... (9 atoms not shown) pdb=" CZ PHE A 30 " occ=0.49 residue: pdb=" N ALA A 60 " occ=0.90 ... (3 atoms not shown) pdb=" CB ALA A 60 " occ=0.90 residue: pdb=" N CYS A 63 " occ=0.86 ... (4 atoms not shown) pdb=" SG CYS A 63 " occ=0.65 residue: pdb=" N VAL A 71 " occ=0.89 ... (5 atoms not shown) pdb=" CG2 VAL A 71 " occ=0.89 residue: pdb=" N ARG A 72 " occ=0.89 ... (9 atoms not shown) pdb=" NH2 ARG A 72 " occ=0.56 residue: pdb=" N GLY A 75 " occ=0.89 ... (2 atoms not shown) pdb=" O GLY A 75 " occ=0.89 residue: pdb=" N GLY A 76 " occ=0.91 ... (2 atoms not shown) pdb=" O GLY A 76 " occ=0.91 residue: pdb=" N VAL A 77 " occ=0.91 ... (5 atoms not shown) pdb=" CG2 VAL A 77 " occ=0.89 residue: pdb=" N SER A 94 " occ=0.81 ... (4 atoms not shown) pdb=" OG SER A 94 " occ=0.83 residue: pdb=" N ARG A 141 " occ=0.91 ... (9 atoms not shown) pdb=" NH2 ARG A 141 " occ=0.54 residue: pdb=" N MET A 164 " occ=0.92 ... (6 atoms not shown) pdb=" CE MET A 164 " occ=0.92 ... (remaining 180 not shown) Time building chain proxies: 12.88, per 1000 atoms: 0.55 Number of scatterers: 23616 At special positions: 0 Unit cell: (119.163, 126.753, 107.019, 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 156 16.00 O 4452 8.00 N 4236 7.00 C 14772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.37 Conformation dependent library (CDL) restraints added in 4.8 seconds 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5760 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 12 sheets defined 54.6% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 29 through 38 removed outlier: 3.538A pdb=" N LYS A 33 " --> pdb=" O PRO A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.575A pdb=" N ALA A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 177 through 197 removed outlier: 3.642A pdb=" N ASN A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 201 through 210 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.808A pdb=" N VAL A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.574A pdb=" N LYS A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'B' and resid 30 through 38 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 105 through 115 removed outlier: 3.574A pdb=" N ALA B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 177 through 197 removed outlier: 3.642A pdb=" N ASN B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 237 through 247 Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.808A pdb=" N VAL B 258 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 removed outlier: 3.574A pdb=" N LYS B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 288 Processing helix chain 'C' and resid 30 through 38 Processing helix chain 'C' and resid 50 through 61 Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 105 through 115 removed outlier: 3.573A pdb=" N ALA C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 177 through 197 removed outlier: 3.641A pdb=" N ASN C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 200 No H-bonds generated for 'chain 'C' and resid 198 through 200' Processing helix chain 'C' and resid 201 through 210 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 237 through 247 Processing helix chain 'C' and resid 255 through 259 removed outlier: 3.807A pdb=" N VAL C 258 " --> pdb=" O GLY C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 removed outlier: 3.575A pdb=" N LYS C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 288 Processing helix chain 'D' and resid 30 through 38 Processing helix chain 'D' and resid 50 through 61 Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'D' and resid 105 through 115 removed outlier: 3.574A pdb=" N ALA D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 161 Processing helix chain 'D' and resid 177 through 197 removed outlier: 3.641A pdb=" N ASN D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 201 through 210 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 237 through 247 Processing helix chain 'D' and resid 255 through 259 removed outlier: 3.808A pdb=" N VAL D 258 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 277 removed outlier: 3.574A pdb=" N LYS D 267 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 288 Processing helix chain 'E' and resid 30 through 38 Processing helix chain 'E' and resid 50 through 61 Processing helix chain 'E' and resid 82 through 93 Processing helix chain 'E' and resid 105 through 115 removed outlier: 3.574A pdb=" N ALA E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 161 Processing helix chain 'E' and resid 177 through 197 removed outlier: 3.642A pdb=" N ASN E 196 " --> pdb=" O ARG E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 201 through 210 Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 237 through 247 Processing helix chain 'E' and resid 255 through 259 removed outlier: 3.808A pdb=" N VAL E 258 " --> pdb=" O GLY E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 277 removed outlier: 3.573A pdb=" N LYS E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 288 Processing helix chain 'F' and resid 30 through 38 Processing helix chain 'F' and resid 50 through 61 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 105 through 115 removed outlier: 3.575A pdb=" N ALA F 109 " --> pdb=" O HIS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 161 Processing helix chain 'F' and resid 177 through 197 removed outlier: 3.642A pdb=" N ASN F 196 " --> pdb=" O ARG F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 200 No H-bonds generated for 'chain 'F' and resid 198 through 200' Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'F' and resid 212 through 223 Processing helix chain 'F' and resid 237 through 247 Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.808A pdb=" N VAL F 258 " --> pdb=" O GLY F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 277 removed outlier: 3.573A pdb=" N LYS F 267 " --> pdb=" O ASP F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 288 Processing helix chain 'G' and resid 30 through 38 Processing helix chain 'G' and resid 50 through 61 Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'G' and resid 105 through 115 removed outlier: 3.573A pdb=" N ALA G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 161 Processing helix chain 'G' and resid 177 through 197 removed outlier: 3.641A pdb=" N ASN G 196 " --> pdb=" O ARG G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 200 No H-bonds generated for 'chain 'G' and resid 198 through 200' Processing helix chain 'G' and resid 201 through 210 Processing helix chain 'G' and resid 212 through 223 Processing helix chain 'G' and resid 237 through 247 Processing helix chain 'G' and resid 255 through 259 removed outlier: 3.808A pdb=" N VAL G 258 " --> pdb=" O GLY G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 277 removed outlier: 3.574A pdb=" N LYS G 267 " --> pdb=" O ASP G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 288 Processing helix chain 'H' and resid 30 through 38 Processing helix chain 'H' and resid 50 through 61 Processing helix chain 'H' and resid 82 through 93 Processing helix chain 'H' and resid 105 through 115 removed outlier: 3.574A pdb=" N ALA H 109 " --> pdb=" O HIS H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 161 Processing helix chain 'H' and resid 177 through 197 removed outlier: 3.641A pdb=" N ASN H 196 " --> pdb=" O ARG H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 201 through 210 Processing helix chain 'H' and resid 212 through 223 Processing helix chain 'H' and resid 237 through 247 Processing helix chain 'H' and resid 255 through 259 removed outlier: 3.808A pdb=" N VAL H 258 " --> pdb=" O GLY H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 277 removed outlier: 3.574A pdb=" N LYS H 267 " --> pdb=" O ASP H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 288 Processing helix chain 'I' and resid 30 through 38 Processing helix chain 'I' and resid 50 through 61 Processing helix chain 'I' and resid 82 through 93 Processing helix chain 'I' and resid 105 through 115 removed outlier: 3.574A pdb=" N ALA I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 161 Processing helix chain 'I' and resid 177 through 197 removed outlier: 3.642A pdb=" N ASN I 196 " --> pdb=" O ARG I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 200 No H-bonds generated for 'chain 'I' and resid 198 through 200' Processing helix chain 'I' and resid 201 through 210 Processing helix chain 'I' and resid 212 through 223 Processing helix chain 'I' and resid 237 through 247 Processing helix chain 'I' and resid 255 through 259 removed outlier: 3.808A pdb=" N VAL I 258 " --> pdb=" O GLY I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 263 through 277 removed outlier: 3.574A pdb=" N LYS I 267 " --> pdb=" O ASP I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 288 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 50 through 61 Processing helix chain 'J' and resid 82 through 93 Processing helix chain 'J' and resid 105 through 115 removed outlier: 3.574A pdb=" N ALA J 109 " --> pdb=" O HIS J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 161 Processing helix chain 'J' and resid 177 through 197 removed outlier: 3.642A pdb=" N ASN J 196 " --> pdb=" O ARG J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 200 No H-bonds generated for 'chain 'J' and resid 198 through 200' Processing helix chain 'J' and resid 201 through 210 Processing helix chain 'J' and resid 212 through 223 Processing helix chain 'J' and resid 237 through 247 Processing helix chain 'J' and resid 255 through 259 removed outlier: 3.807A pdb=" N VAL J 258 " --> pdb=" O GLY J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 277 removed outlier: 3.575A pdb=" N LYS J 267 " --> pdb=" O ASP J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 288 Processing helix chain 'K' and resid 30 through 38 Processing helix chain 'K' and resid 50 through 61 Processing helix chain 'K' and resid 82 through 93 Processing helix chain 'K' and resid 105 through 115 removed outlier: 3.574A pdb=" N ALA K 109 " --> pdb=" O HIS K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 161 Processing helix chain 'K' and resid 177 through 197 removed outlier: 3.642A pdb=" N ASN K 196 " --> pdb=" O ARG K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 200 No H-bonds generated for 'chain 'K' and resid 198 through 200' Processing helix chain 'K' and resid 201 through 210 Processing helix chain 'K' and resid 212 through 223 Processing helix chain 'K' and resid 237 through 247 Processing helix chain 'K' and resid 255 through 259 removed outlier: 3.809A pdb=" N VAL K 258 " --> pdb=" O GLY K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 263 through 277 removed outlier: 3.574A pdb=" N LYS K 267 " --> pdb=" O ASP K 263 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 288 Processing helix chain 'L' and resid 30 through 38 Processing helix chain 'L' and resid 50 through 61 Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'L' and resid 105 through 115 removed outlier: 3.573A pdb=" N ALA L 109 " --> pdb=" O HIS L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 161 Processing helix chain 'L' and resid 177 through 197 removed outlier: 3.642A pdb=" N ASN L 196 " --> pdb=" O ARG L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 200 No H-bonds generated for 'chain 'L' and resid 198 through 200' Processing helix chain 'L' and resid 201 through 210 Processing helix chain 'L' and resid 212 through 223 Processing helix chain 'L' and resid 237 through 247 Processing helix chain 'L' and resid 255 through 259 removed outlier: 3.807A pdb=" N VAL L 258 " --> pdb=" O GLY L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 277 removed outlier: 3.574A pdb=" N LYS L 267 " --> pdb=" O ASP L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 288 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA A 44 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE A 66 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 46 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 65 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ARG A 100 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL A 67 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG A 102 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 97 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP A 121 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA A 99 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER A 123 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA A 101 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 120 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY A 147 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU A 122 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE A 144 " --> pdb=" O MET A 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG A 166 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS A 146 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN A 168 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS A 148 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 251 " --> pdb=" O GLN A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA B 44 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE B 66 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL B 46 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 65 " --> pdb=" O MET B 98 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG B 100 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL B 67 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG B 102 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B 97 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASP B 121 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA B 99 " --> pdb=" O ASP B 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER B 123 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA B 101 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE B 120 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY B 147 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N GLU B 122 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE B 144 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG B 166 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS B 146 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN B 168 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS B 148 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY B 251 " --> pdb=" O GLN B 229 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA C 44 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE C 66 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL C 46 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL C 65 " --> pdb=" O MET C 98 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ARG C 100 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL C 67 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG C 102 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL C 97 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP C 121 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA C 99 " --> pdb=" O ASP C 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER C 123 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA C 101 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE C 120 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLY C 147 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU C 122 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE C 144 " --> pdb=" O MET C 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG C 166 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS C 146 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN C 168 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS C 148 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY C 251 " --> pdb=" O GLN C 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 43 through 48 removed outlier: 6.584A pdb=" N ALA D 44 " --> pdb=" O SER D 64 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE D 66 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL D 46 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL D 65 " --> pdb=" O MET D 98 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG D 100 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL D 67 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG D 102 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL D 97 " --> pdb=" O TYR D 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP D 121 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA D 99 " --> pdb=" O ASP D 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER D 123 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA D 101 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE D 120 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY D 147 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU D 122 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE D 144 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG D 166 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS D 146 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN D 168 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS D 148 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY D 251 " --> pdb=" O GLN D 229 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA E 44 " --> pdb=" O SER E 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE E 66 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL E 46 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL E 65 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG E 100 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL E 67 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N ARG E 102 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL E 97 " --> pdb=" O TYR E 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP E 121 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA E 99 " --> pdb=" O ASP E 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER E 123 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ALA E 101 " --> pdb=" O SER E 123 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE E 120 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY E 147 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU E 122 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE E 144 " --> pdb=" O MET E 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG E 166 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS E 146 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN E 168 " --> pdb=" O CYS E 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS E 148 " --> pdb=" O GLN E 168 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY E 251 " --> pdb=" O GLN E 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA F 44 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE F 66 " --> pdb=" O ALA F 44 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL F 46 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL F 65 " --> pdb=" O MET F 98 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ARG F 100 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL F 67 " --> pdb=" O ARG F 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG F 102 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL F 97 " --> pdb=" O TYR F 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP F 121 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA F 99 " --> pdb=" O ASP F 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER F 123 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA F 101 " --> pdb=" O SER F 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE F 120 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY F 147 " --> pdb=" O ILE F 120 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU F 122 " --> pdb=" O GLY F 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE F 144 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG F 166 " --> pdb=" O PHE F 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS F 146 " --> pdb=" O ARG F 166 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN F 168 " --> pdb=" O CYS F 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS F 148 " --> pdb=" O GLN F 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY F 251 " --> pdb=" O GLN F 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA G 44 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE G 66 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL G 46 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL G 65 " --> pdb=" O MET G 98 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG G 100 " --> pdb=" O VAL G 65 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL G 67 " --> pdb=" O ARG G 100 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N ARG G 102 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL G 97 " --> pdb=" O TYR G 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP G 121 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA G 99 " --> pdb=" O ASP G 121 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER G 123 " --> pdb=" O ALA G 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA G 101 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE G 120 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY G 147 " --> pdb=" O ILE G 120 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU G 122 " --> pdb=" O GLY G 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE G 144 " --> pdb=" O MET G 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG G 166 " --> pdb=" O PHE G 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS G 146 " --> pdb=" O ARG G 166 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLN G 168 " --> pdb=" O CYS G 146 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS G 148 " --> pdb=" O GLN G 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY G 251 " --> pdb=" O GLN G 229 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA H 44 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE H 66 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL H 46 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL H 65 " --> pdb=" O MET H 98 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ARG H 100 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL H 67 " --> pdb=" O ARG H 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG H 102 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL H 97 " --> pdb=" O TYR H 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP H 121 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA H 99 " --> pdb=" O ASP H 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER H 123 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA H 101 " --> pdb=" O SER H 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE H 120 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLY H 147 " --> pdb=" O ILE H 120 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N GLU H 122 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE H 144 " --> pdb=" O MET H 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG H 166 " --> pdb=" O PHE H 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS H 146 " --> pdb=" O ARG H 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN H 168 " --> pdb=" O CYS H 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS H 148 " --> pdb=" O GLN H 168 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY H 251 " --> pdb=" O GLN H 229 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 43 through 48 removed outlier: 6.584A pdb=" N ALA I 44 " --> pdb=" O SER I 64 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE I 66 " --> pdb=" O ALA I 44 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL I 46 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL I 65 " --> pdb=" O MET I 98 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG I 100 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL I 67 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG I 102 " --> pdb=" O VAL I 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL I 97 " --> pdb=" O TYR I 119 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASP I 121 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA I 99 " --> pdb=" O ASP I 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER I 123 " --> pdb=" O ALA I 99 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ALA I 101 " --> pdb=" O SER I 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE I 120 " --> pdb=" O ILE I 145 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY I 147 " --> pdb=" O ILE I 120 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU I 122 " --> pdb=" O GLY I 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE I 144 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ARG I 166 " --> pdb=" O PHE I 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS I 146 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLN I 168 " --> pdb=" O CYS I 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS I 148 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY I 251 " --> pdb=" O GLN I 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA J 44 " --> pdb=" O SER J 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE J 66 " --> pdb=" O ALA J 44 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL J 46 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL J 65 " --> pdb=" O MET J 98 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG J 100 " --> pdb=" O VAL J 65 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL J 67 " --> pdb=" O ARG J 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG J 102 " --> pdb=" O VAL J 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL J 97 " --> pdb=" O TYR J 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP J 121 " --> pdb=" O VAL J 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA J 99 " --> pdb=" O ASP J 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER J 123 " --> pdb=" O ALA J 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA J 101 " --> pdb=" O SER J 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE J 120 " --> pdb=" O ILE J 145 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLY J 147 " --> pdb=" O ILE J 120 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU J 122 " --> pdb=" O GLY J 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE J 144 " --> pdb=" O MET J 164 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ARG J 166 " --> pdb=" O PHE J 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS J 146 " --> pdb=" O ARG J 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN J 168 " --> pdb=" O CYS J 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS J 148 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY J 251 " --> pdb=" O GLN J 229 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA K 44 " --> pdb=" O SER K 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE K 66 " --> pdb=" O ALA K 44 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL K 46 " --> pdb=" O ILE K 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL K 65 " --> pdb=" O MET K 98 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG K 100 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL K 67 " --> pdb=" O ARG K 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG K 102 " --> pdb=" O VAL K 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL K 97 " --> pdb=" O TYR K 119 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP K 121 " --> pdb=" O VAL K 97 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA K 99 " --> pdb=" O ASP K 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER K 123 " --> pdb=" O ALA K 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA K 101 " --> pdb=" O SER K 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE K 120 " --> pdb=" O ILE K 145 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLY K 147 " --> pdb=" O ILE K 120 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N GLU K 122 " --> pdb=" O GLY K 147 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE K 144 " --> pdb=" O MET K 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG K 166 " --> pdb=" O PHE K 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS K 146 " --> pdb=" O ARG K 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN K 168 " --> pdb=" O CYS K 146 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS K 148 " --> pdb=" O GLN K 168 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY K 251 " --> pdb=" O GLN K 229 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 43 through 48 removed outlier: 6.583A pdb=" N ALA L 44 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE L 66 " --> pdb=" O ALA L 44 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL L 46 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL L 65 " --> pdb=" O MET L 98 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG L 100 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL L 67 " --> pdb=" O ARG L 100 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ARG L 102 " --> pdb=" O VAL L 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL L 97 " --> pdb=" O TYR L 119 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASP L 121 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA L 99 " --> pdb=" O ASP L 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER L 123 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA L 101 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE L 120 " --> pdb=" O ILE L 145 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLY L 147 " --> pdb=" O ILE L 120 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N GLU L 122 " --> pdb=" O GLY L 147 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE L 144 " --> pdb=" O MET L 164 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG L 166 " --> pdb=" O PHE L 144 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS L 146 " --> pdb=" O ARG L 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN L 168 " --> pdb=" O CYS L 146 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS L 148 " --> pdb=" O GLN L 168 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY L 251 " --> pdb=" O GLN L 229 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3492 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: 8.21 Time building geometry restraints manager: 10.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8196 1.34 - 1.46: 3311 1.46 - 1.57: 12205 1.57 - 1.69: 0 1.69 - 1.80: 264 Bond restraints: 23976 Sorted by residual: bond pdb=" CB VAL I 181 " pdb=" CG1 VAL I 181 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.46e-01 bond pdb=" CB VAL C 181 " pdb=" CG1 VAL C 181 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.34e-01 bond pdb=" CB VAL J 181 " pdb=" CG1 VAL J 181 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.32e-01 bond pdb=" CB VAL H 181 " pdb=" CG1 VAL H 181 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.21e-01 bond pdb=" CB VAL F 181 " pdb=" CG1 VAL F 181 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 5.05e-01 ... (remaining 23971 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.25: 720 106.25 - 112.50: 12343 112.50 - 118.75: 6685 118.75 - 125.00: 12472 125.00 - 131.25: 192 Bond angle restraints: 32412 Sorted by residual: angle pdb=" N THR E 172 " pdb=" CA THR E 172 " pdb=" C THR E 172 " ideal model delta sigma weight residual 113.38 110.56 2.82 1.17e+00 7.31e-01 5.83e+00 angle pdb=" N THR F 172 " pdb=" CA THR F 172 " pdb=" C THR F 172 " ideal model delta sigma weight residual 113.38 110.56 2.82 1.17e+00 7.31e-01 5.80e+00 angle pdb=" N THR C 172 " pdb=" CA THR C 172 " pdb=" C THR C 172 " ideal model delta sigma weight residual 113.38 110.57 2.81 1.17e+00 7.31e-01 5.77e+00 angle pdb=" N THR K 172 " pdb=" CA THR K 172 " pdb=" C THR K 172 " ideal model delta sigma weight residual 113.38 110.57 2.81 1.17e+00 7.31e-01 5.75e+00 angle pdb=" N THR I 172 " pdb=" CA THR I 172 " pdb=" C THR I 172 " ideal model delta sigma weight residual 113.38 110.58 2.80 1.17e+00 7.31e-01 5.73e+00 ... (remaining 32407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 13092 16.95 - 33.90: 1272 33.90 - 50.85: 300 50.85 - 67.80: 36 67.80 - 84.75: 24 Dihedral angle restraints: 14724 sinusoidal: 5820 harmonic: 8904 Sorted by residual: dihedral pdb=" CA GLU D 122 " pdb=" C GLU D 122 " pdb=" N SER D 123 " pdb=" CA SER D 123 " ideal model delta harmonic sigma weight residual -180.00 -163.99 -16.01 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA GLU H 122 " pdb=" C GLU H 122 " pdb=" N SER H 123 " pdb=" CA SER H 123 " ideal model delta harmonic sigma weight residual 180.00 -164.00 -16.00 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA GLU C 122 " pdb=" C GLU C 122 " pdb=" N SER C 123 " pdb=" CA SER C 123 " ideal model delta harmonic sigma weight residual -180.00 -164.01 -15.99 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 14721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2201 0.031 - 0.061: 1003 0.061 - 0.092: 342 0.092 - 0.122: 181 0.122 - 0.153: 29 Chirality restraints: 3756 Sorted by residual: chirality pdb=" CA ASP C 69 " pdb=" N ASP C 69 " pdb=" C ASP C 69 " pdb=" CB ASP C 69 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA ASP D 69 " pdb=" N ASP D 69 " pdb=" C ASP D 69 " pdb=" CB ASP D 69 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ASP L 69 " pdb=" N ASP L 69 " pdb=" C ASP L 69 " pdb=" CB ASP L 69 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 3753 not shown) Planarity restraints: 4284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP H 82 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO H 83 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO H 83 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 83 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 82 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO B 83 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 83 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 83 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP L 82 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.99e+00 pdb=" N PRO L 83 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO L 83 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 83 " 0.020 5.00e-02 4.00e+02 ... (remaining 4281 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 7465 2.84 - 3.35: 22202 3.35 - 3.87: 39180 3.87 - 4.38: 45440 4.38 - 4.90: 79182 Nonbonded interactions: 193469 Sorted by model distance: nonbonded pdb=" NH2 ARG A 224 " pdb=" OE1 GLN A 229 " model vdw 2.323 2.520 nonbonded pdb=" NH2 ARG D 224 " pdb=" OE1 GLN D 229 " model vdw 2.323 2.520 nonbonded pdb=" NH2 ARG J 224 " pdb=" OE1 GLN J 229 " model vdw 2.324 2.520 nonbonded pdb=" NH2 ARG H 224 " pdb=" OE1 GLN H 229 " model vdw 2.324 2.520 nonbonded pdb=" NH2 ARG E 224 " pdb=" OE1 GLN E 229 " model vdw 2.324 2.520 ... (remaining 193464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.49 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.210 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 63.940 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.160 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: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 23976 Z= 0.224 Angle : 0.515 5.585 32412 Z= 0.317 Chirality : 0.043 0.153 3756 Planarity : 0.004 0.035 4284 Dihedral : 14.285 84.754 8964 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.93 % Allowed : 1.87 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.13), residues: 3096 helix: -0.66 (0.11), residues: 1560 sheet: -0.95 (0.20), residues: 588 loop : -2.35 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 105 PHE 0.008 0.001 PHE L 106 TYR 0.007 0.001 TYR C 213 ARG 0.002 0.000 ARG J 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 291 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8255 (ttp) cc_final: 0.7989 (ttp) REVERT: D 80 MET cc_start: 0.8282 (ttp) cc_final: 0.8048 (ttp) REVERT: F 80 MET cc_start: 0.8207 (ttp) cc_final: 0.7965 (ttp) REVERT: H 80 MET cc_start: 0.8238 (ttp) cc_final: 0.8012 (ttp) REVERT: K 80 MET cc_start: 0.8197 (ttp) cc_final: 0.7989 (ttp) outliers start: 24 outliers final: 0 residues processed: 303 average time/residue: 0.3478 time to fit residues: 167.8496 Evaluate side-chains 232 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 244 optimal weight: 0.2980 chunk 94 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 182 optimal weight: 10.0000 chunk 283 optimal weight: 0.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 139 ASN B 52 ASN B 139 ASN C 52 ASN C 139 ASN D 52 ASN D 139 ASN E 38 GLN E 168 GLN E 273 GLN E 276 GLN F 52 ASN F 139 ASN G 139 ASN H 52 ASN H 133 HIS H 139 ASN I 52 ASN I 139 ASN J 52 ASN J 139 ASN J 168 GLN K 52 ASN K 139 ASN L 52 ASN L 139 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 23976 Z= 0.245 Angle : 0.510 5.478 32412 Z= 0.268 Chirality : 0.044 0.144 3756 Planarity : 0.004 0.029 4284 Dihedral : 3.980 13.812 3360 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.51 % Allowed : 10.32 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 3096 helix: 1.39 (0.12), residues: 1584 sheet: -0.52 (0.22), residues: 588 loop : -1.80 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 105 PHE 0.008 0.001 PHE J 205 TYR 0.017 0.002 TYR B 278 ARG 0.004 0.000 ARG H 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 237 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8307 (ttp) cc_final: 0.8009 (ttp) REVERT: D 80 MET cc_start: 0.8324 (ttp) cc_final: 0.8021 (ttp) outliers start: 13 outliers final: 10 residues processed: 237 average time/residue: 0.2940 time to fit residues: 117.4668 Evaluate side-chains 234 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 224 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain K residue 165 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 192 optimal weight: 0.0770 chunk 78 optimal weight: 7.9990 chunk 283 optimal weight: 0.5980 chunk 306 optimal weight: 0.8980 chunk 252 optimal weight: 0.6980 chunk 281 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN H 52 ASN I 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 23976 Z= 0.134 Angle : 0.459 5.364 32412 Z= 0.238 Chirality : 0.042 0.138 3756 Planarity : 0.003 0.026 4284 Dihedral : 3.679 15.216 3360 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.71 % Allowed : 9.54 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.16), residues: 3096 helix: 2.20 (0.13), residues: 1584 sheet: -0.13 (0.22), residues: 600 loop : -1.47 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 133 PHE 0.008 0.001 PHE G 205 TYR 0.014 0.002 TYR G 278 ARG 0.002 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 246 time to evaluate : 2.764 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 43 residues processed: 272 average time/residue: 0.2866 time to fit residues: 132.1752 Evaluate side-chains 280 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 237 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 6.9990 chunk 213 optimal weight: 0.0040 chunk 147 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 190 optimal weight: 8.9990 chunk 284 optimal weight: 3.9990 chunk 301 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 269 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 ASN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 ASN K 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 23976 Z= 0.319 Angle : 0.525 5.686 32412 Z= 0.272 Chirality : 0.044 0.144 3756 Planarity : 0.004 0.031 4284 Dihedral : 3.801 13.861 3360 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.76 % Allowed : 10.24 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.16), residues: 3096 helix: 2.56 (0.13), residues: 1584 sheet: 0.10 (0.22), residues: 588 loop : -1.51 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 105 PHE 0.008 0.001 PHE D 106 TYR 0.012 0.002 TYR L 278 ARG 0.003 0.000 ARG L 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 219 time to evaluate : 2.830 Fit side-chains REVERT: A 80 MET cc_start: 0.8270 (ttp) cc_final: 0.7946 (ttp) REVERT: D 80 MET cc_start: 0.8282 (ttp) cc_final: 0.7961 (ttp) outliers start: 71 outliers final: 49 residues processed: 266 average time/residue: 0.2824 time to fit residues: 128.1676 Evaluate side-chains 259 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 210 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 165 ILE Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 4 optimal weight: 0.0970 chunk 224 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 270 optimal weight: 0.0370 chunk 76 optimal weight: 5.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 23976 Z= 0.130 Angle : 0.455 5.865 32412 Z= 0.235 Chirality : 0.042 0.135 3756 Planarity : 0.003 0.030 4284 Dihedral : 3.595 13.132 3360 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.99 % Allowed : 10.83 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.16), residues: 3096 helix: 2.82 (0.13), residues: 1584 sheet: 0.29 (0.23), residues: 588 loop : -1.26 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 133 PHE 0.007 0.001 PHE G 230 TYR 0.016 0.001 TYR I 278 ARG 0.004 0.000 ARG I 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 241 time to evaluate : 2.636 Fit side-chains REVERT: A 80 MET cc_start: 0.8239 (ttp) cc_final: 0.7924 (ttp) REVERT: D 80 MET cc_start: 0.8237 (ttp) cc_final: 0.7939 (ttp) outliers start: 51 outliers final: 46 residues processed: 270 average time/residue: 0.2828 time to fit residues: 128.7517 Evaluate side-chains 271 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 225 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 0.5980 chunk 271 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 177 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 301 optimal weight: 4.9990 chunk 250 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 0.0010 chunk 99 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 139 ASN B 136 ASN B 139 ASN C 136 ASN C 139 ASN D 136 ASN D 139 ASN F 136 ASN F 139 ASN ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN G 139 ASN H 136 ASN H 139 ASN ** H 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 ASN I 139 ASN K 136 ASN K 139 ASN L 136 ASN L 139 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23976 Z= 0.135 Angle : 0.458 11.109 32412 Z= 0.233 Chirality : 0.042 0.134 3756 Planarity : 0.003 0.029 4284 Dihedral : 3.494 12.857 3360 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.99 % Allowed : 11.92 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.16), residues: 3096 helix: 2.89 (0.13), residues: 1584 sheet: 0.22 (0.23), residues: 600 loop : -0.93 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 105 PHE 0.006 0.001 PHE F 106 TYR 0.013 0.001 TYR A 278 ARG 0.001 0.000 ARG E 224 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 233 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 273 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8481 (mm-40) REVERT: I 188 MET cc_start: 0.8460 (mmt) cc_final: 0.8201 (mmt) REVERT: J 80 MET cc_start: 0.8309 (ttp) cc_final: 0.8063 (ttp) outliers start: 51 outliers final: 43 residues processed: 259 average time/residue: 0.3095 time to fit residues: 133.9349 Evaluate side-chains 271 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 228 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 80 MET Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 0.0570 chunk 34 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 300 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 139 ASN B 136 ASN B 139 ASN C 136 ASN C 139 ASN D 136 ASN D 139 ASN E 136 ASN E 139 ASN F 136 ASN F 139 ASN ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN G 139 ASN H 136 ASN H 139 ASN ** H 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 ASN I 139 ASN J 136 ASN J 139 ASN K 136 ASN K 139 ASN L 136 ASN L 139 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23976 Z= 0.177 Angle : 0.471 7.828 32412 Z= 0.239 Chirality : 0.042 0.133 3756 Planarity : 0.003 0.029 4284 Dihedral : 3.477 12.989 3360 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.83 % Allowed : 12.89 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.16), residues: 3096 helix: 2.96 (0.13), residues: 1584 sheet: 0.51 (0.23), residues: 576 loop : -0.84 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 105 PHE 0.007 0.001 PHE L 106 TYR 0.013 0.002 TYR I 278 ARG 0.002 0.000 ARG I 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 231 time to evaluate : 2.885 Fit side-chains revert: symmetry clash REVERT: J 80 MET cc_start: 0.8315 (ttp) cc_final: 0.8042 (ttp) outliers start: 47 outliers final: 43 residues processed: 256 average time/residue: 0.2996 time to fit residues: 129.9753 Evaluate side-chains 271 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 228 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 165 ILE Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 179 optimal weight: 0.0010 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 204 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 overall best weight: 3.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 139 ASN B 136 ASN B 139 ASN C 136 ASN C 139 ASN D 136 ASN D 139 ASN E 136 ASN E 139 ASN F 136 ASN F 139 ASN G 136 ASN G 139 ASN H 136 ASN H 139 ASN I 136 ASN I 139 ASN J 136 ASN J 139 ASN K 136 ASN K 139 ASN L 136 ASN L 139 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 23976 Z= 0.375 Angle : 0.552 6.887 32412 Z= 0.283 Chirality : 0.045 0.137 3756 Planarity : 0.003 0.034 4284 Dihedral : 3.778 13.683 3360 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.79 % Allowed : 13.40 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.16), residues: 3096 helix: 2.91 (0.13), residues: 1584 sheet: 0.34 (0.22), residues: 576 loop : -0.74 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 105 PHE 0.008 0.001 PHE H 106 TYR 0.011 0.002 TYR I 278 ARG 0.002 0.000 ARG I 159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 220 time to evaluate : 2.956 Fit side-chains REVERT: D 188 MET cc_start: 0.8399 (mmm) cc_final: 0.8170 (mmt) outliers start: 46 outliers final: 42 residues processed: 246 average time/residue: 0.2846 time to fit residues: 119.9233 Evaluate side-chains 249 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 207 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 165 ILE Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.9980 chunk 288 optimal weight: 0.6980 chunk 262 optimal weight: 4.9990 chunk 280 optimal weight: 0.5980 chunk 168 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 253 optimal weight: 0.9990 chunk 265 optimal weight: 6.9990 chunk 279 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 139 ASN B 136 ASN B 139 ASN C 136 ASN C 139 ASN D 136 ASN D 139 ASN E 136 ASN E 139 ASN F 136 ASN F 139 ASN G 136 ASN G 139 ASN H 136 ASN H 139 ASN I 136 ASN I 139 ASN J 136 ASN J 139 ASN K 136 ASN K 139 ASN L 136 ASN L 139 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23976 Z= 0.156 Angle : 0.484 8.748 32412 Z= 0.246 Chirality : 0.042 0.142 3756 Planarity : 0.003 0.030 4284 Dihedral : 3.576 12.768 3360 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.71 % Allowed : 14.02 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.16), residues: 3096 helix: 3.02 (0.13), residues: 1584 sheet: 0.42 (0.23), residues: 576 loop : -0.58 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 133 PHE 0.007 0.001 PHE K 253 TYR 0.015 0.002 TYR I 278 ARG 0.001 0.000 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 2.866 Fit side-chains REVERT: J 80 MET cc_start: 0.8339 (ttp) cc_final: 0.8002 (ttp) outliers start: 44 outliers final: 43 residues processed: 261 average time/residue: 0.2919 time to fit residues: 130.4122 Evaluate side-chains 270 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 227 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 0.0010 chunk 205 optimal weight: 0.9980 chunk 310 optimal weight: 0.0040 chunk 286 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 139 ASN B 136 ASN B 139 ASN C 136 ASN C 139 ASN D 136 ASN D 139 ASN E 136 ASN E 139 ASN F 136 ASN F 139 ASN G 136 ASN G 139 ASN H 136 ASN H 139 ASN I 136 ASN I 139 ASN J 136 ASN J 139 ASN K 136 ASN K 139 ASN L 136 ASN L 139 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23976 Z= 0.183 Angle : 0.489 7.304 32412 Z= 0.249 Chirality : 0.042 0.150 3756 Planarity : 0.003 0.030 4284 Dihedral : 3.553 13.010 3360 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.71 % Allowed : 14.41 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.16), residues: 3096 helix: 3.03 (0.13), residues: 1584 sheet: 0.44 (0.23), residues: 576 loop : -0.53 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 105 PHE 0.007 0.001 PHE K 253 TYR 0.014 0.002 TYR I 278 ARG 0.001 0.000 ARG B 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 225 time to evaluate : 2.790 Fit side-chains REVERT: J 80 MET cc_start: 0.8334 (ttp) cc_final: 0.7992 (ttp) outliers start: 44 outliers final: 44 residues processed: 253 average time/residue: 0.2860 time to fit residues: 123.0894 Evaluate side-chains 269 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 225 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 3.9990 chunk 263 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 chunk 228 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 103 optimal weight: 0.2980 chunk 254 optimal weight: 2.9990 chunk 31 optimal weight: 0.0670 chunk 45 optimal weight: 3.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 139 ASN B 136 ASN B 139 ASN C 136 ASN C 139 ASN D 136 ASN D 139 ASN E 136 ASN E 139 ASN F 136 ASN F 139 ASN G 136 ASN G 139 ASN H 136 ASN H 139 ASN I 136 ASN I 139 ASN J 136 ASN J 139 ASN K 136 ASN K 139 ASN L 136 ASN L 139 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.072260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.058583 restraints weight = 59550.960| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 4.23 r_work: 0.2683 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23976 Z= 0.133 Angle : 0.481 8.883 32412 Z= 0.243 Chirality : 0.042 0.141 3756 Planarity : 0.003 0.029 4284 Dihedral : 3.448 12.910 3360 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.71 % Allowed : 14.88 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.16), residues: 3096 helix: 3.00 (0.13), residues: 1596 sheet: 0.40 (0.23), residues: 588 loop : -0.21 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 133 PHE 0.006 0.001 PHE F 106 TYR 0.014 0.001 TYR I 278 ARG 0.001 0.000 ARG B 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4273.45 seconds wall clock time: 78 minutes 0.16 seconds (4680.16 seconds total)