Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 11 10:11:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb5_23263/07_2023/7lb5_23263.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb5_23263/07_2023/7lb5_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_23263/07_2023/7lb5_23263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb5_23263/07_2023/7lb5_23263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb5_23263/07_2023/7lb5_23263.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb5_23263/07_2023/7lb5_23263.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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-1.21rc1-5013/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: 10.70, per 1000 atoms: 0.45 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: 8.65 Conformation dependent library (CDL) restraints added in 3.6 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: 1.58 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: 7.57 Time building geometry restraints manager: 9.36 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 15.300 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 55.790 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.150 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.580 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 0 residues processed: 303 average time/residue: 0.3456 time to fit residues: 166.5696 Evaluate side-chains 232 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.702 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9053 ------------------------------------------------------------------------------- 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 133 HIS 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 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: 0.8360 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.022 23976 Z= 0.243 Angle : 0.505 5.440 32412 Z= 0.265 Chirality : 0.044 0.142 3756 Planarity : 0.004 0.029 4284 Dihedral : 3.970 13.921 3360 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.47 % 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: 0.08 (0.15), residues: 3096 helix: 1.35 (0.12), residues: 1584 sheet: -0.51 (0.22), residues: 588 loop : -1.81 (0.21), residues: 924 *********************** 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 248 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 236 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 236 average time/residue: 0.2921 time to fit residues: 117.1957 Evaluate side-chains 235 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 225 time to evaluate : 2.669 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2041 time to fit residues: 7.4756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 283 optimal weight: 0.9980 chunk 306 optimal weight: 7.9990 chunk 252 optimal weight: 4.9990 chunk 281 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 227 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** E 139 ASN F 52 ASN H 52 ASN I 52 ASN J 139 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 23976 Z= 0.169 Angle : 0.469 5.413 32412 Z= 0.243 Chirality : 0.043 0.140 3756 Planarity : 0.003 0.027 4284 Dihedral : 3.723 15.069 3360 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.16), residues: 3096 helix: 2.17 (0.13), residues: 1584 sheet: -0.01 (0.22), residues: 588 loop : -1.60 (0.21), residues: 924 *********************** 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 273 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 239 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 34 residues processed: 266 average time/residue: 0.2931 time to fit residues: 132.0557 Evaluate side-chains 263 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 229 time to evaluate : 2.875 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2196 time to fit residues: 18.1857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 31 optimal weight: 0.0570 chunk 135 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 284 optimal weight: 1.9990 chunk 301 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 23976 Z= 0.255 Angle : 0.495 5.578 32412 Z= 0.257 Chirality : 0.043 0.141 3756 Planarity : 0.003 0.029 4284 Dihedral : 3.731 14.196 3360 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 0.86 % 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: 1.43 (0.16), residues: 3096 helix: 2.56 (0.13), residues: 1584 sheet: 0.16 (0.22), residues: 588 loop : -1.48 (0.21), residues: 924 *********************** 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 248 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 226 time to evaluate : 2.848 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 239 average time/residue: 0.2966 time to fit residues: 118.8008 Evaluate side-chains 227 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 219 time to evaluate : 2.638 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2050 time to fit residues: 6.5797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 208 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 153 optimal weight: 0.6980 chunk 270 optimal weight: 0.2980 chunk 76 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN D 38 GLN E 273 GLN L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 23976 Z= 0.235 Angle : 0.487 5.861 32412 Z= 0.251 Chirality : 0.043 0.138 3756 Planarity : 0.003 0.030 4284 Dihedral : 3.682 13.502 3360 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 0.74 % 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: 1.66 (0.16), residues: 3096 helix: 2.75 (0.13), residues: 1584 sheet: 0.20 (0.23), residues: 588 loop : -1.32 (0.21), residues: 924 *********************** 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 245 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 226 time to evaluate : 2.674 Fit side-chains outliers start: 19 outliers final: 5 residues processed: 237 average time/residue: 0.2917 time to fit residues: 117.5427 Evaluate side-chains 223 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 218 time to evaluate : 2.717 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2029 time to fit residues: 5.5319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 0.0570 chunk 271 optimal weight: 0.0870 chunk 59 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 301 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 139 optimal weight: 0.4980 chunk 25 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.4676 ------------------------------------------------------------------------------- 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 273 GLN 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 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 23976 Z= 0.122 Angle : 0.453 6.654 32412 Z= 0.233 Chirality : 0.042 0.133 3756 Planarity : 0.003 0.027 4284 Dihedral : 3.534 12.908 3360 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.16), residues: 3096 helix: 2.89 (0.13), residues: 1584 sheet: 0.19 (0.23), residues: 600 loop : -0.96 (0.22), residues: 912 *********************** 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 267 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 238 time to evaluate : 2.694 Fit side-chains outliers start: 29 outliers final: 24 residues processed: 257 average time/residue: 0.2905 time to fit residues: 126.5148 Evaluate side-chains 249 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 225 time to evaluate : 2.985 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2104 time to fit residues: 13.6559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 254 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 chunk 188 optimal weight: 0.7980 chunk 183 optimal weight: 0.4980 chunk 138 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8358 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 23976 Z= 0.168 Angle : 0.477 11.323 32412 Z= 0.243 Chirality : 0.042 0.134 3756 Planarity : 0.003 0.028 4284 Dihedral : 3.484 12.966 3360 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.43 % 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: 2.10 (0.16), residues: 3096 helix: 2.96 (0.13), residues: 1584 sheet: 0.36 (0.22), residues: 588 loop : -0.76 (0.22), residues: 924 *********************** 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 242 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 231 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 239 average time/residue: 0.3109 time to fit residues: 123.2445 Evaluate side-chains 235 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 225 time to evaluate : 2.728 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2040 time to fit residues: 7.6060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 179 optimal weight: 0.0670 chunk 90 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 chunk 204 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 overall best weight: 0.7918 ------------------------------------------------------------------------------- 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: 0.8346 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 23976 Z= 0.146 Angle : 0.464 7.771 32412 Z= 0.238 Chirality : 0.042 0.132 3756 Planarity : 0.003 0.028 4284 Dihedral : 3.456 12.887 3360 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.23 % 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: 2.22 (0.16), residues: 3096 helix: 3.02 (0.13), residues: 1584 sheet: 0.37 (0.22), residues: 588 loop : -0.61 (0.22), residues: 924 *********************** 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 238 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 232 time to evaluate : 2.707 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 232 average time/residue: 0.3012 time to fit residues: 117.9496 Evaluate side-chains 234 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 230 time to evaluate : 2.853 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2143 time to fit residues: 5.3910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 7.9990 chunk 288 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 280 optimal weight: 7.9990 chunk 168 optimal weight: 0.0770 chunk 122 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 265 optimal weight: 7.9990 chunk 279 optimal weight: 2.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- 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 ** K 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 ASN L 139 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 23976 Z= 0.260 Angle : 0.515 8.587 32412 Z= 0.262 Chirality : 0.043 0.132 3756 Planarity : 0.003 0.030 4284 Dihedral : 3.602 13.359 3360 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.16), residues: 3096 helix: 3.04 (0.13), residues: 1584 sheet: 0.31 (0.23), residues: 588 loop : -0.68 (0.23), residues: 924 *********************** 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 226 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 223 time to evaluate : 2.867 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 223 average time/residue: 0.3107 time to fit residues: 116.7995 Evaluate side-chains 217 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 215 time to evaluate : 3.186 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2310 time to fit residues: 4.7056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.7099 > 50: distance: 67 - 71: 26.819 distance: 71 - 72: 36.296 distance: 72 - 73: 26.652 distance: 72 - 75: 33.229 distance: 73 - 74: 27.167 distance: 73 - 78: 38.812 distance: 75 - 76: 22.129 distance: 75 - 77: 14.230 distance: 78 - 79: 27.469 distance: 79 - 80: 26.606 distance: 79 - 82: 22.137 distance: 80 - 81: 5.204 distance: 80 - 83: 55.037 distance: 83 - 84: 12.450 distance: 84 - 85: 16.572 distance: 84 - 87: 13.861 distance: 85 - 86: 19.815 distance: 85 - 91: 10.881 distance: 87 - 88: 14.010 distance: 88 - 89: 24.486 distance: 88 - 90: 13.634 distance: 91 - 92: 15.098 distance: 92 - 93: 34.602 distance: 92 - 95: 24.180 distance: 93 - 94: 5.695 distance: 93 - 99: 24.075 distance: 95 - 96: 23.064 distance: 96 - 97: 15.146 distance: 96 - 98: 6.762 distance: 99 - 100: 15.028 distance: 100 - 101: 27.903 distance: 100 - 103: 22.540 distance: 101 - 102: 18.862 distance: 101 - 107: 7.452 distance: 103 - 104: 9.126 distance: 104 - 105: 25.037 distance: 104 - 106: 6.038 distance: 107 - 108: 33.735 distance: 108 - 109: 15.593 distance: 108 - 111: 30.735 distance: 109 - 110: 37.349 distance: 109 - 117: 19.258 distance: 111 - 112: 44.222 distance: 112 - 113: 27.680 distance: 112 - 114: 38.756 distance: 113 - 115: 10.636 distance: 114 - 116: 11.734 distance: 115 - 116: 7.559 distance: 117 - 118: 4.346 distance: 118 - 119: 14.203 distance: 118 - 121: 4.955 distance: 119 - 120: 24.973 distance: 119 - 128: 10.122 distance: 121 - 122: 4.272 distance: 122 - 123: 5.089 distance: 122 - 124: 5.943 distance: 123 - 125: 11.030 distance: 124 - 126: 11.765 distance: 125 - 127: 5.110 distance: 126 - 127: 11.854 distance: 128 - 129: 15.723 distance: 129 - 130: 10.305 distance: 129 - 132: 11.369 distance: 130 - 131: 35.278 distance: 130 - 136: 11.976 distance: 132 - 133: 4.747 distance: 132 - 134: 11.821 distance: 133 - 135: 18.008 distance: 136 - 137: 5.920 distance: 137 - 138: 18.286 distance: 137 - 140: 13.877 distance: 138 - 139: 13.329 distance: 138 - 144: 19.363 distance: 140 - 141: 14.769 distance: 141 - 142: 32.271 distance: 141 - 143: 12.956 distance: 144 - 145: 38.217 distance: 145 - 148: 52.434 distance: 146 - 153: 34.886 distance: 148 - 149: 27.828 distance: 149 - 150: 24.965 distance: 150 - 151: 42.766 distance: 151 - 152: 15.574