Starting phenix.real_space_refine on Fri Mar 6 05:40:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbh_27284/03_2026/8dbh_27284.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbh_27284/03_2026/8dbh_27284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dbh_27284/03_2026/8dbh_27284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbh_27284/03_2026/8dbh_27284.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbh_27284/03_2026/8dbh_27284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbh_27284/03_2026/8dbh_27284.cif" } resolution = 2.2 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.397 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 60 5.49 5 Mg 24 5.21 5 S 204 5.16 5 C 17904 2.51 5 N 5040 2.21 5 O 5652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 204 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28884 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "E" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "F" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "G" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "H" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "I" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "J" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "K" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "L" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 636 residue: pdb=" N HIS A 12 " occ=0.58 ... (8 atoms not shown) pdb=" NE2 HIS A 12 " occ=0.58 residue: pdb=" N ARG A 22 " occ=0.80 ... (9 atoms not shown) pdb=" NH2 ARG A 22 " occ=0.80 residue: pdb=" N GLU A 26 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 26 " occ=0.40 residue: pdb=" N LYS A 29 " occ=0.40 ... (7 atoms not shown) pdb=" NZ LYS A 29 " occ=0.40 residue: pdb=" N LYS A 33 " occ=0.01 ... (7 atoms not shown) pdb=" NZ LYS A 33 " occ=0.01 residue: pdb=" N SER A 36 " occ=0.01 ... (4 atoms not shown) pdb=" OG SER A 36 " occ=0.01 residue: pdb=" N ASN A 37 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN A 37 " occ=0.50 residue: pdb=" N CYS A 41 " occ=0.89 ... (4 atoms not shown) pdb=" SG CYS A 41 " occ=0.89 residue: pdb=" N GLU A 43 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 43 " occ=0.40 residue: pdb=" N GLU A 46 " occ=0.88 ... (7 atoms not shown) pdb=" OE2 GLU A 46 " occ=0.88 residue: pdb=" N SER A 58 " occ=0.10 ... (4 atoms not shown) pdb=" OG SER A 58 " occ=0.10 residue: pdb=" N GLY A 59 " occ=0.01 ... (2 atoms not shown) pdb=" O GLY A 59 " occ=0.01 ... (remaining 624 not shown) Time building chain proxies: 6.38, per 1000 atoms: 0.22 Number of scatterers: 28884 At special positions: 0 Unit cell: (126.531, 138.109, 139.763, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 204 16.00 P 60 15.00 Mg 24 11.99 O 5652 8.00 N 5040 7.00 C 17904 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 - 3.00 Amino acid : True - 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: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7008 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 36 sheets defined 44.0% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 62 through 80 Processing helix chain 'A' and resid 107 through 120 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 226 through 239 Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER A 314 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 Processing helix chain 'B' and resid 62 through 80 Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 226 through 239 Processing helix chain 'B' and resid 256 through 264 Processing helix chain 'B' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER B 314 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 62 through 80 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 161 through 164 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 226 through 239 Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 306 Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER C 314 " --> pdb=" O TYR C 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 Processing helix chain 'D' and resid 62 through 80 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 131 through 138 Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 161 through 164 Processing helix chain 'D' and resid 174 through 186 Processing helix chain 'D' and resid 226 through 239 Processing helix chain 'D' and resid 256 through 264 Processing helix chain 'D' and resid 277 through 284 removed outlier: 3.668A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 306 Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.631A pdb=" N SER D 314 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 24 Processing helix chain 'E' and resid 62 through 80 Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 131 through 138 Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 161 through 164 Processing helix chain 'E' and resid 174 through 186 Processing helix chain 'E' and resid 226 through 239 Processing helix chain 'E' and resid 256 through 264 Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.668A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 306 Processing helix chain 'E' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER E 314 " --> pdb=" O TYR E 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 24 Processing helix chain 'F' and resid 62 through 80 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 131 through 138 Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 161 through 164 Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 226 through 239 Processing helix chain 'F' and resid 256 through 264 Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 306 Processing helix chain 'F' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER F 314 " --> pdb=" O TYR F 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 62 through 80 Processing helix chain 'G' and resid 107 through 120 Processing helix chain 'G' and resid 131 through 138 Processing helix chain 'G' and resid 147 through 159 Processing helix chain 'G' and resid 161 through 164 Processing helix chain 'G' and resid 174 through 186 Processing helix chain 'G' and resid 226 through 239 Processing helix chain 'G' and resid 256 through 264 Processing helix chain 'G' and resid 277 through 284 removed outlier: 3.668A pdb=" N HIS G 283 " --> pdb=" O ASP G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 306 Processing helix chain 'G' and resid 309 through 314 removed outlier: 3.631A pdb=" N SER G 314 " --> pdb=" O TYR G 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 24 Processing helix chain 'H' and resid 62 through 80 Processing helix chain 'H' and resid 107 through 120 Processing helix chain 'H' and resid 131 through 138 Processing helix chain 'H' and resid 147 through 159 Processing helix chain 'H' and resid 161 through 164 Processing helix chain 'H' and resid 174 through 186 Processing helix chain 'H' and resid 226 through 239 Processing helix chain 'H' and resid 256 through 264 Processing helix chain 'H' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS H 283 " --> pdb=" O ASP H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 306 Processing helix chain 'H' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER H 314 " --> pdb=" O TYR H 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 24 Processing helix chain 'I' and resid 62 through 80 Processing helix chain 'I' and resid 107 through 120 Processing helix chain 'I' and resid 131 through 138 Processing helix chain 'I' and resid 147 through 159 Processing helix chain 'I' and resid 161 through 164 Processing helix chain 'I' and resid 174 through 186 Processing helix chain 'I' and resid 226 through 239 Processing helix chain 'I' and resid 256 through 264 Processing helix chain 'I' and resid 277 through 284 removed outlier: 3.668A pdb=" N HIS I 283 " --> pdb=" O ASP I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 292 through 306 Processing helix chain 'I' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER I 314 " --> pdb=" O TYR I 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 24 Processing helix chain 'J' and resid 62 through 80 Processing helix chain 'J' and resid 107 through 120 Processing helix chain 'J' and resid 131 through 138 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 161 through 164 Processing helix chain 'J' and resid 174 through 186 Processing helix chain 'J' and resid 226 through 239 Processing helix chain 'J' and resid 256 through 264 Processing helix chain 'J' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS J 283 " --> pdb=" O ASP J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 306 Processing helix chain 'J' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER J 314 " --> pdb=" O TYR J 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 24 Processing helix chain 'K' and resid 62 through 80 Processing helix chain 'K' and resid 107 through 120 Processing helix chain 'K' and resid 131 through 138 Processing helix chain 'K' and resid 147 through 159 Processing helix chain 'K' and resid 161 through 164 Processing helix chain 'K' and resid 174 through 186 Processing helix chain 'K' and resid 226 through 239 Processing helix chain 'K' and resid 256 through 264 Processing helix chain 'K' and resid 277 through 284 removed outlier: 3.668A pdb=" N HIS K 283 " --> pdb=" O ASP K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 306 Processing helix chain 'K' and resid 309 through 314 removed outlier: 3.633A pdb=" N SER K 314 " --> pdb=" O TYR K 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 24 Processing helix chain 'L' and resid 62 through 80 Processing helix chain 'L' and resid 107 through 120 Processing helix chain 'L' and resid 131 through 138 Processing helix chain 'L' and resid 147 through 159 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'L' and resid 174 through 186 Processing helix chain 'L' and resid 226 through 239 Processing helix chain 'L' and resid 256 through 264 Processing helix chain 'L' and resid 277 through 284 removed outlier: 3.668A pdb=" N HIS L 283 " --> pdb=" O ASP L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 306 Processing helix chain 'L' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER L 314 " --> pdb=" O TYR L 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS A 5 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL A 56 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE A 7 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A 88 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS A 123 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET A 127 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 124 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU A 145 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR A 126 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 208 removed outlier: 6.697A pdb=" N MET A 222 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY A 251 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 268 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS A 250 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS B 5 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL B 56 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE B 7 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL B 53 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL B 88 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS B 123 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET B 127 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 124 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU B 145 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR B 126 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA6, first strand: chain 'B' and resid 205 through 208 removed outlier: 6.697A pdb=" N MET B 222 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY B 251 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS B 250 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS C 5 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL C 56 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE C 7 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL C 88 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS C 123 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET C 127 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE C 124 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU C 145 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR C 126 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 30 through 34 Processing sheet with id=AA9, first strand: chain 'C' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET C 222 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY C 251 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA C 268 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS C 250 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS D 5 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL D 56 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE D 7 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL D 88 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS D 123 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET D 127 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE D 124 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU D 145 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AB3, first strand: chain 'D' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET D 222 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY D 251 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA D 268 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS D 250 " --> pdb=" O THR D 272 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS E 5 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL E 56 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE E 7 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL E 53 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL E 88 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE E 55 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS E 123 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET E 127 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE E 124 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU E 145 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR E 126 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 34 Processing sheet with id=AB6, first strand: chain 'E' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET E 222 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY E 251 " --> pdb=" O MET E 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N HIS E 250 " --> pdb=" O THR E 272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS F 5 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL F 56 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE F 7 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL F 53 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL F 88 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE F 55 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS F 123 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET F 127 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE F 124 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU F 145 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR F 126 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 30 through 34 Processing sheet with id=AB9, first strand: chain 'F' and resid 205 through 208 removed outlier: 6.697A pdb=" N MET F 222 " --> pdb=" O THR F 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY F 251 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS F 250 " --> pdb=" O THR F 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS G 5 " --> pdb=" O TYR G 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL G 56 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE G 7 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL G 53 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL G 88 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE G 55 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS G 123 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET G 127 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE G 124 " --> pdb=" O ASP G 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU G 145 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR G 126 " --> pdb=" O LEU G 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 30 through 34 Processing sheet with id=AC3, first strand: chain 'G' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET G 222 " --> pdb=" O THR G 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY G 251 " --> pdb=" O MET G 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA G 268 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS G 250 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS H 5 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL H 56 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE H 7 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL H 53 " --> pdb=" O THR H 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL H 88 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE H 55 " --> pdb=" O VAL H 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS H 123 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET H 127 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE H 124 " --> pdb=" O ASP H 143 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU H 145 " --> pdb=" O ILE H 124 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR H 126 " --> pdb=" O LEU H 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 30 through 34 Processing sheet with id=AC6, first strand: chain 'H' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET H 222 " --> pdb=" O THR H 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY H 251 " --> pdb=" O MET H 222 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA H 268 " --> pdb=" O VAL H 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS H 250 " --> pdb=" O THR H 272 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS I 5 " --> pdb=" O TYR I 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL I 56 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE I 7 " --> pdb=" O VAL I 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL I 53 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL I 88 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE I 55 " --> pdb=" O VAL I 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS I 123 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET I 127 " --> pdb=" O ILE I 89 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE I 124 " --> pdb=" O ASP I 143 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU I 145 " --> pdb=" O ILE I 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR I 126 " --> pdb=" O LEU I 145 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 30 through 34 Processing sheet with id=AC9, first strand: chain 'I' and resid 205 through 208 removed outlier: 6.697A pdb=" N MET I 222 " --> pdb=" O THR I 249 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY I 251 " --> pdb=" O MET I 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA I 268 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS I 250 " --> pdb=" O THR I 272 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS J 5 " --> pdb=" O TYR J 54 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL J 56 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE J 7 " --> pdb=" O VAL J 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL J 53 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL J 88 " --> pdb=" O VAL J 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE J 55 " --> pdb=" O VAL J 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS J 123 " --> pdb=" O VAL J 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET J 127 " --> pdb=" O ILE J 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE J 124 " --> pdb=" O ASP J 143 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU J 145 " --> pdb=" O ILE J 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR J 126 " --> pdb=" O LEU J 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 30 through 34 Processing sheet with id=AD3, first strand: chain 'J' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET J 222 " --> pdb=" O THR J 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY J 251 " --> pdb=" O MET J 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA J 268 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS J 250 " --> pdb=" O THR J 272 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS K 5 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL K 56 " --> pdb=" O LYS K 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE K 7 " --> pdb=" O VAL K 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL K 53 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL K 88 " --> pdb=" O VAL K 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE K 55 " --> pdb=" O VAL K 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS K 123 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET K 127 " --> pdb=" O ILE K 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE K 124 " --> pdb=" O ASP K 143 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU K 145 " --> pdb=" O ILE K 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR K 126 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 30 through 34 Processing sheet with id=AD6, first strand: chain 'K' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET K 222 " --> pdb=" O THR K 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY K 251 " --> pdb=" O MET K 222 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA K 268 " --> pdb=" O VAL K 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS K 250 " --> pdb=" O THR K 272 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS L 5 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL L 56 " --> pdb=" O LYS L 5 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE L 7 " --> pdb=" O VAL L 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL L 53 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL L 88 " --> pdb=" O VAL L 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE L 55 " --> pdb=" O VAL L 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS L 123 " --> pdb=" O VAL L 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET L 127 " --> pdb=" O ILE L 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE L 124 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU L 145 " --> pdb=" O ILE L 124 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR L 126 " --> pdb=" O LEU L 145 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 30 through 34 Processing sheet with id=AD9, first strand: chain 'L' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET L 222 " --> pdb=" O THR L 249 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY L 251 " --> pdb=" O MET L 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA L 268 " --> pdb=" O VAL L 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS L 250 " --> pdb=" O THR L 272 " (cutoff:3.500A) 1428 hydrogen bonds defined for protein. 3996 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: 5.54 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9333 1.33 - 1.45: 3391 1.45 - 1.57: 16172 1.57 - 1.69: 60 1.69 - 1.81: 300 Bond restraints: 29256 Sorted by residual: bond pdb=" O4 PO4 A 403 " pdb=" P PO4 A 403 " ideal model delta sigma weight residual 1.568 1.497 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O4 PO4 G 403 " pdb=" P PO4 G 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O4 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" O4 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" O4 PO4 K 403 " pdb=" P PO4 K 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 29251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 38097 1.51 - 3.01: 1273 3.01 - 4.52: 242 4.52 - 6.03: 48 6.03 - 7.54: 12 Bond angle restraints: 39672 Sorted by residual: angle pdb=" PB ATP L 401 " pdb=" O3B ATP L 401 " pdb=" PG ATP L 401 " ideal model delta sigma weight residual 139.87 132.33 7.54 1.00e+00 1.00e+00 5.68e+01 angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 132.34 7.53 1.00e+00 1.00e+00 5.66e+01 angle pdb=" PB ATP I 401 " pdb=" O3B ATP I 401 " pdb=" PG ATP I 401 " ideal model delta sigma weight residual 139.87 132.37 7.50 1.00e+00 1.00e+00 5.62e+01 angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 132.38 7.49 1.00e+00 1.00e+00 5.61e+01 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 132.39 7.48 1.00e+00 1.00e+00 5.59e+01 ... (remaining 39667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16036 17.95 - 35.90: 1352 35.90 - 53.85: 432 53.85 - 71.80: 138 71.80 - 89.75: 90 Dihedral angle restraints: 18048 sinusoidal: 7296 harmonic: 10752 Sorted by residual: dihedral pdb=" CA SER K 8 " pdb=" C SER K 8 " pdb=" N GLY K 9 " pdb=" CA GLY K 9 " ideal model delta harmonic sigma weight residual 180.00 160.62 19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER J 8 " pdb=" C SER J 8 " pdb=" N GLY J 9 " pdb=" CA GLY J 9 " ideal model delta harmonic sigma weight residual 180.00 160.62 19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER D 8 " pdb=" C SER D 8 " pdb=" N GLY D 9 " pdb=" CA GLY D 9 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 18045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2634 0.040 - 0.080: 1417 0.080 - 0.120: 489 0.120 - 0.160: 84 0.160 - 0.200: 44 Chirality restraints: 4668 Sorted by residual: chirality pdb=" CG LEU J 248 " pdb=" CB LEU J 248 " pdb=" CD1 LEU J 248 " pdb=" CD2 LEU J 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CG LEU H 248 " pdb=" CB LEU H 248 " pdb=" CD1 LEU H 248 " pdb=" CD2 LEU H 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CG LEU D 248 " pdb=" CB LEU D 248 " pdb=" CD1 LEU D 248 " pdb=" CD2 LEU D 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.69e-01 ... (remaining 4665 not shown) Planarity restraints: 5004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER I 180 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C SER I 180 " -0.030 2.00e-02 2.50e+03 pdb=" O SER I 180 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE I 181 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 180 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C SER F 180 " 0.030 2.00e-02 2.50e+03 pdb=" O SER F 180 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE F 181 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 180 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C SER L 180 " 0.029 2.00e-02 2.50e+03 pdb=" O SER L 180 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE L 181 " -0.010 2.00e-02 2.50e+03 ... (remaining 5001 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 224 2.55 - 3.13: 23022 3.13 - 3.72: 47364 3.72 - 4.31: 66713 4.31 - 4.90: 111238 Nonbonded interactions: 248561 Sorted by model distance: nonbonded pdb="MG MG D 404 " pdb=" O HOH D 501 " model vdw 1.957 2.170 nonbonded pdb="MG MG J 404 " pdb=" O HOH J 501 " model vdw 1.958 2.170 nonbonded pdb="MG MG F 404 " pdb=" O HOH F 501 " model vdw 1.958 2.170 nonbonded pdb="MG MG I 404 " pdb=" O HOH I 501 " model vdw 1.958 2.170 nonbonded pdb="MG MG B 404 " pdb=" O HOH B 501 " model vdw 1.958 2.170 ... (remaining 248556 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 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=0.01 max=1.00 mean=0.91 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: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 25.840 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 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 : 0.007 0.071 29256 Z= 0.322 Angle : 0.694 7.536 39672 Z= 0.437 Chirality : 0.054 0.200 4668 Planarity : 0.003 0.019 5004 Dihedral : 17.531 89.747 11040 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.94 % Allowed : 12.56 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.14), residues: 3660 helix: 1.27 (0.14), residues: 1488 sheet: 0.06 (0.17), residues: 948 loop : -0.38 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 177 TYR 0.023 0.004 TYR D 146 PHE 0.012 0.002 PHE J 189 TRP 0.012 0.003 TRP E 162 HIS 0.005 0.001 HIS H 130 Details of bonding type rmsd covalent geometry : bond 0.00687 (29256) covalent geometry : angle 0.69380 (39672) hydrogen bonds : bond 0.13188 ( 1428) hydrogen bonds : angle 6.05788 ( 3996) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 713 time to evaluate : 1.097 Fit side-chains REVERT: A 29 LYS cc_start: 0.8257 (mttp) cc_final: 0.8042 (mttm) REVERT: B 294 MET cc_start: 0.8204 (pmm) cc_final: 0.7846 (pmm) REVERT: B 298 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7945 (mm-30) REVERT: C 68 MET cc_start: 0.8302 (tpp) cc_final: 0.8098 (mmm) REVERT: D 281 MET cc_start: 0.6999 (mtp) cc_final: 0.6575 (mtm) REVERT: E 29 LYS cc_start: 0.8144 (mttp) cc_final: 0.7888 (mttm) REVERT: E 51 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7671 (mm-30) REVERT: F 51 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7787 (mm-30) REVERT: F 221 ASP cc_start: 0.7814 (p0) cc_final: 0.7448 (p0) REVERT: F 248 LEU cc_start: 0.8548 (mp) cc_final: 0.8335 (mm) REVERT: G 51 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7800 (mm-30) REVERT: G 221 ASP cc_start: 0.7816 (p0) cc_final: 0.7452 (p0) REVERT: H 29 LYS cc_start: 0.8150 (mttp) cc_final: 0.7884 (mttm) REVERT: H 51 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7676 (mm-30) REVERT: I 281 MET cc_start: 0.7010 (mtp) cc_final: 0.6587 (mtm) REVERT: J 29 LYS cc_start: 0.8162 (mttp) cc_final: 0.7831 (mttm) REVERT: J 46 GLU cc_start: 0.8360 (pt0) cc_final: 0.8157 (pt0) REVERT: K 294 MET cc_start: 0.8213 (pmm) cc_final: 0.7849 (pmm) REVERT: K 298 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7942 (mm-30) REVERT: L 29 LYS cc_start: 0.8271 (mttp) cc_final: 0.8043 (mttm) outliers start: 61 outliers final: 26 residues processed: 761 average time/residue: 0.6073 time to fit residues: 544.9587 Evaluate side-chains 605 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 579 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 314 SER Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 314 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN B 263 ASN B 288 GLN C 135 GLN D 288 GLN E 135 GLN F 288 GLN G 288 GLN H 135 GLN I 288 GLN J 135 GLN K 263 ASN K 288 GLN L 38 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.155669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.121925 restraints weight = 24593.399| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.07 r_work: 0.3192 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 648 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29256 Z= 0.141 Angle : 0.537 6.832 39672 Z= 0.304 Chirality : 0.048 0.170 4668 Planarity : 0.003 0.026 5004 Dihedral : 12.675 89.481 4360 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.86 % Allowed : 13.23 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.14), residues: 3660 helix: 1.49 (0.14), residues: 1512 sheet: -0.01 (0.17), residues: 1008 loop : -0.18 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 163 TYR 0.015 0.002 TYR I 146 PHE 0.010 0.002 PHE K 35 TRP 0.012 0.002 TRP H 162 HIS 0.005 0.001 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.00297 (29256) covalent geometry : angle 0.53716 (39672) hydrogen bonds : bond 0.04787 ( 1428) hydrogen bonds : angle 5.04190 ( 3996) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 629 time to evaluate : 1.101 Fit side-chains REVERT: A 188 ASP cc_start: 0.7961 (m-30) cc_final: 0.7561 (m-30) REVERT: B 248 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8304 (mm) REVERT: B 294 MET cc_start: 0.8478 (pmm) cc_final: 0.8165 (pmm) REVERT: D 281 MET cc_start: 0.8599 (mtp) cc_final: 0.8392 (mtm) REVERT: E 51 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8045 (mm-30) REVERT: F 51 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8233 (mm-30) REVERT: F 221 ASP cc_start: 0.7938 (p0) cc_final: 0.7736 (p0) REVERT: G 51 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8226 (mm-30) REVERT: G 221 ASP cc_start: 0.7930 (p0) cc_final: 0.7723 (p0) REVERT: H 51 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8047 (mm-30) REVERT: I 281 MET cc_start: 0.8578 (mtp) cc_final: 0.8374 (mtm) REVERT: K 248 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8303 (mm) REVERT: K 294 MET cc_start: 0.8483 (pmm) cc_final: 0.8164 (pmm) REVERT: L 188 ASP cc_start: 0.7975 (m-30) cc_final: 0.7580 (m-30) outliers start: 90 outliers final: 41 residues processed: 669 average time/residue: 0.6538 time to fit residues: 510.5677 Evaluate side-chains 639 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 596 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 12 HIS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 12 HIS Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 188 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 343 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS A 288 GLN B 263 ASN C 38 GLN D 17 GLN D 288 GLN D 305 ASN E 123 HIS F 17 GLN F 123 HIS F 263 ASN F 288 GLN G 17 GLN G 123 HIS G 263 ASN G 288 GLN H 123 HIS I 17 GLN I 288 GLN I 305 ASN K 263 ASN L 123 HIS L 288 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.138016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.102961 restraints weight = 24628.976| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.05 r_work: 0.2921 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29256 Z= 0.147 Angle : 0.534 6.983 39672 Z= 0.302 Chirality : 0.049 0.199 4668 Planarity : 0.003 0.025 5004 Dihedral : 11.564 82.484 4338 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.61 % Allowed : 13.55 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3660 helix: 1.65 (0.14), residues: 1512 sheet: -0.07 (0.16), residues: 1008 loop : -0.22 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 163 TYR 0.014 0.002 TYR E 146 PHE 0.009 0.002 PHE H 189 TRP 0.011 0.002 TRP H 162 HIS 0.005 0.001 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.00315 (29256) covalent geometry : angle 0.53385 (39672) hydrogen bonds : bond 0.04856 ( 1428) hydrogen bonds : angle 4.93437 ( 3996) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 616 time to evaluate : 0.671 Fit side-chains REVERT: A 188 ASP cc_start: 0.7875 (m-30) cc_final: 0.7436 (m-30) REVERT: B 39 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8389 (mt-10) REVERT: B 248 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8257 (mm) REVERT: B 294 MET cc_start: 0.8446 (pmm) cc_final: 0.8080 (pmm) REVERT: D 51 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8320 (mm-30) REVERT: E 51 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8010 (mm-30) REVERT: F 51 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8260 (mm-30) REVERT: F 69 GLU cc_start: 0.8997 (tt0) cc_final: 0.8660 (tt0) REVERT: F 248 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8361 (mm) REVERT: G 51 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8262 (mm-30) REVERT: G 69 GLU cc_start: 0.8995 (tt0) cc_final: 0.8652 (tt0) REVERT: H 51 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8013 (mm-30) REVERT: J 17 GLN cc_start: 0.9078 (tp40) cc_final: 0.8827 (tp40) REVERT: K 39 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: K 248 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8258 (mm) REVERT: K 294 MET cc_start: 0.8443 (pmm) cc_final: 0.8073 (pmm) REVERT: L 188 ASP cc_start: 0.7860 (m-30) cc_final: 0.7417 (m-30) outliers start: 82 outliers final: 46 residues processed: 651 average time/residue: 0.6678 time to fit residues: 505.4681 Evaluate side-chains 636 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 585 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 12 HIS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 232 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 240 optimal weight: 6.9990 chunk 254 optimal weight: 0.8980 chunk 213 optimal weight: 0.3980 chunk 82 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 253 optimal weight: 0.5980 chunk 291 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN D 288 GLN F 263 ASN F 288 GLN G 263 ASN G 288 GLN I 288 GLN K 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.141528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106496 restraints weight = 24691.435| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.05 r_work: 0.2955 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 29256 Z= 0.114 Angle : 0.486 5.618 39672 Z= 0.275 Chirality : 0.047 0.188 4668 Planarity : 0.003 0.026 5004 Dihedral : 10.662 77.655 4338 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.10 % Allowed : 14.31 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.14), residues: 3660 helix: 1.79 (0.14), residues: 1512 sheet: -0.13 (0.16), residues: 1008 loop : -0.21 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 163 TYR 0.013 0.001 TYR J 146 PHE 0.008 0.001 PHE D 138 TRP 0.010 0.002 TRP A 162 HIS 0.003 0.001 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00233 (29256) covalent geometry : angle 0.48587 (39672) hydrogen bonds : bond 0.04111 ( 1428) hydrogen bonds : angle 4.79069 ( 3996) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 607 time to evaluate : 1.000 Fit side-chains REVERT: A 188 ASP cc_start: 0.7756 (m-30) cc_final: 0.7302 (m-30) REVERT: B 205 MET cc_start: 0.7797 (mtt) cc_final: 0.7566 (mtt) REVERT: B 248 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8386 (mm) REVERT: B 294 MET cc_start: 0.8468 (pmm) cc_final: 0.8086 (pmm) REVERT: C 14 ASP cc_start: 0.8511 (t70) cc_final: 0.8295 (t0) REVERT: D 17 GLN cc_start: 0.9065 (tp-100) cc_final: 0.8816 (tp-100) REVERT: F 51 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8213 (mm-30) REVERT: F 181 ILE cc_start: 0.8480 (mt) cc_final: 0.8267 (mt) REVERT: F 248 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8359 (mm) REVERT: G 51 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8217 (mm-30) REVERT: G 69 GLU cc_start: 0.8996 (tt0) cc_final: 0.8587 (tt0) REVERT: G 181 ILE cc_start: 0.8482 (mt) cc_final: 0.8274 (mt) REVERT: H 51 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7963 (mm-30) REVERT: I 17 GLN cc_start: 0.9069 (tp-100) cc_final: 0.8819 (tp-100) REVERT: J 14 ASP cc_start: 0.8512 (t70) cc_final: 0.8265 (t0) REVERT: K 205 MET cc_start: 0.7794 (mtt) cc_final: 0.7562 (mtt) REVERT: K 248 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8385 (mm) REVERT: K 294 MET cc_start: 0.8464 (pmm) cc_final: 0.8080 (pmm) REVERT: L 188 ASP cc_start: 0.7734 (m-30) cc_final: 0.7282 (m-30) outliers start: 66 outliers final: 40 residues processed: 640 average time/residue: 0.6656 time to fit residues: 495.8142 Evaluate side-chains 612 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 569 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain K residue 282 LYS Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 54 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 204 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 201 optimal weight: 0.5980 chunk 357 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 HIS B 263 ASN B 288 GLN C 38 GLN C 123 HIS D 17 GLN D 123 HIS D 288 GLN F 17 GLN F 263 ASN F 288 GLN G 17 GLN G 263 ASN G 288 GLN I 17 GLN I 123 HIS I 288 GLN J 38 GLN J 123 HIS K 123 HIS K 263 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.099530 restraints weight = 24431.690| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.08 r_work: 0.2895 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29256 Z= 0.199 Angle : 0.571 7.062 39672 Z= 0.323 Chirality : 0.051 0.207 4668 Planarity : 0.003 0.031 5004 Dihedral : 11.838 86.800 4338 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.32 % Allowed : 14.34 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.14), residues: 3660 helix: 1.71 (0.14), residues: 1512 sheet: 0.08 (0.17), residues: 912 loop : -0.38 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 163 TYR 0.018 0.002 TYR J 146 PHE 0.010 0.002 PHE I 138 TRP 0.011 0.003 TRP L 162 HIS 0.006 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00446 (29256) covalent geometry : angle 0.57096 (39672) hydrogen bonds : bond 0.05307 ( 1428) hydrogen bonds : angle 4.91651 ( 3996) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 602 time to evaluate : 1.031 Fit side-chains REVERT: A 188 ASP cc_start: 0.7894 (m-30) cc_final: 0.7570 (m-30) REVERT: B 205 MET cc_start: 0.7810 (mtt) cc_final: 0.7557 (mtt) REVERT: B 294 MET cc_start: 0.8468 (pmm) cc_final: 0.8074 (pmm) REVERT: C 286 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8331 (ptmt) REVERT: F 51 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8249 (mm-30) REVERT: F 208 VAL cc_start: 0.6687 (OUTLIER) cc_final: 0.6487 (p) REVERT: G 51 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8235 (mm-30) REVERT: G 163 ARG cc_start: 0.8548 (mtt90) cc_final: 0.8345 (mtt180) REVERT: H 51 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8082 (mm-30) REVERT: J 286 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8334 (ptmt) REVERT: K 205 MET cc_start: 0.7805 (mtt) cc_final: 0.7553 (mtt) REVERT: K 294 MET cc_start: 0.8461 (pmm) cc_final: 0.8066 (pmm) REVERT: L 188 ASP cc_start: 0.7867 (m-30) cc_final: 0.7455 (m-30) outliers start: 73 outliers final: 42 residues processed: 627 average time/residue: 0.6600 time to fit residues: 482.7020 Evaluate side-chains 630 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 585 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 286 LYS Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 266 optimal weight: 2.9990 chunk 331 optimal weight: 0.5980 chunk 205 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 323 optimal weight: 8.9990 chunk 140 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN B 288 GLN C 38 GLN F 263 ASN F 288 GLN G 263 ASN G 288 GLN I 17 GLN J 38 GLN K 263 ASN K 288 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.137010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.100441 restraints weight = 24353.995| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.08 r_work: 0.2926 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 29256 Z= 0.165 Angle : 0.543 6.871 39672 Z= 0.307 Chirality : 0.049 0.216 4668 Planarity : 0.003 0.028 5004 Dihedral : 11.594 85.290 4338 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.13 % Allowed : 14.66 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.14), residues: 3660 helix: 1.68 (0.14), residues: 1512 sheet: 0.11 (0.17), residues: 912 loop : -0.41 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 163 TYR 0.019 0.002 TYR J 146 PHE 0.010 0.002 PHE I 138 TRP 0.011 0.002 TRP H 162 HIS 0.005 0.001 HIS H 130 Details of bonding type rmsd covalent geometry : bond 0.00365 (29256) covalent geometry : angle 0.54308 (39672) hydrogen bonds : bond 0.04925 ( 1428) hydrogen bonds : angle 4.87074 ( 3996) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 590 time to evaluate : 1.134 Fit side-chains REVERT: B 39 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8362 (mt-10) REVERT: B 205 MET cc_start: 0.7813 (mtt) cc_final: 0.7585 (mtt) REVERT: B 248 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8264 (mm) REVERT: B 294 MET cc_start: 0.8467 (pmm) cc_final: 0.8073 (pmm) REVERT: D 17 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8796 (tp-100) REVERT: G 51 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8225 (mm-30) REVERT: G 248 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8324 (mm) REVERT: H 51 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8105 (mm-30) REVERT: K 39 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8368 (mt-10) REVERT: K 205 MET cc_start: 0.7805 (mtt) cc_final: 0.7576 (mtt) REVERT: K 248 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8263 (mm) REVERT: K 294 MET cc_start: 0.8474 (pmm) cc_final: 0.8081 (pmm) outliers start: 67 outliers final: 46 residues processed: 620 average time/residue: 0.6681 time to fit residues: 481.3321 Evaluate side-chains 633 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 582 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 205 MET Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 258 ILE Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 349 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 332 optimal weight: 1.9990 chunk 298 optimal weight: 7.9990 chunk 222 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 226 optimal weight: 0.6980 chunk 254 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN B 288 GLN D 17 GLN F 288 GLN G 263 ASN G 288 GLN K 263 ASN K 288 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.138744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.102395 restraints weight = 24576.606| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.09 r_work: 0.2931 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29256 Z= 0.130 Angle : 0.508 6.170 39672 Z= 0.287 Chirality : 0.048 0.210 4668 Planarity : 0.003 0.026 5004 Dihedral : 10.968 82.272 4338 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.16 % Allowed : 15.01 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3660 helix: 1.77 (0.14), residues: 1512 sheet: -0.02 (0.16), residues: 948 loop : -0.29 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 163 TYR 0.016 0.002 TYR C 146 PHE 0.009 0.001 PHE D 138 TRP 0.012 0.002 TRP A 162 HIS 0.004 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00278 (29256) covalent geometry : angle 0.50789 (39672) hydrogen bonds : bond 0.04410 ( 1428) hydrogen bonds : angle 4.77856 ( 3996) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 586 time to evaluate : 0.926 Fit side-chains REVERT: B 39 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8293 (mt-10) REVERT: B 205 MET cc_start: 0.7761 (mtt) cc_final: 0.7553 (mtt) REVERT: B 248 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8342 (mm) REVERT: B 294 MET cc_start: 0.8463 (pmm) cc_final: 0.8061 (pmm) REVERT: F 224 ASP cc_start: 0.8346 (t0) cc_final: 0.8112 (t0) REVERT: F 248 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8355 (mm) REVERT: G 51 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8176 (mm-30) REVERT: G 224 ASP cc_start: 0.8337 (t0) cc_final: 0.8119 (t0) REVERT: G 248 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8346 (mm) REVERT: H 51 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8036 (mm-30) REVERT: K 39 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8299 (mt-10) REVERT: K 205 MET cc_start: 0.7753 (mtt) cc_final: 0.7533 (mtt) REVERT: K 248 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8336 (mm) REVERT: K 294 MET cc_start: 0.8467 (pmm) cc_final: 0.8061 (pmm) outliers start: 68 outliers final: 42 residues processed: 617 average time/residue: 0.6664 time to fit residues: 477.8173 Evaluate side-chains 622 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 574 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 282 LYS Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 258 ILE Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 196 optimal weight: 0.8980 chunk 268 optimal weight: 2.9990 chunk 328 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 159 optimal weight: 0.7980 chunk 270 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 355 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN B 288 GLN C 38 GLN F 17 GLN F 263 ASN F 288 GLN G 17 GLN G 263 ASN G 288 GLN J 38 GLN K 263 ASN K 288 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.100480 restraints weight = 24586.770| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.10 r_work: 0.2906 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 29256 Z= 0.164 Angle : 0.541 6.690 39672 Z= 0.305 Chirality : 0.049 0.213 4668 Planarity : 0.003 0.028 5004 Dihedral : 11.376 85.181 4338 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.97 % Allowed : 15.27 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.14), residues: 3660 helix: 1.74 (0.14), residues: 1512 sheet: 0.03 (0.17), residues: 912 loop : -0.42 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 163 TYR 0.019 0.002 TYR J 146 PHE 0.010 0.002 PHE B 138 TRP 0.011 0.002 TRP L 162 HIS 0.005 0.001 HIS H 130 Details of bonding type rmsd covalent geometry : bond 0.00361 (29256) covalent geometry : angle 0.54127 (39672) hydrogen bonds : bond 0.04895 ( 1428) hydrogen bonds : angle 4.82359 ( 3996) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 567 time to evaluate : 0.814 Fit side-chains REVERT: B 39 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8340 (mt-10) REVERT: B 205 MET cc_start: 0.7769 (mtt) cc_final: 0.7559 (mtt) REVERT: B 248 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8266 (mm) REVERT: B 294 MET cc_start: 0.8481 (pmm) cc_final: 0.8079 (pmm) REVERT: C 286 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8304 (ptmt) REVERT: D 17 GLN cc_start: 0.9039 (tp-100) cc_final: 0.8824 (tp-100) REVERT: F 248 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8338 (mm) REVERT: G 51 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8199 (mm-30) REVERT: H 51 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8079 (mm-30) REVERT: J 286 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8298 (ptmt) REVERT: K 39 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8347 (mt-10) REVERT: K 205 MET cc_start: 0.7766 (mtt) cc_final: 0.7554 (mtt) REVERT: K 248 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8267 (mm) REVERT: K 294 MET cc_start: 0.8493 (pmm) cc_final: 0.8091 (pmm) outliers start: 62 outliers final: 44 residues processed: 597 average time/residue: 0.6705 time to fit residues: 465.2727 Evaluate side-chains 611 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 560 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 282 LYS Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 286 LYS Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 112 optimal weight: 4.9990 chunk 292 optimal weight: 1.9990 chunk 342 optimal weight: 8.9990 chunk 355 optimal weight: 0.0980 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 220 optimal weight: 0.0970 chunk 12 optimal weight: 4.9990 chunk 358 optimal weight: 9.9990 chunk 291 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN F 263 ASN F 288 GLN G 263 ASN G 288 GLN K 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.139097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.102120 restraints weight = 24676.012| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.20 r_work: 0.2954 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29256 Z= 0.126 Angle : 0.508 5.998 39672 Z= 0.285 Chirality : 0.048 0.222 4668 Planarity : 0.003 0.026 5004 Dihedral : 10.788 81.531 4338 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.75 % Allowed : 15.65 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3660 helix: 1.81 (0.14), residues: 1512 sheet: -0.06 (0.16), residues: 948 loop : -0.29 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 163 TYR 0.016 0.002 TYR J 146 PHE 0.009 0.001 PHE I 138 TRP 0.013 0.002 TRP A 162 HIS 0.004 0.001 HIS H 130 Details of bonding type rmsd covalent geometry : bond 0.00270 (29256) covalent geometry : angle 0.50783 (39672) hydrogen bonds : bond 0.04301 ( 1428) hydrogen bonds : angle 4.72229 ( 3996) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 576 time to evaluate : 1.096 Fit side-chains REVERT: B 39 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8323 (mt-10) REVERT: B 205 MET cc_start: 0.7752 (mtt) cc_final: 0.7549 (mtt) REVERT: B 248 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8360 (mm) REVERT: B 294 MET cc_start: 0.8494 (pmm) cc_final: 0.8086 (pmm) REVERT: C 286 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8321 (ptmt) REVERT: F 248 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8358 (mm) REVERT: G 51 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8176 (mm-30) REVERT: G 248 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8355 (mm) REVERT: H 51 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8056 (mm-30) REVERT: J 286 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8318 (ptmt) REVERT: K 39 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8325 (mt-10) REVERT: K 205 MET cc_start: 0.7754 (mtt) cc_final: 0.7550 (mtt) REVERT: K 248 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8364 (mm) REVERT: K 294 MET cc_start: 0.8498 (pmm) cc_final: 0.8091 (pmm) outliers start: 55 outliers final: 34 residues processed: 606 average time/residue: 0.6795 time to fit residues: 477.4182 Evaluate side-chains 610 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 568 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 286 LYS Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 164 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 241 optimal weight: 3.9990 chunk 288 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 246 optimal weight: 5.9990 chunk 300 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 193 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN F 263 ASN F 288 GLN G 263 ASN G 288 GLN K 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.102975 restraints weight = 24548.225| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.15 r_work: 0.2936 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29256 Z= 0.123 Angle : 0.506 7.076 39672 Z= 0.283 Chirality : 0.047 0.209 4668 Planarity : 0.003 0.027 5004 Dihedral : 10.530 80.198 4336 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.30 % Allowed : 15.94 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.14), residues: 3660 helix: 1.86 (0.14), residues: 1512 sheet: -0.21 (0.16), residues: 1008 loop : -0.25 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 163 TYR 0.016 0.001 TYR J 146 PHE 0.009 0.001 PHE B 138 TRP 0.013 0.002 TRP A 162 HIS 0.004 0.001 HIS H 130 Details of bonding type rmsd covalent geometry : bond 0.00262 (29256) covalent geometry : angle 0.50575 (39672) hydrogen bonds : bond 0.04221 ( 1428) hydrogen bonds : angle 4.68802 ( 3996) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 572 time to evaluate : 0.932 Fit side-chains REVERT: B 248 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8377 (mm) REVERT: B 294 MET cc_start: 0.8488 (pmm) cc_final: 0.8089 (pmm) REVERT: C 286 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8292 (ptmt) REVERT: F 224 ASP cc_start: 0.8308 (t0) cc_final: 0.7997 (t0) REVERT: F 248 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8374 (mm) REVERT: G 51 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8175 (mm-30) REVERT: G 69 GLU cc_start: 0.9042 (tt0) cc_final: 0.8827 (tt0) REVERT: G 248 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8377 (mm) REVERT: H 51 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8051 (mm-30) REVERT: J 286 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8294 (ptmt) REVERT: K 205 MET cc_start: 0.7745 (mtt) cc_final: 0.7544 (mtt) REVERT: K 248 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8378 (mm) REVERT: K 294 MET cc_start: 0.8488 (pmm) cc_final: 0.8089 (pmm) outliers start: 41 outliers final: 35 residues processed: 594 average time/residue: 0.6896 time to fit residues: 475.3119 Evaluate side-chains 607 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 566 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 286 LYS Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 193 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 235 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 133 optimal weight: 0.0870 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN B 288 GLN F 263 ASN F 288 GLN G 263 ASN G 288 GLN I 17 GLN J 38 GLN K 263 ASN K 288 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.138955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.102340 restraints weight = 24781.053| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.10 r_work: 0.2929 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29256 Z= 0.136 Angle : 0.520 7.050 39672 Z= 0.291 Chirality : 0.048 0.209 4668 Planarity : 0.003 0.027 5004 Dihedral : 10.674 81.768 4336 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.34 % Allowed : 16.03 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.14), residues: 3660 helix: 1.84 (0.14), residues: 1512 sheet: -0.22 (0.16), residues: 1008 loop : -0.26 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 163 TYR 0.016 0.002 TYR C 146 PHE 0.009 0.001 PHE I 138 TRP 0.012 0.002 TRP L 162 HIS 0.004 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00293 (29256) covalent geometry : angle 0.52006 (39672) hydrogen bonds : bond 0.04426 ( 1428) hydrogen bonds : angle 4.69918 ( 3996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14473.71 seconds wall clock time: 245 minutes 50.52 seconds (14750.52 seconds total)