Starting phenix.real_space_refine on Tue Jun 24 16:19:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbh_27284/06_2025/8dbh_27284.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbh_27284/06_2025/8dbh_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_27284/06_2025/8dbh_27284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbh_27284/06_2025/8dbh_27284.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbh_27284/06_2025/8dbh_27284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbh_27284/06_2025/8dbh_27284.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.397 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.67, per 1000 atoms: 0.54 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: 6.70 Conformation dependent library (CDL) restraints added in 3.5 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: 3.42 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: 9.94 Time building geometry restraints manager: 7.94 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: 0.25 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 1.820 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: 1.220 Check model and map are aligned: 0.180 Set scattering table: 0.280 Process input model: 60.360 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.130 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:10.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.120 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (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 TRP 0.012 0.003 TRP E 162 HIS 0.005 0.001 HIS H 130 PHE 0.012 0.002 PHE J 189 TYR 0.023 0.004 TYR D 146 ARG 0.004 0.001 ARG F 177 Details of bonding type rmsd hydrogen bonds : bond 0.13188 ( 1428) hydrogen bonds : angle 6.05788 ( 3996) covalent geometry : bond 0.00687 (29256) covalent geometry : angle 0.69380 (39672) *********************** 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 : 3.837 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: 1.4312 time to fit residues: 1284.1913 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 : 3.216 ------------------------------------------------------------------------------- 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 303 optimal weight: 0.0060 chunk 272 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 184 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 326 optimal weight: 2.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.155553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.121833 restraints weight = 24489.262| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.07 r_work: 0.3190 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 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 = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1350 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= 0.140 Angle : 0.535 6.803 39672 Z= 0.303 Chirality : 0.048 0.170 4668 Planarity : 0.003 0.024 5004 Dihedral : 12.808 88.138 4360 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.74 % Allowed : 13.55 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3660 helix: 1.50 (0.14), residues: 1512 sheet: -0.01 (0.17), residues: 1008 loop : -0.19 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 162 HIS 0.005 0.001 HIS E 130 PHE 0.010 0.002 PHE B 138 TYR 0.015 0.002 TYR D 146 ARG 0.004 0.000 ARG K 163 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 1428) hydrogen bonds : angle 5.05172 ( 3996) covalent geometry : bond 0.00295 (29256) covalent geometry : angle 0.53524 (39672) *********************** 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 715 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 629 time to evaluate : 3.028 Fit side-chains REVERT: A 188 ASP cc_start: 0.7979 (m-30) cc_final: 0.7579 (m-30) REVERT: B 248 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8305 (mm) REVERT: B 294 MET cc_start: 0.8467 (pmm) cc_final: 0.8143 (pmm) REVERT: D 281 MET cc_start: 0.8576 (mtp) cc_final: 0.8373 (mtm) REVERT: E 51 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8041 (mm-30) REVERT: E 294 MET cc_start: 0.9011 (pmm) cc_final: 0.8716 (pmm) REVERT: F 51 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8230 (mm-30) REVERT: F 221 ASP cc_start: 0.7921 (p0) cc_final: 0.7707 (p0) REVERT: G 51 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8217 (mm-30) REVERT: G 221 ASP cc_start: 0.7930 (p0) cc_final: 0.7715 (p0) REVERT: H 51 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8045 (mm-30) REVERT: H 294 MET cc_start: 0.9013 (pmm) cc_final: 0.8717 (pmm) REVERT: I 281 MET cc_start: 0.8552 (mtp) cc_final: 0.8348 (mtm) REVERT: K 248 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8303 (mm) REVERT: K 294 MET cc_start: 0.8472 (pmm) cc_final: 0.8145 (pmm) REVERT: L 188 ASP cc_start: 0.7985 (m-30) cc_final: 0.7591 (m-30) outliers start: 86 outliers final: 41 residues processed: 665 average time/residue: 1.4306 time to fit residues: 1110.3293 Evaluate side-chains 632 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 589 time to evaluate : 3.332 ------------------------------------------------------------------------------- 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 143 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 340 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 334 optimal weight: 2.9990 chunk 355 optimal weight: 4.9990 chunk 293 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 C 123 HIS D 12 HIS 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 12 HIS I 17 GLN I 288 GLN I 305 ASN J 123 HIS K 263 ASN L 123 HIS L 288 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.102119 restraints weight = 24447.535| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.05 r_work: 0.2905 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- 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 = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 29256 Z= 0.169 Angle : 0.558 7.164 39672 Z= 0.316 Chirality : 0.050 0.201 4668 Planarity : 0.003 0.029 5004 Dihedral : 11.930 83.797 4338 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.99 % Allowed : 13.23 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.14), residues: 3660 helix: 1.61 (0.14), residues: 1512 sheet: 0.04 (0.17), residues: 972 loop : -0.36 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 162 HIS 0.007 0.001 HIS J 130 PHE 0.010 0.002 PHE D 138 TYR 0.016 0.002 TYR E 146 ARG 0.005 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.05160 ( 1428) hydrogen bonds : angle 4.98168 ( 3996) covalent geometry : bond 0.00373 (29256) covalent geometry : angle 0.55762 (39672) *********************** 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 704 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 610 time to evaluate : 3.381 Fit side-chains REVERT: A 188 ASP cc_start: 0.7891 (m-30) cc_final: 0.7455 (m-30) REVERT: A 286 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8169 (ptmt) REVERT: B 39 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8400 (mt-10) REVERT: B 294 MET cc_start: 0.8434 (pmm) cc_final: 0.8070 (pmm) REVERT: D 51 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8341 (mm-30) REVERT: E 51 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8025 (mm-30) REVERT: E 294 MET cc_start: 0.9020 (pmm) cc_final: 0.8734 (pmm) REVERT: F 51 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8275 (mm-30) REVERT: F 248 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8351 (mm) REVERT: G 51 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8225 (mm-30) REVERT: H 51 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8025 (mm-30) REVERT: H 294 MET cc_start: 0.9021 (pmm) cc_final: 0.8736 (pmm) REVERT: J 17 GLN cc_start: 0.9088 (tp40) cc_final: 0.8830 (tp40) REVERT: K 294 MET cc_start: 0.8433 (pmm) cc_final: 0.8068 (pmm) REVERT: L 188 ASP cc_start: 0.7878 (m-30) cc_final: 0.7440 (m-30) REVERT: L 286 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8172 (ptmt) outliers start: 94 outliers final: 47 residues processed: 656 average time/residue: 1.3348 time to fit residues: 1028.5053 Evaluate side-chains 642 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 591 time to evaluate : 3.316 ------------------------------------------------------------------------------- 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 A residue 286 LYS Chi-restraints excluded: chain B residue 39 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 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 270 VAL 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 F residue 270 VAL 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 G residue 270 VAL 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 H residue 270 VAL 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 118 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER 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 Chi-restraints excluded: chain L residue 286 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 151 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 253 optimal weight: 0.7980 chunk 290 optimal weight: 9.9990 chunk 306 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 276 optimal weight: 0.9990 chunk 315 optimal weight: 0.9990 chunk 49 optimal weight: 0.0010 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 263 ASN C 38 GLN F 263 ASN F 288 GLN G 263 ASN G 288 GLN K 263 ASN L 288 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.140233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.104950 restraints weight = 24851.760| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.06 r_work: 0.2968 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1925 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= 0.115 Angle : 0.492 5.969 39672 Z= 0.279 Chirality : 0.047 0.190 4668 Planarity : 0.003 0.025 5004 Dihedral : 10.847 78.702 4338 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.13 % Allowed : 14.34 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.14), residues: 3660 helix: 1.75 (0.14), residues: 1512 sheet: -0.13 (0.16), residues: 1008 loop : -0.25 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 162 HIS 0.003 0.001 HIS F 12 PHE 0.009 0.001 PHE D 138 TYR 0.013 0.001 TYR J 146 ARG 0.006 0.000 ARG I 22 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 1428) hydrogen bonds : angle 4.82856 ( 3996) covalent geometry : bond 0.00237 (29256) covalent geometry : angle 0.49223 (39672) *********************** 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 676 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 609 time to evaluate : 3.402 Fit side-chains REVERT: A 188 ASP cc_start: 0.7799 (m-30) cc_final: 0.7349 (m-30) REVERT: B 205 MET cc_start: 0.7805 (mtt) cc_final: 0.7561 (mtt) REVERT: B 294 MET cc_start: 0.8459 (pmm) cc_final: 0.8079 (pmm) REVERT: C 14 ASP cc_start: 0.8516 (t70) cc_final: 0.8295 (t0) REVERT: D 17 GLN cc_start: 0.9059 (tp-100) cc_final: 0.8826 (tp-100) REVERT: E 294 MET cc_start: 0.9009 (pmm) cc_final: 0.8725 (pmm) REVERT: F 51 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8234 (mm-30) REVERT: F 69 GLU cc_start: 0.8904 (tt0) cc_final: 0.8518 (tt0) REVERT: F 181 ILE cc_start: 0.8491 (mt) cc_final: 0.8284 (mt) REVERT: F 248 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8351 (mm) REVERT: G 51 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8229 (mm-30) REVERT: G 69 GLU cc_start: 0.8988 (tt0) cc_final: 0.8597 (tt0) REVERT: G 181 ILE cc_start: 0.8494 (mt) cc_final: 0.8292 (mt) REVERT: H 51 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7989 (mm-30) REVERT: H 294 MET cc_start: 0.9004 (pmm) cc_final: 0.8718 (pmm) REVERT: I 17 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8828 (tp-100) REVERT: J 14 ASP cc_start: 0.8515 (t70) cc_final: 0.8271 (t0) REVERT: K 205 MET cc_start: 0.7809 (mtt) cc_final: 0.7566 (mtt) REVERT: K 248 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8358 (mm) REVERT: K 294 MET cc_start: 0.8451 (pmm) cc_final: 0.8069 (pmm) REVERT: L 188 ASP cc_start: 0.7780 (m-30) cc_final: 0.7324 (m-30) outliers start: 67 outliers final: 37 residues processed: 643 average time/residue: 1.3830 time to fit residues: 1042.2002 Evaluate side-chains 622 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 583 time to evaluate : 3.092 ------------------------------------------------------------------------------- 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 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 C residue 258 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 J residue 258 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 300 optimal weight: 6.9990 chunk 339 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 F 263 ASN F 288 GLN G 17 GLN G 263 ASN G 288 GLN I 123 HIS J 38 GLN K 123 HIS K 263 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.102213 restraints weight = 24516.022| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.06 r_work: 0.2934 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1912 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= 0.155 Angle : 0.533 6.686 39672 Z= 0.301 Chirality : 0.049 0.213 4668 Planarity : 0.003 0.027 5004 Dihedral : 11.260 82.482 4338 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.04 % Allowed : 14.95 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 3660 helix: 1.76 (0.14), residues: 1512 sheet: 0.03 (0.17), residues: 912 loop : -0.38 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 162 HIS 0.005 0.001 HIS H 130 PHE 0.009 0.002 PHE D 138 TYR 0.016 0.002 TYR C 146 ARG 0.005 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.04827 ( 1428) hydrogen bonds : angle 4.84259 ( 3996) covalent geometry : bond 0.00338 (29256) covalent geometry : angle 0.53255 (39672) *********************** 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 667 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 603 time to evaluate : 3.106 Fit side-chains REVERT: A 188 ASP cc_start: 0.7814 (m-30) cc_final: 0.7385 (m-30) REVERT: A 286 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8222 (ptmt) REVERT: B 39 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8354 (mt-10) REVERT: B 205 MET cc_start: 0.7866 (mtt) cc_final: 0.7627 (mtt) REVERT: B 294 MET cc_start: 0.8465 (pmm) cc_final: 0.8082 (pmm) REVERT: E 294 MET cc_start: 0.9029 (pmm) cc_final: 0.8727 (pmm) REVERT: F 51 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8254 (mm-30) REVERT: F 69 GLU cc_start: 0.8925 (tt0) cc_final: 0.8610 (tt0) REVERT: F 248 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8369 (mm) REVERT: G 51 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8242 (mm-30) REVERT: G 69 GLU cc_start: 0.9004 (tt0) cc_final: 0.8646 (tt0) REVERT: H 51 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8044 (mm-30) REVERT: H 294 MET cc_start: 0.9029 (pmm) cc_final: 0.8728 (pmm) REVERT: K 39 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: K 205 MET cc_start: 0.7789 (mtt) cc_final: 0.7553 (mtt) REVERT: K 248 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8273 (mm) REVERT: K 294 MET cc_start: 0.8460 (pmm) cc_final: 0.8073 (pmm) REVERT: L 188 ASP cc_start: 0.7806 (m-30) cc_final: 0.7386 (m-30) REVERT: L 286 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8226 (ptmt) outliers start: 64 outliers final: 44 residues processed: 632 average time/residue: 1.4218 time to fit residues: 1047.4100 Evaluate side-chains 641 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 591 time to evaluate : 3.541 ------------------------------------------------------------------------------- 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 A residue 286 LYS 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 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 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 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 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 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 Chi-restraints excluded: chain L residue 286 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 226 optimal weight: 0.3980 chunk 89 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 284 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 204 optimal weight: 0.0010 chunk 188 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- 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 K 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.140636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.104965 restraints weight = 24585.015| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.06 r_work: 0.2973 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2085 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 : 0.484 5.659 39672 Z= 0.273 Chirality : 0.047 0.197 4668 Planarity : 0.003 0.024 5004 Dihedral : 10.483 78.138 4338 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.04 % Allowed : 15.30 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.14), residues: 3660 helix: 1.84 (0.14), residues: 1512 sheet: -0.19 (0.16), residues: 1008 loop : -0.22 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 162 HIS 0.003 0.001 HIS C 130 PHE 0.009 0.001 PHE I 138 TYR 0.014 0.001 TYR J 146 ARG 0.006 0.000 ARG K 163 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 1428) hydrogen bonds : angle 4.72084 ( 3996) covalent geometry : bond 0.00235 (29256) covalent geometry : angle 0.48445 (39672) *********************** 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 663 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 599 time to evaluate : 3.376 Fit side-chains REVERT: B 39 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8289 (mt-10) REVERT: B 205 MET cc_start: 0.7770 (mtt) cc_final: 0.7566 (mtt) REVERT: B 294 MET cc_start: 0.8457 (pmm) cc_final: 0.8078 (pmm) REVERT: C 14 ASP cc_start: 0.8512 (t70) cc_final: 0.8289 (t0) REVERT: C 205 MET cc_start: 0.7862 (mtp) cc_final: 0.7648 (ptp) REVERT: D 17 GLN cc_start: 0.9070 (tp-100) cc_final: 0.8777 (tp-100) REVERT: E 294 MET cc_start: 0.8997 (pmm) cc_final: 0.8712 (pmm) REVERT: F 51 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8218 (mm-30) REVERT: F 248 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8385 (mm) REVERT: G 51 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8193 (mm-30) REVERT: G 69 GLU cc_start: 0.9004 (tt0) cc_final: 0.8662 (tt0) REVERT: H 51 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7997 (mm-30) REVERT: H 294 MET cc_start: 0.9002 (pmm) cc_final: 0.8717 (pmm) REVERT: I 17 GLN cc_start: 0.9072 (tp-100) cc_final: 0.8778 (tp-100) REVERT: J 205 MET cc_start: 0.7866 (mtp) cc_final: 0.7658 (ptp) REVERT: K 205 MET cc_start: 0.7771 (mtt) cc_final: 0.7569 (mtt) REVERT: K 248 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8377 (mm) REVERT: K 294 MET cc_start: 0.8466 (pmm) cc_final: 0.8082 (pmm) outliers start: 64 outliers final: 40 residues processed: 632 average time/residue: 1.4675 time to fit residues: 1077.2861 Evaluate side-chains 617 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 574 time to evaluate : 3.151 ------------------------------------------------------------------------------- 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 39 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 258 ILE 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 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 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 J residue 62 GLU Chi-restraints excluded: chain J residue 118 VAL 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 45 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 257 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 296 optimal weight: 1.9990 chunk 317 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 315 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 123 HIS F 263 ASN F 288 GLN G 263 ASN G 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 = 0.3573 r_free = 0.3573 target = 0.139378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.103032 restraints weight = 24768.450| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.10 r_work: 0.2951 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2088 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= 0.123 Angle : 0.493 5.783 39672 Z= 0.278 Chirality : 0.047 0.186 4668 Planarity : 0.003 0.026 5004 Dihedral : 10.451 78.329 4337 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.69 % Allowed : 15.78 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.14), residues: 3660 helix: 1.86 (0.14), residues: 1512 sheet: -0.21 (0.16), residues: 1008 loop : -0.20 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 162 HIS 0.004 0.001 HIS E 130 PHE 0.008 0.001 PHE D 138 TYR 0.015 0.001 TYR C 146 ARG 0.006 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 1428) hydrogen bonds : angle 4.70742 ( 3996) covalent geometry : bond 0.00259 (29256) covalent geometry : angle 0.49293 (39672) *********************** 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 630 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 577 time to evaluate : 3.230 Fit side-chains REVERT: B 39 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8325 (mt-10) REVERT: B 69 GLU cc_start: 0.9083 (tt0) cc_final: 0.8765 (tt0) REVERT: B 294 MET cc_start: 0.8471 (pmm) cc_final: 0.8067 (pmm) REVERT: C 205 MET cc_start: 0.7866 (mtp) cc_final: 0.7658 (ptp) REVERT: C 286 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8287 (ptmt) REVERT: D 17 GLN cc_start: 0.9066 (tp-100) cc_final: 0.8809 (tp-100) REVERT: E 294 MET cc_start: 0.8968 (pmm) cc_final: 0.8657 (pmm) REVERT: F 51 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8170 (mm-30) REVERT: F 69 GLU cc_start: 0.9060 (tt0) cc_final: 0.8840 (tt0) REVERT: F 224 ASP cc_start: 0.8317 (t0) cc_final: 0.8004 (t0) REVERT: F 248 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8370 (mm) REVERT: G 51 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8162 (mm-30) REVERT: G 69 GLU cc_start: 0.9026 (tt0) cc_final: 0.8684 (tt0) REVERT: H 51 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7985 (mm-30) REVERT: H 294 MET cc_start: 0.8965 (pmm) cc_final: 0.8653 (pmm) REVERT: I 17 GLN cc_start: 0.9070 (tp-100) cc_final: 0.8813 (tp-100) REVERT: J 205 MET cc_start: 0.7849 (mtp) cc_final: 0.7643 (ptp) REVERT: J 286 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8285 (ptmt) REVERT: K 39 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8301 (mt-10) REVERT: K 248 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8357 (mm) REVERT: K 294 MET cc_start: 0.8458 (pmm) cc_final: 0.8054 (pmm) outliers start: 53 outliers final: 38 residues processed: 604 average time/residue: 1.5342 time to fit residues: 1082.4491 Evaluate side-chains 613 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 569 time to evaluate : 3.561 ------------------------------------------------------------------------------- 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 39 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 25 LEU 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 248 LEU Chi-restraints excluded: chain F residue 249 THR 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 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 25 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 118 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 193 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 chunk 250 optimal weight: 0.0570 chunk 288 optimal weight: 7.9990 chunk 140 optimal weight: 0.1980 chunk 172 optimal weight: 7.9990 chunk 265 optimal weight: 0.9980 chunk 218 optimal weight: 8.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- 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 17 GLN G 263 ASN G 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 = 0.3575 r_free = 0.3575 target = 0.139493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.103134 restraints weight = 24797.677| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.10 r_work: 0.2949 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29256 Z= 0.125 Angle : 0.495 5.705 39672 Z= 0.279 Chirality : 0.047 0.208 4668 Planarity : 0.003 0.023 5004 Dihedral : 10.407 78.015 4336 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.56 % Allowed : 16.00 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.14), residues: 3660 helix: 1.87 (0.14), residues: 1512 sheet: -0.20 (0.16), residues: 1008 loop : -0.23 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 162 HIS 0.004 0.001 HIS H 130 PHE 0.008 0.001 PHE I 138 TYR 0.016 0.002 TYR J 146 ARG 0.006 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 1428) hydrogen bonds : angle 4.68977 ( 3996) covalent geometry : bond 0.00265 (29256) covalent geometry : angle 0.49486 (39672) *********************** 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 619 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 570 time to evaluate : 3.082 Fit side-chains REVERT: B 69 GLU cc_start: 0.9072 (tt0) cc_final: 0.8748 (tt0) REVERT: B 294 MET cc_start: 0.8461 (pmm) cc_final: 0.8054 (pmm) REVERT: C 286 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8308 (ptmt) REVERT: D 17 GLN cc_start: 0.9070 (tp-100) cc_final: 0.8803 (tp-100) REVERT: D 224 ASP cc_start: 0.8324 (t0) cc_final: 0.8037 (t0) REVERT: D 248 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8310 (mm) REVERT: E 294 MET cc_start: 0.8965 (pmm) cc_final: 0.8655 (pmm) REVERT: F 51 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8172 (mm-30) REVERT: F 69 GLU cc_start: 0.9058 (tt0) cc_final: 0.8844 (tt0) REVERT: F 248 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8371 (mm) REVERT: G 51 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8189 (mm-30) REVERT: G 69 GLU cc_start: 0.9029 (tt0) cc_final: 0.8759 (tt0) REVERT: G 248 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8380 (mm) REVERT: H 294 MET cc_start: 0.8960 (pmm) cc_final: 0.8649 (pmm) REVERT: I 17 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8803 (tp-100) REVERT: I 224 ASP cc_start: 0.8322 (t0) cc_final: 0.8024 (t0) REVERT: I 248 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8309 (mm) REVERT: J 286 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8306 (ptmt) REVERT: K 248 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8351 (mm) REVERT: K 294 MET cc_start: 0.8474 (pmm) cc_final: 0.8065 (pmm) outliers start: 49 outliers final: 38 residues processed: 594 average time/residue: 1.4110 time to fit residues: 976.1620 Evaluate side-chains 607 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 562 time to evaluate : 3.124 ------------------------------------------------------------------------------- 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 26 GLU Chi-restraints excluded: chain B residue 39 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 25 LEU Chi-restraints excluded: chain D residue 248 LEU 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 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 I residue 248 LEU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 118 VAL 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 309 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 218 optimal weight: 8.9990 chunk 302 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 237 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 K 263 ASN K 288 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.138098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.101449 restraints weight = 24618.037| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.10 r_work: 0.2916 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2061 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= 0.151 Angle : 0.525 6.320 39672 Z= 0.296 Chirality : 0.048 0.207 4668 Planarity : 0.003 0.025 5004 Dihedral : 10.873 81.662 4336 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.84 % Allowed : 15.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.14), residues: 3660 helix: 1.82 (0.14), residues: 1512 sheet: -0.14 (0.16), residues: 972 loop : -0.35 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 162 HIS 0.004 0.001 HIS E 130 PHE 0.009 0.001 PHE I 138 TYR 0.018 0.002 TYR J 146 ARG 0.005 0.000 ARG K 163 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 1428) hydrogen bonds : angle 4.73687 ( 3996) covalent geometry : bond 0.00329 (29256) covalent geometry : angle 0.52463 (39672) *********************** 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 627 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 569 time to evaluate : 3.221 Fit side-chains REVERT: B 39 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8354 (mt-10) REVERT: B 69 GLU cc_start: 0.9074 (tt0) cc_final: 0.8809 (tt0) REVERT: B 294 MET cc_start: 0.8487 (pmm) cc_final: 0.8088 (pmm) REVERT: C 286 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8297 (ptmt) REVERT: D 17 GLN cc_start: 0.9067 (tp-100) cc_final: 0.8793 (tp-100) REVERT: E 294 MET cc_start: 0.8980 (pmm) cc_final: 0.8667 (pmm) REVERT: F 51 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8206 (mm-30) REVERT: F 69 GLU cc_start: 0.9061 (tt0) cc_final: 0.8721 (tt0) REVERT: F 248 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8364 (mm) REVERT: G 51 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8225 (mm-30) REVERT: G 69 GLU cc_start: 0.9032 (tt0) cc_final: 0.8695 (tt0) REVERT: G 248 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8354 (mm) REVERT: H 294 MET cc_start: 0.8986 (pmm) cc_final: 0.8676 (pmm) REVERT: I 17 GLN cc_start: 0.9066 (tp-100) cc_final: 0.8795 (tp-100) REVERT: J 286 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8289 (ptmt) REVERT: K 39 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: K 248 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8299 (mm) REVERT: K 294 MET cc_start: 0.8490 (pmm) cc_final: 0.8085 (pmm) outliers start: 58 outliers final: 35 residues processed: 599 average time/residue: 1.4847 time to fit residues: 1033.6814 Evaluate side-chains 615 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 573 time to evaluate : 3.137 ------------------------------------------------------------------------------- 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 39 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 25 LEU 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 248 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 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 118 VAL 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 187 optimal weight: 4.9990 chunk 317 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 204 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 274 optimal weight: 0.9990 chunk 303 optimal weight: 7.9990 chunk 333 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 HIS B 263 ASN C 38 GLN D 12 HIS F 263 ASN F 288 GLN G 263 ASN G 288 GLN I 12 HIS 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 = 0.3530 r_free = 0.3530 target = 0.135776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.099389 restraints weight = 24549.533| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.14 r_work: 0.2891 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 29256 Z= 0.240 Angle : 0.613 7.281 39672 Z= 0.344 Chirality : 0.053 0.242 4668 Planarity : 0.004 0.037 5004 Dihedral : 12.253 87.901 4336 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.72 % Allowed : 15.97 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.14), residues: 3660 helix: 1.63 (0.14), residues: 1512 sheet: -0.04 (0.16), residues: 972 loop : -0.46 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP L 162 HIS 0.007 0.001 HIS A 130 PHE 0.010 0.002 PHE B 138 TYR 0.025 0.003 TYR C 146 ARG 0.007 0.001 ARG F 163 Details of bonding type rmsd hydrogen bonds : bond 0.05631 ( 1428) hydrogen bonds : angle 4.94634 ( 3996) covalent geometry : bond 0.00546 (29256) covalent geometry : angle 0.61321 (39672) ********************** 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 658 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 604 time to evaluate : 3.539 Fit side-chains REVERT: B 294 MET cc_start: 0.8465 (pmm) cc_final: 0.8053 (pmm) REVERT: C 286 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8363 (ptmt) REVERT: D 17 GLN cc_start: 0.9056 (tp-100) cc_final: 0.8769 (tp-100) REVERT: E 294 MET cc_start: 0.8983 (pmm) cc_final: 0.8648 (pmm) REVERT: F 51 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8241 (mm-30) REVERT: F 282 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7887 (mtmm) REVERT: G 51 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8254 (mm-30) REVERT: G 282 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7884 (mtmm) REVERT: H 294 MET cc_start: 0.8984 (pmm) cc_final: 0.8650 (pmm) REVERT: I 17 GLN cc_start: 0.9060 (tp-100) cc_final: 0.8743 (tp-100) REVERT: J 286 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8356 (ptmt) REVERT: K 294 MET cc_start: 0.8467 (pmm) cc_final: 0.8049 (pmm) outliers start: 54 outliers final: 37 residues processed: 626 average time/residue: 1.4998 time to fit residues: 1089.3587 Evaluate side-chains 617 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 576 time to evaluate : 3.319 ------------------------------------------------------------------------------- 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 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 258 ILE Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 25 LEU 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 F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 282 LYS Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 118 VAL 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 I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 118 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 260 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 292 optimal weight: 2.9990 chunk 267 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 249 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 288 GLN I 17 GLN J 38 GLN K 263 ASN K 288 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.139738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.103456 restraints weight = 24590.758| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.09 r_work: 0.2955 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2160 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= 0.120 Angle : 0.507 7.371 39672 Z= 0.285 Chirality : 0.048 0.226 4668 Planarity : 0.003 0.026 5004 Dihedral : 10.851 82.597 4336 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.34 % Allowed : 16.32 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.14), residues: 3660 helix: 1.79 (0.14), residues: 1512 sheet: -0.16 (0.16), residues: 1008 loop : -0.27 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 162 HIS 0.004 0.001 HIS E 130 PHE 0.008 0.001 PHE D 138 TYR 0.016 0.001 TYR J 146 ARG 0.007 0.000 ARG F 163 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 1428) hydrogen bonds : angle 4.72940 ( 3996) covalent geometry : bond 0.00254 (29256) covalent geometry : angle 0.50691 (39672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31295.95 seconds wall clock time: 538 minutes 42.89 seconds (32322.89 seconds total)