Starting phenix.real_space_refine on Wed Mar 4 14:47:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbl_27289/03_2026/8dbl_27289.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbl_27289/03_2026/8dbl_27289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dbl_27289/03_2026/8dbl_27289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbl_27289/03_2026/8dbl_27289.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbl_27289/03_2026/8dbl_27289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbl_27289/03_2026/8dbl_27289.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.334 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 24 5.49 5 Mg 12 5.21 5 S 102 5.16 5 C 8922 2.51 5 N 2490 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14358 Number of models: 1 Model: "" Number of chains: 18 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: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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} Residues with excluded nonbonded symmetry interactions: 318 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 306 not shown) Time building chain proxies: 2.90, per 1000 atoms: 0.20 Number of scatterers: 14358 At special positions: 0 Unit cell: (122.728, 130.134, 77.234, 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 102 16.00 P 24 15.00 Mg 12 11.99 O 2808 8.00 N 2490 7.00 C 8922 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: 1.20 Conformation dependent library (CDL) restraints added in 563.0 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 43.4% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 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 removed outlier: 3.525A pdb=" N PHE A 138 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' 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 283 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 315 Processing helix chain 'B' and resid 12 through 23 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 removed outlier: 3.525A pdb=" N PHE B 138 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' 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 283 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 315 Processing helix chain 'C' and resid 12 through 23 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 removed outlier: 3.525A pdb=" N PHE C 138 " --> pdb=" O GLN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' 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 283 removed outlier: 3.666A 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 315 Processing helix chain 'D' and resid 12 through 23 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 removed outlier: 3.525A pdb=" N PHE D 138 " --> pdb=" O GLN D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' 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 283 removed outlier: 3.667A 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 315 Processing helix chain 'E' and resid 12 through 23 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 removed outlier: 3.526A pdb=" N PHE E 138 " --> pdb=" O GLN E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' 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 283 removed outlier: 3.666A 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 315 Processing helix chain 'F' and resid 12 through 23 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 removed outlier: 3.524A pdb=" N PHE F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 171 through 173 No H-bonds generated for 'chain 'F' and resid 171 through 173' 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 283 removed outlier: 3.666A 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 315 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.157A pdb=" N LYS A 5 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL A 56 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE A 7 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL A 88 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS A 123 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET A 127 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE A 124 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU A 145 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 6.701A 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: 3.775A pdb=" N SER A 169 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 249 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET A 222 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY A 251 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL A 244 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL A 270 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA A 246 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR A 272 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU A 248 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 269 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE A 290 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 271 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.156A pdb=" N LYS B 5 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL B 56 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE B 7 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 53 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL B 88 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS B 123 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET B 127 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 124 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU B 145 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 6.702A 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: 3.775A pdb=" N SER B 169 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 249 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET B 222 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY B 251 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL B 244 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL B 270 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA B 246 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR B 272 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU B 248 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 269 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE B 290 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 271 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.157A pdb=" N LYS C 5 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL C 56 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE C 7 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL C 88 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS C 123 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET C 127 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE C 124 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU C 145 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 6.701A 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: 3.775A pdb=" N SER C 169 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR C 249 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET C 222 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY C 251 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL C 244 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL C 270 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA C 246 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR C 272 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU C 248 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL C 269 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE C 290 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL C 271 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.156A pdb=" N LYS D 5 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL D 56 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE D 7 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL D 88 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS D 123 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET D 127 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE D 124 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU D 145 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 6.701A 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: 3.775A pdb=" N SER D 169 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR D 249 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET D 222 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY D 251 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL D 244 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL D 270 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA D 246 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR D 272 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU D 248 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL D 269 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE D 290 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 271 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.156A pdb=" N LYS E 5 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL E 56 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE E 7 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL E 53 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL E 88 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE E 55 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS E 123 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET E 127 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE E 124 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU E 145 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 6.702A 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: 3.776A pdb=" N SER E 169 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR E 249 " --> pdb=" O ASP E 220 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET E 222 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY E 251 " --> pdb=" O MET E 222 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL E 244 " --> pdb=" O ALA E 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL E 270 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA E 246 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N THR E 272 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU E 248 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL E 269 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE E 290 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL E 271 " --> pdb=" O ILE E 290 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.157A pdb=" N LYS F 5 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL F 56 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE F 7 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL F 53 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL F 88 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE F 55 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS F 123 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET F 127 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE F 124 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU F 145 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 6.702A 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: 3.775A pdb=" N SER F 169 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR F 249 " --> pdb=" O ASP F 220 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET F 222 " --> pdb=" O THR F 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY F 251 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL F 244 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL F 270 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA F 246 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR F 272 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU F 248 " --> pdb=" O THR F 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL F 269 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE F 290 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL F 271 " --> pdb=" O ILE F 290 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1800 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: 2.22 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4775 1.34 - 1.46: 2118 1.46 - 1.57: 7471 1.57 - 1.69: 24 1.69 - 1.81: 150 Bond restraints: 14538 Sorted by residual: bond pdb=" C1 PRP B 401 " pdb=" O4 PRP B 401 " ideal model delta sigma weight residual 1.656 1.420 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1 PRP A 401 " pdb=" O4 PRP A 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1 PRP C 401 " pdb=" O4 PRP C 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1 PRP F 401 " pdb=" O4 PRP F 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1 PRP D 401 " pdb=" O4 PRP D 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.38e+02 ... (remaining 14533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 19102 1.95 - 3.91: 465 3.91 - 5.86: 89 5.86 - 7.81: 30 7.81 - 9.76: 12 Bond angle restraints: 19698 Sorted by residual: angle pdb=" C THR E 272 " pdb=" CA THR E 272 " pdb=" CB THR E 272 " ideal model delta sigma weight residual 109.51 117.38 -7.87 1.71e+00 3.42e-01 2.12e+01 angle pdb=" C THR C 272 " pdb=" CA THR C 272 " pdb=" CB THR C 272 " ideal model delta sigma weight residual 109.51 117.37 -7.86 1.71e+00 3.42e-01 2.11e+01 angle pdb=" C THR A 272 " pdb=" CA THR A 272 " pdb=" CB THR A 272 " ideal model delta sigma weight residual 109.51 117.37 -7.86 1.71e+00 3.42e-01 2.11e+01 angle pdb=" C THR B 272 " pdb=" CA THR B 272 " pdb=" CB THR B 272 " ideal model delta sigma weight residual 109.51 117.36 -7.85 1.71e+00 3.42e-01 2.11e+01 angle pdb=" C THR F 272 " pdb=" CA THR F 272 " pdb=" CB THR F 272 " ideal model delta sigma weight residual 109.51 117.34 -7.83 1.71e+00 3.42e-01 2.10e+01 ... (remaining 19693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 8013 17.71 - 35.41: 660 35.41 - 53.12: 207 53.12 - 70.82: 60 70.82 - 88.53: 36 Dihedral angle restraints: 8976 sinusoidal: 3600 harmonic: 5376 Sorted by residual: dihedral pdb=" CA GLU C 62 " pdb=" C GLU C 62 " pdb=" N ILE C 63 " pdb=" CA ILE C 63 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU E 62 " pdb=" C GLU E 62 " pdb=" N ILE E 63 " pdb=" CA ILE E 63 " ideal model delta harmonic sigma weight residual -180.00 -160.93 -19.07 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU B 62 " pdb=" C GLU B 62 " pdb=" N ILE B 63 " pdb=" CA ILE B 63 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 8973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1333 0.041 - 0.082: 659 0.082 - 0.124: 267 0.124 - 0.165: 45 0.165 - 0.206: 30 Chirality restraints: 2334 Sorted by residual: chirality pdb=" CA THR D 272 " pdb=" N THR D 272 " pdb=" C THR D 272 " pdb=" CB THR D 272 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR E 272 " pdb=" N THR E 272 " pdb=" C THR E 272 " pdb=" CB THR E 272 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR F 272 " pdb=" N THR F 272 " pdb=" C THR F 272 " pdb=" CB THR F 272 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2331 not shown) Planarity restraints: 2496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 221 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" CG ASP E 221 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP E 221 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP E 221 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 221 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.93e+00 pdb=" CG ASP C 221 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP C 221 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP C 221 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 221 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" CG ASP F 221 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP F 221 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP F 221 " -0.015 2.00e-02 2.50e+03 ... (remaining 2493 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 108 2.49 - 3.09: 10320 3.09 - 3.69: 22423 3.69 - 4.30: 34207 4.30 - 4.90: 55860 Nonbonded interactions: 122918 Sorted by model distance: nonbonded pdb=" O3B PRP E 401 " pdb="MG MG E 403 " model vdw 1.885 2.170 nonbonded pdb=" O3B PRP C 401 " pdb="MG MG C 403 " model vdw 1.886 2.170 nonbonded pdb=" O1B PRP F 401 " pdb="MG MG F 403 " model vdw 1.886 2.170 nonbonded pdb=" O3B PRP A 401 " pdb="MG MG A 403 " model vdw 1.886 2.170 nonbonded pdb=" O1B PRP D 401 " pdb="MG MG D 403 " model vdw 1.886 2.170 ... (remaining 122913 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.610 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.440 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.011 0.236 14538 Z= 0.534 Angle : 0.823 9.765 19698 Z= 0.454 Chirality : 0.057 0.206 2334 Planarity : 0.003 0.024 2496 Dihedral : 16.538 88.531 5472 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.67 % Allowed : 15.27 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1830 helix: 1.25 (0.20), residues: 738 sheet: -0.62 (0.24), residues: 522 loop : -0.54 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 156 TYR 0.027 0.004 TYR B 245 PHE 0.017 0.002 PHE E 138 TRP 0.016 0.003 TRP F 162 HIS 0.003 0.001 HIS E 193 Details of bonding type rmsd covalent geometry : bond 0.01102 (14538) covalent geometry : angle 0.82307 (19698) hydrogen bonds : bond 0.15501 ( 648) hydrogen bonds : angle 5.67944 ( 1800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 322 time to evaluate : 0.465 Fit side-chains REVERT: A 5 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8431 (mmpt) REVERT: A 115 MET cc_start: 0.8598 (mtp) cc_final: 0.8244 (mtp) REVERT: A 127 MET cc_start: 0.8545 (ttm) cc_final: 0.8273 (ttm) REVERT: A 220 ASP cc_start: 0.8493 (t0) cc_final: 0.8267 (t70) REVERT: A 222 MET cc_start: 0.7806 (ptp) cc_final: 0.7530 (ptp) REVERT: A 267 GLU cc_start: 0.7586 (tp30) cc_final: 0.7162 (tp30) REVERT: B 122 ASP cc_start: 0.8460 (m-30) cc_final: 0.8248 (m-30) REVERT: B 220 ASP cc_start: 0.8601 (t0) cc_final: 0.8173 (t0) REVERT: C 38 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7382 (mp-120) REVERT: C 122 ASP cc_start: 0.8624 (m-30) cc_final: 0.8372 (m-30) REVERT: C 220 ASP cc_start: 0.8648 (t0) cc_final: 0.8328 (t70) REVERT: D 38 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7383 (mp-120) REVERT: D 220 ASP cc_start: 0.8649 (t0) cc_final: 0.8391 (t70) REVERT: E 5 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8457 (mmpt) REVERT: E 122 ASP cc_start: 0.8447 (m-30) cc_final: 0.8239 (m-30) REVERT: E 220 ASP cc_start: 0.8597 (t0) cc_final: 0.8164 (t0) REVERT: F 5 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8429 (mmpt) REVERT: F 115 MET cc_start: 0.8588 (mtp) cc_final: 0.8224 (mtp) REVERT: F 127 MET cc_start: 0.8570 (ttm) cc_final: 0.8294 (ttm) REVERT: F 220 ASP cc_start: 0.8510 (t0) cc_final: 0.8270 (t70) REVERT: F 267 GLU cc_start: 0.7575 (tp30) cc_final: 0.7133 (tp30) outliers start: 42 outliers final: 26 residues processed: 353 average time/residue: 0.6087 time to fit residues: 233.3469 Evaluate side-chains 315 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 284 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 285 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 HIS B 288 GLN C 277 GLN C 288 GLN D 277 GLN D 288 GLN E 288 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.159791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.121617 restraints weight = 13655.610| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.43 r_work: 0.3215 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 324 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14538 Z= 0.135 Angle : 0.496 4.127 19698 Z= 0.276 Chirality : 0.048 0.172 2334 Planarity : 0.003 0.021 2496 Dihedral : 8.633 68.525 2166 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.64 % Allowed : 12.85 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.21), residues: 1830 helix: 1.75 (0.20), residues: 714 sheet: -0.38 (0.24), residues: 486 loop : 0.01 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 177 TYR 0.016 0.002 TYR D 311 PHE 0.010 0.001 PHE D 138 TRP 0.012 0.002 TRP B 162 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00299 (14538) covalent geometry : angle 0.49612 (19698) hydrogen bonds : bond 0.04117 ( 648) hydrogen bonds : angle 4.84710 ( 1800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 325 time to evaluate : 0.482 Fit side-chains REVERT: A 5 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8688 (mmpt) REVERT: A 17 GLN cc_start: 0.9146 (tp40) cc_final: 0.8863 (tp40) REVERT: A 68 MET cc_start: 0.8718 (tpp) cc_final: 0.8508 (mmm) REVERT: A 96 ARG cc_start: 0.8786 (mtm180) cc_final: 0.8537 (mtm180) REVERT: A 97 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7550 (mp10) REVERT: A 127 MET cc_start: 0.9046 (ttm) cc_final: 0.8793 (ttm) REVERT: A 178 VAL cc_start: 0.8261 (m) cc_final: 0.7851 (t) REVERT: A 180 SER cc_start: 0.8343 (t) cc_final: 0.8063 (t) REVERT: A 220 ASP cc_start: 0.8612 (t0) cc_final: 0.8382 (t70) REVERT: A 222 MET cc_start: 0.8282 (ptp) cc_final: 0.7732 (ptp) REVERT: A 311 TYR cc_start: 0.8571 (t80) cc_final: 0.8353 (t80) REVERT: B 17 GLN cc_start: 0.9077 (tp40) cc_final: 0.8875 (tp-100) REVERT: B 97 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7966 (mm110) REVERT: B 122 ASP cc_start: 0.8807 (m-30) cc_final: 0.8479 (m-30) REVERT: B 220 ASP cc_start: 0.8688 (t0) cc_final: 0.8169 (t0) REVERT: C 17 GLN cc_start: 0.9061 (tp40) cc_final: 0.8693 (tp40) REVERT: C 68 MET cc_start: 0.8583 (tpp) cc_final: 0.8281 (tpt) REVERT: C 79 ILE cc_start: 0.9170 (pt) cc_final: 0.8887 (mm) REVERT: C 122 ASP cc_start: 0.9010 (m-30) cc_final: 0.8690 (m-30) REVERT: C 158 ASN cc_start: 0.7487 (m-40) cc_final: 0.7179 (m-40) REVERT: C 220 ASP cc_start: 0.8736 (t0) cc_final: 0.8397 (t70) REVERT: C 282 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8127 (mtpp) REVERT: D 17 GLN cc_start: 0.9094 (tp40) cc_final: 0.8693 (tp40) REVERT: D 68 MET cc_start: 0.8564 (tpp) cc_final: 0.8259 (tpt) REVERT: D 79 ILE cc_start: 0.9185 (pt) cc_final: 0.8886 (mm) REVERT: D 158 ASN cc_start: 0.7594 (m-40) cc_final: 0.7298 (m-40) REVERT: D 220 ASP cc_start: 0.8730 (t0) cc_final: 0.8405 (t70) REVERT: D 282 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8218 (mtpp) REVERT: E 5 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8732 (mmpt) REVERT: E 17 GLN cc_start: 0.9097 (tp40) cc_final: 0.8885 (tp-100) REVERT: E 97 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7959 (mm110) REVERT: E 122 ASP cc_start: 0.8805 (m-30) cc_final: 0.8506 (m-30) REVERT: E 220 ASP cc_start: 0.8691 (t0) cc_final: 0.8144 (t0) REVERT: F 5 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8685 (mmpt) REVERT: F 68 MET cc_start: 0.8735 (tpp) cc_final: 0.8525 (mmm) REVERT: F 97 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7548 (mp10) REVERT: F 127 MET cc_start: 0.9034 (ttm) cc_final: 0.8770 (ttm) REVERT: F 180 SER cc_start: 0.8238 (t) cc_final: 0.8013 (t) REVERT: F 220 ASP cc_start: 0.8635 (t0) cc_final: 0.8392 (t70) REVERT: F 222 MET cc_start: 0.8196 (ptp) cc_final: 0.7798 (ptp) REVERT: F 278 GLU cc_start: 0.7662 (mp0) cc_final: 0.7365 (pm20) outliers start: 73 outliers final: 24 residues processed: 372 average time/residue: 0.5864 time to fit residues: 237.6181 Evaluate side-chains 325 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 292 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 31 VAL 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 259 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 LYS Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 82 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 167 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 130 HIS A 283 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN B 283 HIS C 37 ASN C 283 HIS D 37 ASN D 283 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 283 HIS F 37 ASN F 97 GLN F 130 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.103752 restraints weight = 13760.183| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.48 r_work: 0.2987 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14538 Z= 0.130 Angle : 0.485 4.162 19698 Z= 0.267 Chirality : 0.047 0.165 2334 Planarity : 0.003 0.022 2496 Dihedral : 7.024 51.485 2148 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.44 % Allowed : 14.38 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.21), residues: 1830 helix: 1.90 (0.20), residues: 714 sheet: -0.29 (0.25), residues: 486 loop : -0.06 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 22 TYR 0.017 0.002 TYR E 311 PHE 0.011 0.001 PHE A 138 TRP 0.010 0.002 TRP E 162 HIS 0.004 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00292 (14538) covalent geometry : angle 0.48487 (19698) hydrogen bonds : bond 0.03980 ( 648) hydrogen bonds : angle 4.65708 ( 1800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 310 time to evaluate : 0.502 Fit side-chains REVERT: A 5 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8602 (mmpt) REVERT: A 17 GLN cc_start: 0.9108 (tp40) cc_final: 0.8829 (tp40) REVERT: A 97 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7578 (mp10) REVERT: A 178 VAL cc_start: 0.8230 (m) cc_final: 0.7867 (t) REVERT: A 180 SER cc_start: 0.8209 (t) cc_final: 0.7963 (t) REVERT: A 220 ASP cc_start: 0.8648 (t0) cc_final: 0.8348 (t70) REVERT: A 222 MET cc_start: 0.8283 (ptp) cc_final: 0.7586 (ptp) REVERT: A 259 SER cc_start: 0.8437 (p) cc_final: 0.8205 (p) REVERT: A 282 LYS cc_start: 0.8279 (mtpp) cc_final: 0.7963 (tttm) REVERT: A 311 TYR cc_start: 0.8592 (t80) cc_final: 0.8330 (t80) REVERT: B 22 ARG cc_start: 0.8807 (mtp85) cc_final: 0.8577 (mtp85) REVERT: B 122 ASP cc_start: 0.8913 (m-30) cc_final: 0.8567 (m-30) REVERT: B 127 MET cc_start: 0.9092 (ttm) cc_final: 0.8869 (tpp) REVERT: B 220 ASP cc_start: 0.8720 (t0) cc_final: 0.8230 (t0) REVERT: C 17 GLN cc_start: 0.9069 (tp40) cc_final: 0.8708 (tp40) REVERT: C 29 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8690 (mtpt) REVERT: C 38 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7243 (mp-120) REVERT: C 68 MET cc_start: 0.8730 (tpp) cc_final: 0.8342 (tpt) REVERT: C 79 ILE cc_start: 0.9140 (pt) cc_final: 0.8885 (mm) REVERT: C 122 ASP cc_start: 0.9101 (m-30) cc_final: 0.8799 (m-30) REVERT: C 158 ASN cc_start: 0.7414 (m-40) cc_final: 0.7013 (m110) REVERT: C 220 ASP cc_start: 0.8758 (t0) cc_final: 0.8363 (t70) REVERT: C 222 MET cc_start: 0.8337 (ptp) cc_final: 0.7949 (ptm) REVERT: C 281 MET cc_start: 0.8599 (mtp) cc_final: 0.8288 (mtp) REVERT: C 282 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8201 (mtpp) REVERT: D 17 GLN cc_start: 0.9090 (tp40) cc_final: 0.8739 (tp40) REVERT: D 29 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8721 (mtpt) REVERT: D 68 MET cc_start: 0.8727 (tpp) cc_final: 0.8335 (tpt) REVERT: D 79 ILE cc_start: 0.9143 (pt) cc_final: 0.8883 (mm) REVERT: D 158 ASN cc_start: 0.7387 (m-40) cc_final: 0.7099 (m-40) REVERT: D 220 ASP cc_start: 0.8776 (t0) cc_final: 0.8361 (t70) REVERT: D 222 MET cc_start: 0.8322 (ptp) cc_final: 0.7931 (ptm) REVERT: D 282 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8199 (mtpp) REVERT: E 5 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8609 (mmpt) REVERT: E 22 ARG cc_start: 0.8802 (mtp85) cc_final: 0.8578 (mtp85) REVERT: E 122 ASP cc_start: 0.8928 (m-30) cc_final: 0.8631 (m-30) REVERT: E 127 MET cc_start: 0.9100 (ttm) cc_final: 0.8878 (tpp) REVERT: E 220 ASP cc_start: 0.8689 (t0) cc_final: 0.8212 (t0) REVERT: F 5 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8645 (mmpt) REVERT: F 37 ASN cc_start: 0.8827 (p0) cc_final: 0.8622 (p0) REVERT: F 97 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: F 222 MET cc_start: 0.8203 (ptp) cc_final: 0.7926 (ptp) REVERT: F 259 SER cc_start: 0.8366 (p) cc_final: 0.8134 (p) outliers start: 54 outliers final: 22 residues processed: 340 average time/residue: 0.5954 time to fit residues: 220.0437 Evaluate side-chains 322 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 292 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 38 GLN 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 270 VAL Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 314 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 129 optimal weight: 1.9990 chunk 67 optimal weight: 0.0030 chunk 60 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 158 optimal weight: 0.4980 chunk 13 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 17 GLN B 97 GLN B 283 HIS B 288 GLN C 37 ASN C 283 HIS D 37 ASN D 283 HIS E 17 GLN E 263 ASN E 283 HIS E 288 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.143514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.103614 restraints weight = 13843.171| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.47 r_work: 0.2995 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14538 Z= 0.124 Angle : 0.474 4.269 19698 Z= 0.261 Chirality : 0.047 0.164 2334 Planarity : 0.003 0.022 2496 Dihedral : 6.670 46.422 2142 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.50 % Allowed : 15.59 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1830 helix: 1.97 (0.20), residues: 714 sheet: -0.08 (0.26), residues: 408 loop : -0.24 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 96 TYR 0.018 0.002 TYR E 311 PHE 0.011 0.001 PHE E 35 TRP 0.009 0.002 TRP E 162 HIS 0.003 0.001 HIS E 193 Details of bonding type rmsd covalent geometry : bond 0.00279 (14538) covalent geometry : angle 0.47360 (19698) hydrogen bonds : bond 0.03758 ( 648) hydrogen bonds : angle 4.55590 ( 1800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 305 time to evaluate : 0.550 Fit side-chains REVERT: A 17 GLN cc_start: 0.9103 (tp40) cc_final: 0.8831 (tp40) REVERT: A 178 VAL cc_start: 0.8246 (m) cc_final: 0.7875 (t) REVERT: A 180 SER cc_start: 0.8196 (t) cc_final: 0.7984 (t) REVERT: A 220 ASP cc_start: 0.8655 (t0) cc_final: 0.8339 (t70) REVERT: A 222 MET cc_start: 0.8321 (ptp) cc_final: 0.7631 (ptp) REVERT: A 259 SER cc_start: 0.8394 (p) cc_final: 0.8164 (p) REVERT: A 278 GLU cc_start: 0.7631 (mp0) cc_final: 0.7228 (pm20) REVERT: A 311 TYR cc_start: 0.8579 (t80) cc_final: 0.8317 (t80) REVERT: B 22 ARG cc_start: 0.8798 (mtp85) cc_final: 0.8477 (mtp85) REVERT: B 122 ASP cc_start: 0.8946 (m-30) cc_final: 0.8598 (m-30) REVERT: B 220 ASP cc_start: 0.8769 (t0) cc_final: 0.8248 (t0) REVERT: B 282 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8244 (mtpp) REVERT: C 17 GLN cc_start: 0.9067 (tp40) cc_final: 0.8753 (tp40) REVERT: C 29 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8694 (mtpt) REVERT: C 38 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7243 (mp-120) REVERT: C 68 MET cc_start: 0.8745 (tpp) cc_final: 0.8329 (tpt) REVERT: C 122 ASP cc_start: 0.9117 (m-30) cc_final: 0.8819 (m-30) REVERT: C 220 ASP cc_start: 0.8789 (t0) cc_final: 0.8343 (t70) REVERT: C 222 MET cc_start: 0.8410 (ptp) cc_final: 0.7978 (ptm) REVERT: C 281 MET cc_start: 0.8673 (mtp) cc_final: 0.8293 (mtp) REVERT: C 282 LYS cc_start: 0.8459 (mtpp) cc_final: 0.8219 (mtpp) REVERT: D 17 GLN cc_start: 0.9079 (tp40) cc_final: 0.8725 (tp40) REVERT: D 29 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8702 (mtpt) REVERT: D 68 MET cc_start: 0.8741 (tpp) cc_final: 0.8356 (tpt) REVERT: D 79 ILE cc_start: 0.9103 (pt) cc_final: 0.8899 (mm) REVERT: D 158 ASN cc_start: 0.7432 (m-40) cc_final: 0.7193 (m110) REVERT: D 220 ASP cc_start: 0.8794 (t0) cc_final: 0.8459 (t70) REVERT: D 222 MET cc_start: 0.8406 (ptp) cc_final: 0.8115 (ptm) REVERT: D 282 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8219 (mtpp) REVERT: E 22 ARG cc_start: 0.8812 (mtp85) cc_final: 0.8499 (mtp85) REVERT: E 97 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8077 (mm110) REVERT: E 122 ASP cc_start: 0.8962 (m-30) cc_final: 0.8638 (m-30) REVERT: E 191 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6603 (mt) REVERT: E 205 MET cc_start: 0.5682 (ptp) cc_final: 0.5418 (ptm) REVERT: E 220 ASP cc_start: 0.8733 (t0) cc_final: 0.8252 (t0) REVERT: E 282 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8197 (mtpp) REVERT: F 37 ASN cc_start: 0.8820 (p0) cc_final: 0.8550 (p0) REVERT: F 278 GLU cc_start: 0.7637 (mp0) cc_final: 0.7173 (pm20) outliers start: 55 outliers final: 22 residues processed: 334 average time/residue: 0.6004 time to fit residues: 218.0613 Evaluate side-chains 326 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 297 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 34 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN B 263 ASN B 283 HIS B 288 GLN ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 283 HIS ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 283 HIS E 288 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.140755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.100387 restraints weight = 13886.015| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.48 r_work: 0.2939 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14538 Z= 0.200 Angle : 0.546 4.751 19698 Z= 0.298 Chirality : 0.049 0.166 2334 Planarity : 0.003 0.023 2496 Dihedral : 6.546 54.132 2130 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.13 % Allowed : 14.06 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1830 helix: 1.84 (0.20), residues: 714 sheet: -0.34 (0.24), residues: 480 loop : -0.13 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 301 TYR 0.016 0.002 TYR F 146 PHE 0.013 0.002 PHE C 138 TRP 0.009 0.002 TRP E 162 HIS 0.004 0.001 HIS E 193 Details of bonding type rmsd covalent geometry : bond 0.00463 (14538) covalent geometry : angle 0.54566 (19698) hydrogen bonds : bond 0.04440 ( 648) hydrogen bonds : angle 4.66370 ( 1800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 286 time to evaluate : 0.518 Fit side-chains REVERT: A 17 GLN cc_start: 0.9137 (tp40) cc_final: 0.8808 (tp40) REVERT: A 22 ARG cc_start: 0.8723 (mtp85) cc_final: 0.8483 (mtp85) REVERT: A 97 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.7261 (mp10) REVERT: A 122 ASP cc_start: 0.9032 (m-30) cc_final: 0.8763 (m-30) REVERT: A 178 VAL cc_start: 0.8282 (m) cc_final: 0.7893 (t) REVERT: A 222 MET cc_start: 0.8460 (ptp) cc_final: 0.7936 (ptp) REVERT: A 259 SER cc_start: 0.8427 (p) cc_final: 0.8222 (p) REVERT: B 22 ARG cc_start: 0.8846 (mtp85) cc_final: 0.8587 (mtp85) REVERT: B 122 ASP cc_start: 0.8961 (m-30) cc_final: 0.8691 (m-30) REVERT: B 191 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7174 (mt) REVERT: B 220 ASP cc_start: 0.8821 (t0) cc_final: 0.8325 (t0) REVERT: B 282 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8258 (mtpp) REVERT: C 17 GLN cc_start: 0.9047 (tp40) cc_final: 0.8791 (tp40) REVERT: C 29 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8654 (mtpt) REVERT: C 68 MET cc_start: 0.8809 (tpp) cc_final: 0.8418 (tpt) REVERT: C 122 ASP cc_start: 0.9129 (m-30) cc_final: 0.8761 (m-30) REVERT: C 220 ASP cc_start: 0.8769 (t0) cc_final: 0.8343 (t70) REVERT: C 278 GLU cc_start: 0.7552 (mp0) cc_final: 0.7174 (pm20) REVERT: C 282 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8289 (mtpp) REVERT: C 314 SER cc_start: 0.6777 (OUTLIER) cc_final: 0.6296 (p) REVERT: D 17 GLN cc_start: 0.9061 (tp40) cc_final: 0.8818 (tp40) REVERT: D 29 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8655 (mtpt) REVERT: D 68 MET cc_start: 0.8800 (tpp) cc_final: 0.8406 (tpt) REVERT: D 79 ILE cc_start: 0.9230 (pt) cc_final: 0.8845 (mm) REVERT: D 220 ASP cc_start: 0.8810 (t0) cc_final: 0.8482 (t70) REVERT: D 282 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8275 (mtpp) REVERT: D 314 SER cc_start: 0.6748 (OUTLIER) cc_final: 0.6289 (p) REVERT: E 22 ARG cc_start: 0.8827 (mtp85) cc_final: 0.8560 (mtp85) REVERT: E 122 ASP cc_start: 0.8950 (m-30) cc_final: 0.8688 (m-30) REVERT: E 191 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6933 (mt) REVERT: E 220 ASP cc_start: 0.8819 (t0) cc_final: 0.8295 (t0) REVERT: E 282 LYS cc_start: 0.8431 (mtpp) cc_final: 0.8213 (mtpp) REVERT: F 22 ARG cc_start: 0.8737 (mtp85) cc_final: 0.8498 (mtp85) REVERT: F 97 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7197 (mp10) outliers start: 65 outliers final: 27 residues processed: 331 average time/residue: 0.5962 time to fit residues: 214.8980 Evaluate side-chains 324 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 286 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 314 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 163 optimal weight: 0.0770 chunk 99 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 170 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 97 GLN B 283 HIS C 283 HIS D 283 HIS E 283 HIS F 37 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104193 restraints weight = 13889.307| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.48 r_work: 0.3000 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14538 Z= 0.111 Angle : 0.456 4.322 19698 Z= 0.252 Chirality : 0.046 0.166 2334 Planarity : 0.003 0.023 2496 Dihedral : 6.142 55.501 2130 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.75 % Allowed : 14.31 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1830 helix: 1.97 (0.20), residues: 714 sheet: -0.19 (0.26), residues: 408 loop : -0.31 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 49 TYR 0.022 0.002 TYR C 311 PHE 0.010 0.001 PHE C 138 TRP 0.009 0.002 TRP F 162 HIS 0.003 0.001 HIS E 193 Details of bonding type rmsd covalent geometry : bond 0.00249 (14538) covalent geometry : angle 0.45567 (19698) hydrogen bonds : bond 0.03527 ( 648) hydrogen bonds : angle 4.48608 ( 1800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 308 time to evaluate : 0.485 Fit side-chains REVERT: A 17 GLN cc_start: 0.9086 (tp40) cc_final: 0.8790 (tp40) REVERT: A 97 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: A 122 ASP cc_start: 0.9015 (m-30) cc_final: 0.8728 (m-30) REVERT: A 178 VAL cc_start: 0.8243 (m) cc_final: 0.7878 (t) REVERT: A 180 SER cc_start: 0.8211 (t) cc_final: 0.7996 (t) REVERT: A 222 MET cc_start: 0.8484 (ptp) cc_final: 0.7867 (ptp) REVERT: A 278 GLU cc_start: 0.7659 (mp0) cc_final: 0.7175 (pm20) REVERT: A 311 TYR cc_start: 0.8608 (t80) cc_final: 0.8369 (t80) REVERT: B 122 ASP cc_start: 0.8954 (m-30) cc_final: 0.8611 (m-30) REVERT: B 191 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7085 (mt) REVERT: B 220 ASP cc_start: 0.8770 (t0) cc_final: 0.8258 (t0) REVERT: B 282 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8248 (mtpp) REVERT: C 17 GLN cc_start: 0.9075 (tp40) cc_final: 0.8773 (tp40) REVERT: C 29 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8672 (mtpt) REVERT: C 68 MET cc_start: 0.8728 (tpp) cc_final: 0.8318 (tpt) REVERT: C 208 VAL cc_start: 0.4828 (OUTLIER) cc_final: 0.4563 (m) REVERT: C 220 ASP cc_start: 0.8779 (t0) cc_final: 0.8329 (t70) REVERT: C 222 MET cc_start: 0.8257 (ptp) cc_final: 0.7854 (ptm) REVERT: C 281 MET cc_start: 0.8431 (mtp) cc_final: 0.8178 (mtp) REVERT: C 282 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8202 (mtpp) REVERT: D 17 GLN cc_start: 0.9085 (tp40) cc_final: 0.8758 (tp40) REVERT: D 29 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8686 (mtpt) REVERT: D 68 MET cc_start: 0.8725 (tpp) cc_final: 0.8310 (tpt) REVERT: D 220 ASP cc_start: 0.8800 (t0) cc_final: 0.8466 (t70) REVERT: D 222 MET cc_start: 0.8301 (ptp) cc_final: 0.7995 (ptm) REVERT: D 282 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8175 (mtpp) REVERT: E 22 ARG cc_start: 0.8766 (mtp85) cc_final: 0.8443 (mtp85) REVERT: E 97 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7966 (mm110) REVERT: E 122 ASP cc_start: 0.8954 (m-30) cc_final: 0.8657 (m-30) REVERT: E 191 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6995 (mt) REVERT: E 220 ASP cc_start: 0.8784 (t0) cc_final: 0.8271 (t0) REVERT: E 282 LYS cc_start: 0.8405 (mtpp) cc_final: 0.8181 (mtpp) REVERT: F 22 ARG cc_start: 0.8635 (mtp85) cc_final: 0.8380 (mtp85) REVERT: F 97 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.7355 (mp10) REVERT: F 278 GLU cc_start: 0.7547 (mp0) cc_final: 0.7095 (pm20) outliers start: 59 outliers final: 26 residues processed: 348 average time/residue: 0.5769 time to fit residues: 219.0374 Evaluate side-chains 331 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 295 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 LYS Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 80 optimal weight: 8.9990 chunk 113 optimal weight: 0.3980 chunk 111 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 134 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 263 ASN B 283 HIS B 288 GLN C 283 HIS E 263 ASN E 283 HIS E 288 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.104643 restraints weight = 13790.554| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.49 r_work: 0.3007 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.002 0.027 14538 Z= 0.110 Angle : 0.452 4.367 19698 Z= 0.250 Chirality : 0.046 0.162 2334 Planarity : 0.003 0.023 2496 Dihedral : 5.859 51.016 2130 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.31 % Allowed : 15.20 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.20), residues: 1830 helix: 2.01 (0.20), residues: 714 sheet: -0.20 (0.26), residues: 408 loop : -0.29 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 49 TYR 0.022 0.002 TYR E 311 PHE 0.009 0.001 PHE B 138 TRP 0.009 0.002 TRP F 162 HIS 0.003 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00246 (14538) covalent geometry : angle 0.45225 (19698) hydrogen bonds : bond 0.03428 ( 648) hydrogen bonds : angle 4.37646 ( 1800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 0.530 Fit side-chains REVERT: A 17 GLN cc_start: 0.9089 (tp40) cc_final: 0.8818 (tp40) REVERT: A 97 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7351 (mp10) REVERT: A 178 VAL cc_start: 0.8331 (m) cc_final: 0.7962 (t) REVERT: A 180 SER cc_start: 0.8235 (t) cc_final: 0.8028 (t) REVERT: A 222 MET cc_start: 0.8383 (ptp) cc_final: 0.7784 (ptp) REVERT: A 278 GLU cc_start: 0.7689 (mp0) cc_final: 0.7195 (pm20) REVERT: A 311 TYR cc_start: 0.8624 (t80) cc_final: 0.8393 (t80) REVERT: B 22 ARG cc_start: 0.8802 (mtp85) cc_final: 0.8580 (mtp85) REVERT: B 122 ASP cc_start: 0.8936 (m-30) cc_final: 0.8601 (m-30) REVERT: B 191 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7114 (mt) REVERT: B 220 ASP cc_start: 0.8792 (t0) cc_final: 0.8292 (t0) REVERT: C 17 GLN cc_start: 0.9066 (tp40) cc_final: 0.8769 (tp40) REVERT: C 29 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8683 (mtpt) REVERT: C 68 MET cc_start: 0.8766 (tpp) cc_final: 0.8344 (tpt) REVERT: C 122 ASP cc_start: 0.9102 (m-30) cc_final: 0.8703 (m-30) REVERT: C 222 MET cc_start: 0.8343 (ptp) cc_final: 0.8135 (ptm) REVERT: C 282 LYS cc_start: 0.8421 (mtpp) cc_final: 0.8141 (mtpp) REVERT: C 314 SER cc_start: 0.6728 (OUTLIER) cc_final: 0.6248 (p) REVERT: D 17 GLN cc_start: 0.9083 (tp40) cc_final: 0.8747 (tp40) REVERT: D 68 MET cc_start: 0.8768 (tpp) cc_final: 0.8326 (tpt) REVERT: D 220 ASP cc_start: 0.8822 (t0) cc_final: 0.8499 (t70) REVERT: D 222 MET cc_start: 0.8342 (ptp) cc_final: 0.8015 (ptm) REVERT: D 282 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8175 (mtpp) REVERT: D 314 SER cc_start: 0.6700 (OUTLIER) cc_final: 0.6243 (p) REVERT: E 97 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8020 (mm110) REVERT: E 122 ASP cc_start: 0.8946 (m-30) cc_final: 0.8638 (m-30) REVERT: E 191 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7049 (mt) REVERT: E 220 ASP cc_start: 0.8801 (t0) cc_final: 0.8315 (t0) REVERT: E 282 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8316 (mtpp) REVERT: F 278 GLU cc_start: 0.7564 (mp0) cc_final: 0.7115 (pm20) outliers start: 52 outliers final: 22 residues processed: 334 average time/residue: 0.5933 time to fit residues: 215.9958 Evaluate side-chains 331 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 301 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 118 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 160 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN B 283 HIS B 288 GLN E 283 HIS E 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.103706 restraints weight = 13827.934| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.49 r_work: 0.2991 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14538 Z= 0.125 Angle : 0.469 4.373 19698 Z= 0.259 Chirality : 0.047 0.164 2334 Planarity : 0.003 0.029 2496 Dihedral : 5.825 52.403 2129 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.80 % Allowed : 15.59 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.20), residues: 1830 helix: 2.00 (0.20), residues: 714 sheet: -0.21 (0.26), residues: 408 loop : -0.27 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 184 TYR 0.019 0.002 TYR F 311 PHE 0.010 0.001 PHE E 138 TRP 0.008 0.002 TRP E 162 HIS 0.003 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00286 (14538) covalent geometry : angle 0.46941 (19698) hydrogen bonds : bond 0.03596 ( 648) hydrogen bonds : angle 4.39446 ( 1800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 300 time to evaluate : 0.336 Fit side-chains REVERT: A 17 GLN cc_start: 0.9092 (tp40) cc_final: 0.8821 (tp40) REVERT: A 97 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7288 (mp10) REVERT: A 122 ASP cc_start: 0.9003 (m-30) cc_final: 0.8753 (m-30) REVERT: A 178 VAL cc_start: 0.8318 (m) cc_final: 0.7945 (t) REVERT: A 180 SER cc_start: 0.8235 (t) cc_final: 0.8026 (t) REVERT: A 222 MET cc_start: 0.8384 (ptp) cc_final: 0.7760 (ptp) REVERT: A 278 GLU cc_start: 0.7668 (mp0) cc_final: 0.7164 (pm20) REVERT: A 311 TYR cc_start: 0.8654 (t80) cc_final: 0.8388 (t80) REVERT: B 22 ARG cc_start: 0.8809 (mtp85) cc_final: 0.8560 (mtp85) REVERT: B 97 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8066 (mm110) REVERT: B 122 ASP cc_start: 0.8947 (m-30) cc_final: 0.8624 (m-30) REVERT: B 127 MET cc_start: 0.9047 (ttm) cc_final: 0.8842 (tpp) REVERT: B 191 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7160 (mt) REVERT: B 205 MET cc_start: 0.5257 (ptp) cc_final: 0.4694 (ptm) REVERT: B 220 ASP cc_start: 0.8812 (t0) cc_final: 0.8313 (t0) REVERT: C 17 GLN cc_start: 0.9082 (tp40) cc_final: 0.8725 (tp40) REVERT: C 29 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8678 (mtpt) REVERT: C 68 MET cc_start: 0.8775 (tpp) cc_final: 0.8367 (tpt) REVERT: C 220 ASP cc_start: 0.8816 (t0) cc_final: 0.8391 (t70) REVERT: C 222 MET cc_start: 0.8325 (ptp) cc_final: 0.7897 (ptm) REVERT: C 282 LYS cc_start: 0.8469 (mtpp) cc_final: 0.8225 (mtpp) REVERT: C 314 SER cc_start: 0.6721 (OUTLIER) cc_final: 0.6254 (p) REVERT: D 17 GLN cc_start: 0.9087 (tp40) cc_final: 0.8832 (tp40) REVERT: D 68 MET cc_start: 0.8769 (tpp) cc_final: 0.8322 (tpt) REVERT: D 222 MET cc_start: 0.8344 (ptp) cc_final: 0.8131 (ptm) REVERT: D 282 LYS cc_start: 0.8455 (mtpp) cc_final: 0.8215 (mtpp) REVERT: D 314 SER cc_start: 0.6697 (OUTLIER) cc_final: 0.6254 (p) REVERT: E 97 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8046 (mm110) REVERT: E 122 ASP cc_start: 0.8964 (m-30) cc_final: 0.8672 (m-30) REVERT: E 127 MET cc_start: 0.9048 (ttm) cc_final: 0.8841 (tpp) REVERT: E 191 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7112 (mt) REVERT: E 220 ASP cc_start: 0.8808 (t0) cc_final: 0.8319 (t0) REVERT: E 282 LYS cc_start: 0.8518 (mtpp) cc_final: 0.8313 (mtpp) REVERT: F 278 GLU cc_start: 0.7592 (mp0) cc_final: 0.7139 (pm20) outliers start: 44 outliers final: 28 residues processed: 332 average time/residue: 0.5922 time to fit residues: 214.1935 Evaluate side-chains 335 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 299 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 171 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS E 263 ASN E 283 HIS E 288 GLN F 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.099769 restraints weight = 13929.486| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.48 r_work: 0.2926 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14538 Z= 0.243 Angle : 0.589 5.627 19698 Z= 0.321 Chirality : 0.051 0.167 2334 Planarity : 0.004 0.032 2496 Dihedral : 6.290 57.658 2129 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.24 % Allowed : 15.52 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.20), residues: 1830 helix: 1.79 (0.20), residues: 714 sheet: -0.27 (0.26), residues: 408 loop : -0.22 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 184 TYR 0.017 0.003 TYR A 146 PHE 0.014 0.002 PHE C 138 TRP 0.008 0.003 TRP B 154 HIS 0.004 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00566 (14538) covalent geometry : angle 0.58905 (19698) hydrogen bonds : bond 0.04609 ( 648) hydrogen bonds : angle 4.66636 ( 1800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 283 time to evaluate : 0.460 Fit side-chains REVERT: A 97 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: A 122 ASP cc_start: 0.9061 (m-30) cc_final: 0.8808 (m-30) REVERT: A 178 VAL cc_start: 0.8269 (m) cc_final: 0.7897 (t) REVERT: A 222 MET cc_start: 0.8527 (ptp) cc_final: 0.8005 (ptp) REVERT: A 267 GLU cc_start: 0.8098 (tp30) cc_final: 0.7659 (tp30) REVERT: A 311 TYR cc_start: 0.8740 (t80) cc_final: 0.8490 (t80) REVERT: B 97 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8051 (mm110) REVERT: B 122 ASP cc_start: 0.8957 (m-30) cc_final: 0.8700 (m-30) REVERT: B 191 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7248 (mt) REVERT: C 17 GLN cc_start: 0.9049 (tp40) cc_final: 0.8784 (tp40) REVERT: C 29 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8634 (mtpt) REVERT: C 68 MET cc_start: 0.8828 (tpp) cc_final: 0.8385 (tpt) REVERT: C 122 ASP cc_start: 0.9140 (m-30) cc_final: 0.8780 (m-30) REVERT: C 282 LYS cc_start: 0.8524 (mtpp) cc_final: 0.8290 (mtpp) REVERT: C 314 SER cc_start: 0.6728 (OUTLIER) cc_final: 0.6262 (p) REVERT: D 29 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8631 (mtpt) REVERT: D 68 MET cc_start: 0.8831 (tpp) cc_final: 0.8390 (tpt) REVERT: D 220 ASP cc_start: 0.8804 (t0) cc_final: 0.8466 (t70) REVERT: D 278 GLU cc_start: 0.7565 (mp0) cc_final: 0.7346 (mp0) REVERT: D 282 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8243 (mtpp) REVERT: D 314 SER cc_start: 0.6732 (OUTLIER) cc_final: 0.6280 (p) REVERT: E 97 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8062 (mm110) REVERT: E 122 ASP cc_start: 0.8968 (m-30) cc_final: 0.8727 (m-30) REVERT: E 191 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7196 (mt) REVERT: E 282 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8195 (mtpp) REVERT: F 38 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7779 (mp-120) REVERT: F 97 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7302 (mp10) outliers start: 51 outliers final: 28 residues processed: 319 average time/residue: 0.5729 time to fit residues: 199.3638 Evaluate side-chains 322 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 282 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 99 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 151 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 283 HIS F 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.102400 restraints weight = 13881.207| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.48 r_work: 0.2971 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14538 Z= 0.143 Angle : 0.497 4.511 19698 Z= 0.275 Chirality : 0.047 0.164 2334 Planarity : 0.003 0.029 2496 Dihedral : 5.980 47.244 2129 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.67 % Allowed : 16.28 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.20), residues: 1830 helix: 1.83 (0.20), residues: 714 sheet: -0.29 (0.26), residues: 408 loop : -0.27 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 184 TYR 0.025 0.002 TYR C 311 PHE 0.012 0.001 PHE E 138 TRP 0.009 0.002 TRP E 162 HIS 0.005 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00328 (14538) covalent geometry : angle 0.49694 (19698) hydrogen bonds : bond 0.03824 ( 648) hydrogen bonds : angle 4.53753 ( 1800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 301 time to evaluate : 0.487 Fit side-chains REVERT: A 17 GLN cc_start: 0.9118 (tp40) cc_final: 0.8811 (tp40) REVERT: A 97 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: A 122 ASP cc_start: 0.9048 (m-30) cc_final: 0.8786 (m-30) REVERT: A 178 VAL cc_start: 0.8260 (m) cc_final: 0.7892 (t) REVERT: A 180 SER cc_start: 0.8148 (t) cc_final: 0.7932 (t) REVERT: A 222 MET cc_start: 0.8430 (ptp) cc_final: 0.7820 (ptp) REVERT: A 278 GLU cc_start: 0.7680 (mp0) cc_final: 0.7237 (pm20) REVERT: A 311 TYR cc_start: 0.8674 (t80) cc_final: 0.8460 (t80) REVERT: B 97 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8036 (mm110) REVERT: B 122 ASP cc_start: 0.8949 (m-30) cc_final: 0.8644 (m-30) REVERT: B 127 MET cc_start: 0.9069 (ttm) cc_final: 0.8792 (tpp) REVERT: B 191 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7193 (mt) REVERT: B 205 MET cc_start: 0.5645 (ptp) cc_final: 0.5220 (ptm) REVERT: B 220 ASP cc_start: 0.8830 (t0) cc_final: 0.8308 (t0) REVERT: C 17 GLN cc_start: 0.9090 (tp40) cc_final: 0.8796 (tp40) REVERT: C 29 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8639 (mtpt) REVERT: C 68 MET cc_start: 0.8772 (tpp) cc_final: 0.8339 (tpt) REVERT: C 220 ASP cc_start: 0.8802 (t0) cc_final: 0.8374 (t70) REVERT: C 282 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8256 (mtpp) REVERT: C 314 SER cc_start: 0.6705 (OUTLIER) cc_final: 0.6235 (p) REVERT: D 17 GLN cc_start: 0.9083 (tp40) cc_final: 0.8722 (tp40) REVERT: D 68 MET cc_start: 0.8770 (tpp) cc_final: 0.8401 (tpt) REVERT: D 220 ASP cc_start: 0.8808 (t0) cc_final: 0.8464 (t70) REVERT: D 278 GLU cc_start: 0.7535 (mp0) cc_final: 0.7312 (mp0) REVERT: D 282 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8248 (mtpp) REVERT: D 314 SER cc_start: 0.6712 (OUTLIER) cc_final: 0.6261 (p) REVERT: E 68 MET cc_start: 0.8920 (tpt) cc_final: 0.8698 (tpp) REVERT: E 122 ASP cc_start: 0.8974 (m-30) cc_final: 0.8687 (m-30) REVERT: E 127 MET cc_start: 0.9068 (ttm) cc_final: 0.8778 (tpp) REVERT: E 191 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7126 (mt) REVERT: E 220 ASP cc_start: 0.8804 (t0) cc_final: 0.8310 (t0) REVERT: E 282 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8204 (mtpp) REVERT: F 278 GLU cc_start: 0.7639 (mp0) cc_final: 0.7139 (pm20) outliers start: 42 outliers final: 28 residues processed: 331 average time/residue: 0.5795 time to fit residues: 209.2807 Evaluate side-chains 323 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 286 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 283 HIS C 38 GLN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.142867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.102356 restraints weight = 13849.943| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.49 r_work: 0.2963 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14538 Z= 0.146 Angle : 0.500 4.467 19698 Z= 0.277 Chirality : 0.048 0.164 2334 Planarity : 0.003 0.029 2496 Dihedral : 5.883 41.348 2129 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.61 % Allowed : 16.60 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 1830 helix: 1.86 (0.20), residues: 714 sheet: -0.29 (0.26), residues: 408 loop : -0.28 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 184 TYR 0.027 0.002 TYR C 311 PHE 0.012 0.002 PHE C 138 TRP 0.009 0.002 TRP E 162 HIS 0.005 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00337 (14538) covalent geometry : angle 0.50031 (19698) hydrogen bonds : bond 0.03845 ( 648) hydrogen bonds : angle 4.48680 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6082.58 seconds wall clock time: 104 minutes 3.34 seconds (6243.34 seconds total)