Starting phenix.real_space_refine on Fri Jul 3 13:22:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dbl_27289/07_2026/8dbl_27289.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbl_27289/07_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_27289/07_2026/8dbl_27289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbl_27289/07_2026/8dbl_27289.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbl_27289/07_2026/8dbl_27289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbl_27289/07_2026/8dbl_27289.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dbl_27289/07_2026/8dbl_27289.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dbl_27289/07_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-6108/lib/python3.11/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: 3.05, per 1000 atoms: 0.21 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: 1.17 Conformation dependent library (CDL) restraints added in 700.3 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: 0.36 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: 2.37 Time building geometry restraints manager: 1.54 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: 7902 17.71 - 35.41: 648 35.41 - 53.12: 192 53.12 - 70.82: 60 70.82 - 88.53: 36 Dihedral angle restraints: 8838 sinusoidal: 3462 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 8835 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: 0.05 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.660 Find NCS groups from input model: 0.150 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:7.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 : 16.470 88.531 5334 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/Z covalent geometry : bond 0.01102 / 0.53 (14538) covalent geometry : angle 0.82307 / 0.45 (19698) hydrogen bonds : bond 0.15501 / 10.00 ( 648) hydrogen bonds : angle 5.67944 / 4.05 ( 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 : 0.525 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: 0.6279 time to fit residues: 241.7883 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 : 0.545 ------------------------------------------------------------------------------- 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... B 283 HIS B 288 GLN C 277 GLN C 288 GLN D 277 GLN D 288 GLN E 97 GLN E 288 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.159530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.121300 restraints weight = 13642.223| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.42 r_work: 0.3214 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 324 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14538 Z= 0.137 Angle : 0.498 4.104 19698 Z= 0.277 Chirality : 0.047 0.170 2334 Planarity : 0.003 0.021 2496 Dihedral : 7.210 71.311 2028 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.77 % Allowed : 12.72 % 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: 0.55 (0.20), residues: 1830 helix: 1.39 (0.20), residues: 756 sheet: -0.39 (0.24), residues: 486 loop : -0.10 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 243 TYR 0.015 0.002 TYR D 311 PHE 0.010 0.001 PHE C 138 TRP 0.012 0.002 TRP B 162 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (14538) covalent geometry : angle 0.49812 / 0.28 (19698) hydrogen bonds : bond 0.04190 / 2.74 ( 648) hydrogen bonds : angle 4.87040 / 3.47 ( 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 394 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 319 time to evaluate : 0.603 Fit side-chains REVERT: A 5 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8640 (mmpt) REVERT: A 17 GLN cc_start: 0.9151 (tp40) cc_final: 0.8846 (tp40) REVERT: A 68 MET cc_start: 0.8718 (tpp) cc_final: 0.8502 (mmm) REVERT: A 96 ARG cc_start: 0.8765 (mtm180) cc_final: 0.8519 (mtm180) REVERT: A 97 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7543 (mp10) REVERT: A 127 MET cc_start: 0.9047 (ttm) cc_final: 0.8795 (ttm) REVERT: A 178 VAL cc_start: 0.8239 (m) cc_final: 0.7848 (t) REVERT: A 180 SER cc_start: 0.8360 (t) cc_final: 0.8078 (t) REVERT: A 220 ASP cc_start: 0.8618 (t0) cc_final: 0.8388 (t70) REVERT: A 222 MET cc_start: 0.8302 (ptp) cc_final: 0.7676 (ptp) REVERT: A 311 TYR cc_start: 0.8568 (t80) cc_final: 0.8334 (t80) REVERT: B 17 GLN cc_start: 0.9084 (tp40) cc_final: 0.8880 (tp-100) REVERT: B 97 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7962 (mm110) REVERT: B 122 ASP cc_start: 0.8808 (m-30) cc_final: 0.8483 (m-30) REVERT: B 220 ASP cc_start: 0.8693 (t0) cc_final: 0.8177 (t0) REVERT: C 17 GLN cc_start: 0.9069 (tp40) cc_final: 0.8703 (tp40) REVERT: C 68 MET cc_start: 0.8635 (tpp) cc_final: 0.8263 (tpt) REVERT: C 79 ILE cc_start: 0.9160 (pt) cc_final: 0.8855 (mm) REVERT: C 122 ASP cc_start: 0.9010 (m-30) cc_final: 0.8686 (m-30) REVERT: C 220 ASP cc_start: 0.8741 (t0) cc_final: 0.8402 (t70) REVERT: C 282 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8132 (mtpp) REVERT: D 17 GLN cc_start: 0.9105 (tp40) cc_final: 0.8709 (tp40) REVERT: D 68 MET cc_start: 0.8630 (tpp) cc_final: 0.8254 (tpt) REVERT: D 79 ILE cc_start: 0.9185 (pt) cc_final: 0.8861 (mm) REVERT: D 158 ASN cc_start: 0.7605 (m-40) cc_final: 0.7310 (m-40) REVERT: D 220 ASP cc_start: 0.8734 (t0) cc_final: 0.8413 (t70) REVERT: D 282 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8161 (mtpp) REVERT: E 5 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8700 (mmpt) REVERT: E 17 GLN cc_start: 0.9105 (tp40) cc_final: 0.8892 (tp-100) REVERT: E 122 ASP cc_start: 0.8807 (m-30) cc_final: 0.8497 (m-30) REVERT: E 220 ASP cc_start: 0.8695 (t0) cc_final: 0.8180 (t0) REVERT: F 5 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8642 (mmpt) REVERT: F 68 MET cc_start: 0.8702 (tpp) cc_final: 0.8486 (mmm) REVERT: F 79 ILE cc_start: 0.9142 (pt) cc_final: 0.8937 (mm) REVERT: F 97 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7541 (mp10) REVERT: F 127 MET cc_start: 0.9035 (ttm) cc_final: 0.8770 (ttm) REVERT: F 180 SER cc_start: 0.8235 (t) cc_final: 0.8009 (t) REVERT: F 220 ASP cc_start: 0.8624 (t0) cc_final: 0.8388 (t70) REVERT: F 222 MET cc_start: 0.8205 (ptp) cc_final: 0.7800 (ptp) REVERT: F 278 GLU cc_start: 0.7660 (mp0) cc_final: 0.7351 (pm20) REVERT: F 311 TYR cc_start: 0.8661 (t80) cc_final: 0.8458 (t80) outliers start: 75 outliers final: 24 residues processed: 367 average time/residue: 0.6321 time to fit residues: 253.3291 Evaluate side-chains 329 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 297 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 22 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 167 optimal weight: 0.1980 chunk 119 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN A 130 HIS A 283 HIS B 97 GLN B 283 HIS C 37 ASN C 283 HIS D 37 ASN D 130 HIS E 283 HIS F 97 GLN F 130 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.143479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104122 restraints weight = 13790.639| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.48 r_work: 0.3001 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1640 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= 0.123 Angle : 0.475 4.161 19698 Z= 0.262 Chirality : 0.047 0.164 2334 Planarity : 0.003 0.022 2496 Dihedral : 5.438 45.023 2010 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.05 % Allowed : 14.50 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.93 (0.20), residues: 1830 helix: 1.93 (0.20), residues: 714 sheet: -0.16 (0.26), residues: 414 loop : -0.17 (0.24), residues: 702 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 0.010 0.001 PHE F 138 TRP 0.010 0.002 TRP E 162 HIS 0.003 0.001 HIS E 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (14538) covalent geometry : angle 0.47492 / 0.26 (19698) hydrogen bonds : bond 0.03893 / 2.55 ( 648) hydrogen bonds : angle 4.63710 / 3.29 ( 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 359 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 311 time to evaluate : 0.532 Fit side-chains REVERT: A 5 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8646 (mmpt) REVERT: A 17 GLN cc_start: 0.9110 (tp40) cc_final: 0.8830 (tp40) REVERT: A 97 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7599 (mp10) REVERT: A 178 VAL cc_start: 0.8234 (m) cc_final: 0.7862 (t) REVERT: A 180 SER cc_start: 0.8226 (t) cc_final: 0.7975 (t) REVERT: A 220 ASP cc_start: 0.8639 (t0) cc_final: 0.8352 (t70) REVERT: A 222 MET cc_start: 0.8303 (ptp) cc_final: 0.7611 (ptp) REVERT: A 259 SER cc_start: 0.8429 (p) cc_final: 0.8193 (p) REVERT: A 282 LYS cc_start: 0.8277 (mtpp) cc_final: 0.7967 (tttm) REVERT: A 311 TYR cc_start: 0.8566 (t80) cc_final: 0.8313 (t80) REVERT: B 22 ARG cc_start: 0.8797 (mtp85) cc_final: 0.8478 (mtp85) REVERT: B 122 ASP cc_start: 0.8920 (m-30) cc_final: 0.8580 (m-30) REVERT: B 127 MET cc_start: 0.9084 (ttm) cc_final: 0.8812 (tpp) REVERT: B 220 ASP cc_start: 0.8695 (t0) cc_final: 0.8219 (t0) REVERT: C 17 GLN cc_start: 0.9070 (tp40) cc_final: 0.8714 (tp40) REVERT: C 29 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8719 (mtpt) REVERT: C 68 MET cc_start: 0.8740 (tpp) cc_final: 0.8355 (tpt) REVERT: C 79 ILE cc_start: 0.9118 (pt) cc_final: 0.8889 (mm) REVERT: C 122 ASP cc_start: 0.9102 (m-30) cc_final: 0.8797 (m-30) REVERT: C 220 ASP cc_start: 0.8768 (t0) cc_final: 0.8368 (t70) REVERT: C 222 MET cc_start: 0.8331 (ptp) cc_final: 0.7944 (ptm) REVERT: C 281 MET cc_start: 0.8682 (mtp) cc_final: 0.8345 (mtp) REVERT: C 282 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8217 (mtpp) REVERT: D 17 GLN cc_start: 0.9084 (tp40) cc_final: 0.8713 (tp40) REVERT: D 29 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8707 (mtpt) REVERT: D 68 MET cc_start: 0.8738 (tpp) cc_final: 0.8348 (tpt) REVERT: D 79 ILE cc_start: 0.9124 (pt) cc_final: 0.8891 (mm) REVERT: D 158 ASN cc_start: 0.7389 (m-40) cc_final: 0.7105 (m-40) REVERT: D 220 ASP cc_start: 0.8765 (t0) cc_final: 0.8381 (t70) REVERT: D 222 MET cc_start: 0.8326 (ptp) cc_final: 0.7959 (ptm) REVERT: D 282 LYS cc_start: 0.8463 (mtpp) cc_final: 0.8193 (mtpp) REVERT: E 5 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8634 (mmpt) REVERT: E 22 ARG cc_start: 0.8796 (mtp85) cc_final: 0.8571 (mtp85) REVERT: E 97 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8065 (mm110) REVERT: E 122 ASP cc_start: 0.8927 (m-30) cc_final: 0.8606 (m-30) REVERT: E 127 MET cc_start: 0.9095 (ttm) cc_final: 0.8828 (tpp) REVERT: E 220 ASP cc_start: 0.8681 (t0) cc_final: 0.8182 (t0) REVERT: F 5 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8637 (mmpt) REVERT: F 97 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: F 220 ASP cc_start: 0.8671 (t0) cc_final: 0.8371 (t70) REVERT: F 222 MET cc_start: 0.8200 (ptp) cc_final: 0.7767 (ptp) REVERT: F 259 SER cc_start: 0.8353 (p) cc_final: 0.8131 (p) REVERT: F 311 TYR cc_start: 0.8619 (t80) cc_final: 0.8400 (t80) outliers start: 48 outliers final: 21 residues processed: 341 average time/residue: 0.6185 time to fit residues: 230.0482 Evaluate side-chains 325 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 296 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 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 97 GLN 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 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: 0.7980 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN A 283 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 97 GLN B 263 ASN B 283 HIS B 288 GLN C 37 ASN C 283 HIS D 37 ASN D 283 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN E 263 ASN E 283 HIS E 288 GLN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN F 97 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.141701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.101761 restraints weight = 13864.127| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.47 r_work: 0.2964 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14538 Z= 0.166 Angle : 0.513 4.332 19698 Z= 0.282 Chirality : 0.048 0.167 2334 Planarity : 0.003 0.022 2496 Dihedral : 5.585 48.729 2004 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.56 % Allowed : 15.14 % Favored : 81.30 % 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: 0.88 (0.20), residues: 1830 helix: 1.91 (0.20), residues: 714 sheet: -0.26 (0.25), residues: 480 loop : -0.13 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.017 0.002 TYR E 311 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/Z covalent geometry : bond 0.00383 / 0.17 (14538) covalent geometry : angle 0.51254 / 0.28 (19698) hydrogen bonds : bond 0.04185 / 2.73 ( 648) hydrogen bonds : angle 4.63840 / 3.29 ( 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 352 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 296 time to evaluate : 0.556 Fit side-chains REVERT: A 5 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8590 (mmpt) REVERT: A 17 GLN cc_start: 0.9123 (tp40) cc_final: 0.8804 (tp40) REVERT: A 178 VAL cc_start: 0.8246 (m) cc_final: 0.7867 (t) REVERT: A 180 SER cc_start: 0.8191 (t) cc_final: 0.7978 (t) REVERT: A 220 ASP cc_start: 0.8656 (t0) cc_final: 0.8354 (t70) REVERT: A 222 MET cc_start: 0.8350 (ptp) cc_final: 0.7658 (ptp) REVERT: A 259 SER cc_start: 0.8386 (p) cc_final: 0.8184 (p) REVERT: A 278 GLU cc_start: 0.7777 (mp0) cc_final: 0.7476 (pm20) REVERT: A 311 TYR cc_start: 0.8660 (t80) cc_final: 0.8367 (t80) REVERT: B 22 ARG cc_start: 0.8828 (mtp85) cc_final: 0.8510 (mtp85) REVERT: B 122 ASP cc_start: 0.8938 (m-30) cc_final: 0.8625 (m-30) REVERT: B 220 ASP cc_start: 0.8804 (t0) cc_final: 0.8306 (t0) REVERT: B 282 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8244 (mtpp) REVERT: C 17 GLN cc_start: 0.9079 (tp40) cc_final: 0.8776 (tp40) REVERT: C 29 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8700 (mtpt) REVERT: C 38 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7205 (mp-120) REVERT: C 68 MET cc_start: 0.8763 (tpp) cc_final: 0.8360 (tpt) REVERT: C 79 ILE cc_start: 0.9167 (pt) cc_final: 0.8866 (mm) REVERT: C 122 ASP cc_start: 0.9120 (m-30) cc_final: 0.8858 (m-30) REVERT: C 220 ASP cc_start: 0.8787 (t0) cc_final: 0.8354 (t70) REVERT: C 222 MET cc_start: 0.8458 (ptp) cc_final: 0.8029 (ptm) REVERT: C 282 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8251 (mtpp) REVERT: C 314 SER cc_start: 0.6859 (OUTLIER) cc_final: 0.6376 (p) REVERT: D 5 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8444 (mmpt) REVERT: D 17 GLN cc_start: 0.9081 (tp40) cc_final: 0.8839 (tp40) REVERT: D 29 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8702 (mtpt) REVERT: D 68 MET cc_start: 0.8761 (tpp) cc_final: 0.8356 (tpt) REVERT: D 79 ILE cc_start: 0.9173 (pt) cc_final: 0.8863 (mm) REVERT: D 158 ASN cc_start: 0.7483 (m-40) cc_final: 0.7189 (m-40) REVERT: D 220 ASP cc_start: 0.8785 (t0) cc_final: 0.8481 (t70) REVERT: D 222 MET cc_start: 0.8427 (ptp) cc_final: 0.8117 (ptm) REVERT: D 282 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8224 (mtpp) REVERT: D 314 SER cc_start: 0.6824 (OUTLIER) cc_final: 0.6360 (p) REVERT: E 5 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8569 (mmpt) REVERT: E 22 ARG cc_start: 0.8815 (mtp85) cc_final: 0.8504 (mtp85) REVERT: E 62 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7770 (mm-30) REVERT: E 97 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8080 (mm110) REVERT: E 122 ASP cc_start: 0.8941 (m-30) cc_final: 0.8665 (m-30) REVERT: E 191 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7030 (mt) REVERT: E 220 ASP cc_start: 0.8770 (t0) cc_final: 0.8276 (t0) REVERT: E 282 LYS cc_start: 0.8408 (mtpp) cc_final: 0.8195 (mtpp) REVERT: F 5 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8596 (mmpt) REVERT: F 220 ASP cc_start: 0.8693 (t0) cc_final: 0.8378 (t70) REVERT: F 278 GLU cc_start: 0.7718 (mp0) cc_final: 0.7260 (pm20) outliers start: 56 outliers final: 27 residues processed: 330 average time/residue: 0.5702 time to fit residues: 205.3203 Evaluate side-chains 335 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 295 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 63 ILE 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 282 LYS 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 C residue 282 LYS Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 5 LYS 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 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 5 LYS 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 314 SER Chi-restraints excluded: chain F residue 5 LYS 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 Chi-restraints excluded: chain F residue 314 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 34 optimal weight: 4.9990 chunk 114 optimal weight: 0.4980 chunk 152 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 69 optimal weight: 0.0170 chunk 21 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3638 r_free = 0.3638 target = 0.144521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.104970 restraints weight = 13981.909| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.46 r_work: 0.3013 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14538 Z= 0.109 Angle : 0.451 4.317 19698 Z= 0.249 Chirality : 0.046 0.166 2334 Planarity : 0.002 0.023 2496 Dihedral : 5.216 47.510 2004 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.37 % Allowed : 14.82 % 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: 0.93 (0.20), residues: 1830 helix: 2.01 (0.20), residues: 714 sheet: -0.11 (0.26), residues: 408 loop : -0.30 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 49 TYR 0.021 0.002 TYR D 311 PHE 0.010 0.001 PHE C 138 TRP 0.009 0.002 TRP A 162 HIS 0.002 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (14538) covalent geometry : angle 0.45079 / 0.25 (19698) hydrogen bonds : bond 0.03489 / 2.29 ( 648) hydrogen bonds : angle 4.47480 / 3.17 ( 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 360 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 307 time to evaluate : 0.446 Fit side-chains REVERT: A 17 GLN cc_start: 0.9103 (tp40) cc_final: 0.8810 (tp40) REVERT: A 97 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: A 178 VAL cc_start: 0.8245 (m) cc_final: 0.7876 (t) REVERT: A 180 SER cc_start: 0.8214 (t) cc_final: 0.8007 (t) REVERT: A 220 ASP cc_start: 0.8650 (t0) cc_final: 0.8343 (t70) REVERT: A 222 MET cc_start: 0.8381 (ptp) cc_final: 0.7719 (ptp) REVERT: A 278 GLU cc_start: 0.7743 (mp0) cc_final: 0.7383 (pm20) REVERT: A 311 TYR cc_start: 0.8574 (t80) cc_final: 0.8311 (t80) REVERT: B 122 ASP cc_start: 0.8958 (m-30) cc_final: 0.8614 (m-30) REVERT: B 127 MET cc_start: 0.9057 (ttm) cc_final: 0.8851 (tpp) REVERT: B 191 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7073 (mt) REVERT: B 220 ASP cc_start: 0.8754 (t0) cc_final: 0.8268 (t0) REVERT: C 29 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8719 (mtpt) REVERT: C 68 MET cc_start: 0.8768 (tpp) cc_final: 0.8344 (tpt) REVERT: C 122 ASP cc_start: 0.9113 (m-30) cc_final: 0.8835 (m-30) REVERT: C 208 VAL cc_start: 0.4865 (OUTLIER) cc_final: 0.4616 (m) REVERT: C 220 ASP cc_start: 0.8796 (t0) cc_final: 0.8367 (t70) REVERT: C 222 MET cc_start: 0.8428 (ptp) cc_final: 0.8015 (ptm) REVERT: C 281 MET cc_start: 0.8367 (mtp) cc_final: 0.8132 (mtp) REVERT: C 282 LYS cc_start: 0.8400 (mtpp) cc_final: 0.8138 (mtpp) REVERT: D 17 GLN cc_start: 0.9077 (tp40) cc_final: 0.8735 (tp40) REVERT: D 29 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8695 (mtpt) REVERT: D 68 MET cc_start: 0.8768 (tpp) cc_final: 0.8339 (tpt) REVERT: D 220 ASP cc_start: 0.8787 (t0) cc_final: 0.8393 (t70) REVERT: D 222 MET cc_start: 0.8422 (ptp) cc_final: 0.8036 (ptm) REVERT: D 282 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8229 (mtpp) REVERT: E 62 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7760 (mm-30) REVERT: E 97 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8006 (mm110) REVERT: E 122 ASP cc_start: 0.8950 (m-30) cc_final: 0.8657 (m-30) REVERT: E 191 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6752 (mt) REVERT: E 220 ASP cc_start: 0.8749 (t0) cc_final: 0.8489 (t70) REVERT: E 282 LYS cc_start: 0.8408 (mtpp) cc_final: 0.8199 (mtpp) REVERT: F 97 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.7347 (mp10) REVERT: F 278 GLU cc_start: 0.7603 (mp0) cc_final: 0.7171 (pm20) outliers start: 53 outliers final: 19 residues processed: 342 average time/residue: 0.5675 time to fit residues: 212.1223 Evaluate side-chains 324 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 296 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 191 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain 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 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 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 43 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 170 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 HIS B 263 ASN B 283 HIS B 288 GLN C 283 HIS D 283 HIS E 263 ASN E 283 HIS E 288 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.104046 restraints weight = 13854.028| |-----------------------------------------------------------------------------| 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: 0.2883 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2008 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= 0.119 Angle : 0.465 4.350 19698 Z= 0.257 Chirality : 0.047 0.163 2334 Planarity : 0.003 0.026 2496 Dihedral : 4.879 34.222 1992 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.63 % Allowed : 15.14 % 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: 0.94 (0.20), residues: 1830 helix: 2.04 (0.20), residues: 714 sheet: -0.18 (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 0.021 0.002 TYR E 311 PHE 0.010 0.001 PHE E 138 TRP 0.008 0.002 TRP B 162 HIS 0.003 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (14538) covalent geometry : angle 0.46450 / 0.26 (19698) hydrogen bonds : bond 0.03590 / 2.35 ( 648) hydrogen bonds : angle 4.43754 / 3.15 ( 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 352 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 295 time to evaluate : 0.353 Fit side-chains REVERT: A 17 GLN cc_start: 0.9084 (tp40) cc_final: 0.8786 (tp40) REVERT: A 97 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.7297 (mp10) REVERT: A 178 VAL cc_start: 0.8321 (m) cc_final: 0.7945 (t) REVERT: A 180 SER cc_start: 0.8169 (t) cc_final: 0.7956 (t) REVERT: A 220 ASP cc_start: 0.8663 (t0) cc_final: 0.8341 (t70) REVERT: A 222 MET cc_start: 0.8398 (ptp) cc_final: 0.7722 (ptp) REVERT: A 278 GLU cc_start: 0.7743 (mp0) cc_final: 0.7321 (pm20) REVERT: A 311 TYR cc_start: 0.8600 (t80) cc_final: 0.8358 (t80) REVERT: B 22 ARG cc_start: 0.8823 (mtp85) cc_final: 0.8551 (mtp85) REVERT: B 97 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8032 (mm110) REVERT: B 122 ASP cc_start: 0.8948 (m-30) cc_final: 0.8607 (m-30) REVERT: B 127 MET cc_start: 0.9109 (ttm) cc_final: 0.8751 (tpp) REVERT: B 191 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7092 (mt) REVERT: B 220 ASP cc_start: 0.8752 (t0) cc_final: 0.8248 (t0) REVERT: C 29 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8705 (mtpt) REVERT: C 68 MET cc_start: 0.8766 (tpp) cc_final: 0.8313 (tpt) REVERT: C 122 ASP cc_start: 0.9129 (m-30) cc_final: 0.8830 (m-30) REVERT: C 208 VAL cc_start: 0.4765 (OUTLIER) cc_final: 0.4500 (m) REVERT: C 220 ASP cc_start: 0.8804 (t0) cc_final: 0.8348 (t70) REVERT: C 222 MET cc_start: 0.8460 (ptp) cc_final: 0.8005 (ptm) REVERT: C 282 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8202 (mtpp) REVERT: C 314 SER cc_start: 0.6766 (OUTLIER) cc_final: 0.6295 (p) REVERT: D 17 GLN cc_start: 0.9083 (tp40) cc_final: 0.8723 (tp40) REVERT: D 29 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8694 (mtpt) REVERT: D 68 MET cc_start: 0.8766 (tpp) cc_final: 0.8315 (tpt) REVERT: D 220 ASP cc_start: 0.8780 (t0) cc_final: 0.8444 (t70) REVERT: D 222 MET cc_start: 0.8444 (ptp) cc_final: 0.8117 (ptm) REVERT: D 282 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8180 (mtpp) REVERT: D 314 SER cc_start: 0.6763 (OUTLIER) cc_final: 0.6307 (p) REVERT: E 22 ARG cc_start: 0.8815 (mtp85) cc_final: 0.8541 (mtp85) REVERT: E 62 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7764 (mm-30) REVERT: E 97 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8092 (mm110) REVERT: E 115 MET cc_start: 0.9195 (mtp) cc_final: 0.8916 (mtp) REVERT: E 122 ASP cc_start: 0.8949 (m-30) cc_final: 0.8633 (m-30) REVERT: E 191 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7088 (mt) REVERT: E 220 ASP cc_start: 0.8747 (t0) cc_final: 0.8240 (t0) REVERT: E 282 LYS cc_start: 0.8455 (mtpp) cc_final: 0.8249 (mtpp) REVERT: F 97 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.7318 (mp10) REVERT: F 278 GLU cc_start: 0.7606 (mp0) cc_final: 0.7150 (pm20) outliers start: 57 outliers final: 24 residues processed: 338 average time/residue: 0.5848 time to fit residues: 216.1688 Evaluate side-chains 332 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 296 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 97 GLN 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 237 LEU Chi-restraints excluded: chain B residue 249 THR 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 80 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN B 283 HIS B 288 GLN ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.140770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.100137 restraints weight = 13843.309| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.48 r_work: 0.2923 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 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 = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14538 Z= 0.225 Angle : 0.569 4.801 19698 Z= 0.311 Chirality : 0.050 0.167 2334 Planarity : 0.003 0.027 2496 Dihedral : 5.398 30.910 1992 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.31 % Allowed : 14.44 % Favored : 82.25 % 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: 1.84 (0.20), residues: 714 sheet: -0.40 (0.24), residues: 480 loop : -0.13 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 184 TYR 0.017 0.003 TYR E 311 PHE 0.014 0.002 PHE E 138 TRP 0.008 0.003 TRP B 154 HIS 0.005 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.23 (14538) covalent geometry : angle 0.56890 / 0.31 (19698) hydrogen bonds : bond 0.04546 / 2.96 ( 648) hydrogen bonds : angle 4.64457 / 3.30 ( 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 340 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 288 time to evaluate : 0.589 Fit side-chains REVERT: A 97 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.7281 (mp10) REVERT: A 122 ASP cc_start: 0.9064 (m-30) cc_final: 0.8802 (m-30) REVERT: A 178 VAL cc_start: 0.8268 (m) cc_final: 0.7890 (t) REVERT: A 222 MET cc_start: 0.8478 (ptp) cc_final: 0.8000 (ptp) REVERT: A 278 GLU cc_start: 0.7781 (mp0) cc_final: 0.7431 (pm20) REVERT: B 62 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7806 (mm-30) REVERT: B 122 ASP cc_start: 0.8950 (m-30) cc_final: 0.8666 (m-30) REVERT: B 191 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7217 (mt) REVERT: C 29 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8632 (mtpt) REVERT: C 68 MET cc_start: 0.8819 (tpp) cc_final: 0.8372 (tpt) REVERT: C 122 ASP cc_start: 0.9136 (m-30) cc_final: 0.8791 (m-30) REVERT: C 191 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.7012 (mt) REVERT: C 220 ASP cc_start: 0.8761 (t0) cc_final: 0.8353 (t70) REVERT: C 222 MET cc_start: 0.8433 (ptp) cc_final: 0.7965 (ptm) REVERT: C 282 LYS cc_start: 0.8513 (mtpp) cc_final: 0.8271 (mtpp) REVERT: C 314 SER cc_start: 0.6749 (OUTLIER) cc_final: 0.6281 (p) REVERT: D 17 GLN cc_start: 0.9044 (tp40) cc_final: 0.8788 (tp40) REVERT: D 29 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8641 (mtpt) REVERT: D 68 MET cc_start: 0.8812 (tpp) cc_final: 0.8364 (tpt) REVERT: D 122 ASP cc_start: 0.9104 (m-30) cc_final: 0.8874 (m-30) REVERT: D 158 ASN cc_start: 0.7412 (m110) cc_final: 0.7192 (m-40) REVERT: D 220 ASP cc_start: 0.8746 (t0) cc_final: 0.8439 (t70) REVERT: D 278 GLU cc_start: 0.7545 (mp0) cc_final: 0.7315 (mp0) REVERT: D 282 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8259 (mtpp) REVERT: D 314 SER cc_start: 0.6738 (OUTLIER) cc_final: 0.6293 (p) REVERT: E 62 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7853 (mm-30) REVERT: E 122 ASP cc_start: 0.8956 (m-30) cc_final: 0.8713 (m-30) REVERT: E 127 MET cc_start: 0.9113 (ttm) cc_final: 0.8888 (tpp) REVERT: E 191 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7191 (mt) REVERT: E 282 LYS cc_start: 0.8463 (mtpp) cc_final: 0.8259 (mtpp) REVERT: F 97 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7304 (mp10) outliers start: 52 outliers final: 27 residues processed: 330 average time/residue: 0.6112 time to fit residues: 220.5649 Evaluate side-chains 313 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 276 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 191 LEU 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 307 GLU 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 69 optimal weight: 0.2980 chunk 160 optimal weight: 0.0050 chunk 152 optimal weight: 0.8980 chunk 174 optimal weight: 0.0040 chunk 132 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 283 HIS D 283 HIS E 283 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105956 restraints weight = 13914.632| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.49 r_work: 0.3023 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14538 Z= 0.099 Angle : 0.445 4.372 19698 Z= 0.247 Chirality : 0.046 0.168 2334 Planarity : 0.003 0.024 2496 Dihedral : 4.802 35.987 1992 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.48 % Allowed : 15.39 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.88 (0.20), residues: 1830 helix: 1.97 (0.20), residues: 714 sheet: -0.22 (0.26), residues: 408 loop : -0.28 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 184 TYR 0.025 0.002 TYR D 311 PHE 0.008 0.001 PHE A 138 TRP 0.010 0.002 TRP F 162 HIS 0.002 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (14538) covalent geometry : angle 0.44517 / 0.25 (19698) hydrogen bonds : bond 0.03314 / 2.17 ( 648) hydrogen bonds : angle 4.40536 / 3.12 ( 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 334 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 295 time to evaluate : 0.545 Fit side-chains REVERT: A 17 GLN cc_start: 0.9068 (tp40) cc_final: 0.8782 (tp40) REVERT: A 97 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7278 (mp10) REVERT: A 122 ASP cc_start: 0.8995 (m-30) cc_final: 0.8726 (m-30) REVERT: A 178 VAL cc_start: 0.8229 (m) cc_final: 0.7873 (t) REVERT: A 180 SER cc_start: 0.8169 (t) cc_final: 0.7956 (t) REVERT: A 222 MET cc_start: 0.8413 (ptp) cc_final: 0.7829 (ptp) REVERT: A 278 GLU cc_start: 0.7716 (mp0) cc_final: 0.7290 (pm20) REVERT: A 311 TYR cc_start: 0.8572 (t80) cc_final: 0.8344 (t80) REVERT: B 122 ASP cc_start: 0.8928 (m-30) cc_final: 0.8575 (m-30) REVERT: B 127 MET cc_start: 0.9021 (ttm) cc_final: 0.8764 (tpp) REVERT: B 191 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7069 (mt) REVERT: B 205 MET cc_start: 0.5336 (ptp) cc_final: 0.4860 (ptm) REVERT: B 220 ASP cc_start: 0.8762 (t0) cc_final: 0.8263 (t0) REVERT: B 282 LYS cc_start: 0.8746 (mtpp) cc_final: 0.8357 (mttt) REVERT: C 29 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8695 (mtpt) REVERT: C 68 MET cc_start: 0.8726 (tpp) cc_final: 0.8349 (tpt) REVERT: C 122 ASP cc_start: 0.9125 (m-30) cc_final: 0.8833 (m-30) REVERT: C 191 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6842 (mt) REVERT: C 208 VAL cc_start: 0.4708 (OUTLIER) cc_final: 0.4428 (m) REVERT: C 220 ASP cc_start: 0.8766 (t0) cc_final: 0.8347 (t70) REVERT: C 222 MET cc_start: 0.8314 (ptp) cc_final: 0.7891 (ptm) REVERT: C 282 LYS cc_start: 0.8481 (mtpp) cc_final: 0.8240 (mtpp) REVERT: D 17 GLN cc_start: 0.9067 (tp40) cc_final: 0.8774 (tp40) REVERT: D 68 MET cc_start: 0.8733 (tpp) cc_final: 0.8283 (tpt) REVERT: D 222 MET cc_start: 0.8305 (ptp) cc_final: 0.8102 (ptm) REVERT: D 278 GLU cc_start: 0.7491 (mp0) cc_final: 0.7248 (mp0) REVERT: D 282 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8182 (mtpp) REVERT: E 68 MET cc_start: 0.8884 (tpt) cc_final: 0.8651 (tpp) REVERT: E 97 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7903 (mm110) REVERT: E 122 ASP cc_start: 0.8940 (m-30) cc_final: 0.8597 (m-30) REVERT: E 191 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6998 (mt) REVERT: E 220 ASP cc_start: 0.8754 (t0) cc_final: 0.8266 (t0) REVERT: F 97 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7351 (mp10) REVERT: F 278 GLU cc_start: 0.7534 (mp0) cc_final: 0.7089 (pm20) outliers start: 39 outliers final: 18 residues processed: 325 average time/residue: 0.6027 time to fit residues: 213.2314 Evaluate side-chains 323 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 296 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 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 191 LEU 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 171 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 161 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN A 283 HIS B 12 HIS B 263 ASN B 283 HIS B 288 GLN ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN E 283 HIS E 288 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.100220 restraints weight = 13900.193| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.49 r_work: 0.2939 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14538 Z= 0.222 Angle : 0.570 4.516 19698 Z= 0.311 Chirality : 0.050 0.165 2334 Planarity : 0.003 0.026 2496 Dihedral : 5.358 32.077 1991 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.86 % Allowed : 15.78 % Favored : 81.36 % 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: -0.28 (0.26), residues: 408 loop : -0.23 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 184 TYR 0.021 0.003 TYR D 311 PHE 0.014 0.002 PHE C 138 TRP 0.008 0.003 TRP E 154 HIS 0.004 0.001 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (14538) covalent geometry : angle 0.57030 / 0.31 (19698) hydrogen bonds : bond 0.04445 / 2.89 ( 648) hydrogen bonds : angle 4.59437 / 3.26 ( 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 318 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 0.488 Fit side-chains REVERT: A 97 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7269 (mp10) REVERT: A 122 ASP cc_start: 0.9078 (m-30) cc_final: 0.8824 (m-30) REVERT: A 178 VAL cc_start: 0.8263 (m) cc_final: 0.7899 (t) REVERT: A 222 MET cc_start: 0.8513 (ptp) cc_final: 0.8005 (ptp) REVERT: A 278 GLU cc_start: 0.7789 (mp0) cc_final: 0.7435 (pm20) REVERT: A 311 TYR cc_start: 0.8724 (t80) cc_final: 0.8462 (t80) REVERT: B 62 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7807 (mm-30) REVERT: B 97 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8050 (mm110) REVERT: B 122 ASP cc_start: 0.8974 (m-30) cc_final: 0.8693 (m-30) REVERT: B 127 MET cc_start: 0.9120 (ttm) cc_final: 0.8811 (tpp) REVERT: B 191 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7278 (mt) REVERT: C 29 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8631 (mtpt) REVERT: C 68 MET cc_start: 0.8821 (tpp) cc_final: 0.8381 (tpt) REVERT: C 122 ASP cc_start: 0.9147 (m-30) cc_final: 0.8796 (m-30) REVERT: C 191 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.7020 (mt) REVERT: C 282 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8280 (mtpp) REVERT: D 17 GLN cc_start: 0.9054 (tp40) cc_final: 0.8788 (tp40) REVERT: D 29 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8640 (mtpt) REVERT: D 68 MET cc_start: 0.8827 (tpp) cc_final: 0.8425 (tpt) REVERT: D 278 GLU cc_start: 0.7561 (mp0) cc_final: 0.7306 (mp0) REVERT: D 282 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8260 (mtpp) REVERT: E 62 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7905 (mm-30) REVERT: E 97 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8073 (mm110) REVERT: E 122 ASP cc_start: 0.8964 (m-30) cc_final: 0.8714 (m-30) REVERT: E 191 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7200 (mt) REVERT: F 97 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7248 (mp10) REVERT: F 278 GLU cc_start: 0.7706 (mp0) cc_final: 0.7215 (pm20) outliers start: 45 outliers final: 25 residues processed: 305 average time/residue: 0.6057 time to fit residues: 201.6294 Evaluate side-chains 305 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 270 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 A residue 282 LYS 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 C residue 29 LYS Chi-restraints excluded: chain C residue 191 LEU 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 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 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 237 LEU Chi-restraints excluded: chain E residue 249 THR 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: 0.9980 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 103 optimal weight: 0.3980 chunk 161 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 114 optimal weight: 0.0370 chunk 132 optimal weight: 5.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 HIS B 283 HIS D 158 ASN D 283 HIS E 283 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104772 restraints weight = 13893.895| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.48 r_work: 0.3010 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14538 Z= 0.110 Angle : 0.462 4.370 19698 Z= 0.256 Chirality : 0.046 0.168 2334 Planarity : 0.003 0.022 2496 Dihedral : 4.866 34.594 1991 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.29 % Allowed : 16.22 % 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: 0.84 (0.20), residues: 1830 helix: 1.93 (0.20), residues: 714 sheet: -0.27 (0.26), residues: 408 loop : -0.27 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 184 TYR 0.025 0.002 TYR D 311 PHE 0.010 0.001 PHE C 138 TRP 0.010 0.002 TRP F 162 HIS 0.003 0.001 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (14538) covalent geometry : angle 0.46183 / 0.26 (19698) hydrogen bonds : bond 0.03431 / 2.24 ( 648) hydrogen bonds : angle 4.39525 / 3.11 ( 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 324 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 0.419 Fit side-chains REVERT: A 17 GLN cc_start: 0.9092 (tp40) cc_final: 0.8742 (tp40) REVERT: A 96 ARG cc_start: 0.8756 (mtm180) cc_final: 0.8391 (mtm180) REVERT: A 97 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: A 122 ASP cc_start: 0.9023 (m-30) cc_final: 0.8760 (m-30) REVERT: A 178 VAL cc_start: 0.8229 (m) cc_final: 0.7879 (t) REVERT: A 180 SER cc_start: 0.8181 (t) cc_final: 0.7973 (t) REVERT: A 222 MET cc_start: 0.8415 (ptp) cc_final: 0.7869 (ptp) REVERT: A 278 GLU cc_start: 0.7736 (mp0) cc_final: 0.7310 (pm20) REVERT: A 311 TYR cc_start: 0.8618 (t80) cc_final: 0.8400 (t80) REVERT: B 97 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7994 (mm110) REVERT: B 122 ASP cc_start: 0.8948 (m-30) cc_final: 0.8615 (m-30) REVERT: B 191 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7169 (mt) REVERT: B 205 MET cc_start: 0.5591 (ptp) cc_final: 0.5055 (ptm) REVERT: B 220 ASP cc_start: 0.8773 (t0) cc_final: 0.8273 (t0) REVERT: B 282 LYS cc_start: 0.8761 (mtpp) cc_final: 0.8361 (mttt) REVERT: C 29 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8719 (mtpt) REVERT: C 68 MET cc_start: 0.8767 (tpp) cc_final: 0.8373 (tpt) REVERT: C 122 ASP cc_start: 0.9130 (m-30) cc_final: 0.8840 (m-30) REVERT: C 191 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6882 (mt) REVERT: C 208 VAL cc_start: 0.4707 (OUTLIER) cc_final: 0.4426 (m) REVERT: C 220 ASP cc_start: 0.8746 (t0) cc_final: 0.8310 (t70) REVERT: C 222 MET cc_start: 0.8300 (ptp) cc_final: 0.7871 (ptm) REVERT: C 282 LYS cc_start: 0.8466 (mtpp) cc_final: 0.8187 (mtpp) REVERT: D 17 GLN cc_start: 0.9091 (tp40) cc_final: 0.8755 (tp40) REVERT: D 68 MET cc_start: 0.8778 (tpp) cc_final: 0.8357 (tpt) REVERT: D 278 GLU cc_start: 0.7518 (mp0) cc_final: 0.7268 (mp0) REVERT: D 282 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8189 (mtpp) REVERT: E 22 ARG cc_start: 0.8797 (mtp85) cc_final: 0.8522 (mtp85) REVERT: E 62 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7815 (mm-30) REVERT: E 97 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7952 (mm110) REVERT: E 122 ASP cc_start: 0.8957 (m-30) cc_final: 0.8647 (m-30) REVERT: E 191 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7056 (mt) REVERT: E 205 MET cc_start: 0.5461 (ptp) cc_final: 0.4959 (ptm) REVERT: E 220 ASP cc_start: 0.8764 (t0) cc_final: 0.8274 (t0) REVERT: F 96 ARG cc_start: 0.8728 (mtm180) cc_final: 0.8426 (mtm180) REVERT: F 97 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7320 (mp10) REVERT: F 205 MET cc_start: 0.5460 (ptp) cc_final: 0.4915 (ptm) REVERT: F 243 ARG cc_start: 0.6165 (mtp85) cc_final: 0.5892 (mtm-85) REVERT: F 278 GLU cc_start: 0.7549 (mp0) cc_final: 0.7039 (pm20) outliers start: 36 outliers final: 20 residues processed: 317 average time/residue: 0.6164 time to fit residues: 212.3305 Evaluate side-chains 306 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 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 C residue 29 LYS Chi-restraints excluded: chain C residue 191 LEU 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 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 F residue 97 GLN Chi-restraints excluded: chain F residue 207 LEU 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: 2.9990 chunk 66 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 283 HIS B 288 GLN ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 HIS E 12 HIS E 283 HIS E 288 GLN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.099532 restraints weight = 13866.494| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.49 r_work: 0.2912 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14538 Z= 0.261 Angle : 0.613 4.771 19698 Z= 0.333 Chirality : 0.052 0.168 2334 Planarity : 0.004 0.026 2496 Dihedral : 5.524 36.784 1990 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.67 % Allowed : 16.35 % Favored : 80.98 % 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: 0.70 (0.20), residues: 1830 helix: 1.71 (0.20), residues: 714 sheet: -0.34 (0.26), residues: 408 loop : -0.22 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 184 TYR 0.022 0.003 TYR D 311 PHE 0.015 0.002 PHE C 138 TRP 0.008 0.003 TRP B 154 HIS 0.008 0.001 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.26 (14538) covalent geometry : angle 0.61331 / 0.33 (19698) hydrogen bonds : bond 0.04682 / 3.04 ( 648) hydrogen bonds : angle 4.66582 / 3.31 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6092.07 seconds wall clock time: 104 minutes 26.69 seconds (6266.69 seconds total)