Starting phenix.real_space_refine on Tue Nov 18 14:53:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbo_27293/11_2025/8dbo_27293.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbo_27293/11_2025/8dbo_27293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dbo_27293/11_2025/8dbo_27293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbo_27293/11_2025/8dbo_27293.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dbo_27293/11_2025/8dbo_27293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbo_27293/11_2025/8dbo_27293.map" } resolution = 2.5 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= 0.347 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 30 5.49 5 Mg 12 5.21 5 S 102 5.16 5 C 9210 2.51 5 N 2628 2.21 5 O 2898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14880 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2416 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.74, per 1000 atoms: 0.18 Number of scatterers: 14880 At special positions: 0 Unit cell: (120.35, 126.99, 75.53, 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 30 15.00 Mg 12 11.99 O 2898 8.00 N 2628 7.00 C 9210 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: 1.26 Conformation dependent library (CDL) restraints added in 693.0 milliseconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 18 sheets defined 43.4% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 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 Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 161 through 164 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 263 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.708A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 309 through 314 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 Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 161 through 164 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 263 Processing helix chain 'B' and resid 277 through 284 removed outlier: 3.708A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 Processing helix chain 'B' and resid 309 through 314 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 Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 161 through 164 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 263 Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.708A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 306 Processing helix chain 'C' and resid 309 through 314 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 Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 161 through 164 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 263 Processing helix chain 'D' and resid 277 through 284 removed outlier: 3.708A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 306 Processing helix chain 'D' and resid 309 through 314 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 Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 161 through 164 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 263 Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.708A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 306 Processing helix chain 'E' and resid 309 through 314 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 Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 161 through 164 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 263 Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.707A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 306 Processing helix chain 'F' and resid 309 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.121A pdb=" N LYS A 5 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL A 56 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE A 7 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL A 88 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET A 127 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 124 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU A 145 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR A 126 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 208 removed outlier: 6.117A pdb=" N ILE A 167 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A 192 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER A 169 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS A 194 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR A 249 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET A 222 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLY A 251 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A 244 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA A 268 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 272 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS A 250 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLN A 288 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 269 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE A 290 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.564A 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: 6.121A pdb=" N LYS B 5 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL B 56 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE B 7 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 53 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL B 88 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET B 127 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 124 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU B 145 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR B 126 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA6, first strand: chain 'B' and resid 205 through 208 removed outlier: 6.117A pdb=" N ILE B 167 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE B 192 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER B 169 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS B 194 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 249 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N MET B 222 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY B 251 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 244 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 272 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS B 250 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLN B 288 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 269 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE B 290 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.564A 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: 6.121A pdb=" N LYS C 5 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL C 56 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE C 7 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL C 88 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET C 127 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 124 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU C 145 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR C 126 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 30 through 34 Processing sheet with id=AA9, first strand: chain 'C' and resid 205 through 208 removed outlier: 6.117A pdb=" N ILE C 167 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE C 192 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER C 169 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LYS C 194 " --> pdb=" O SER C 169 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR C 249 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET C 222 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLY C 251 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C 244 " --> pdb=" O PHE C 266 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA C 268 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 272 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS C 250 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLN C 288 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL C 269 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.443A 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: 6.121A pdb=" N LYS D 5 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL D 56 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE D 7 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL D 88 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET D 127 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE D 124 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU D 145 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AB3, first strand: chain 'D' and resid 205 through 208 removed outlier: 6.117A pdb=" N ILE D 167 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE D 192 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER D 169 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS D 194 " --> pdb=" O SER D 169 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR D 249 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET D 222 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLY D 251 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL D 244 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA D 268 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR D 272 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N HIS D 250 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLN D 288 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL D 269 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.443A 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: 6.121A pdb=" N LYS E 5 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL E 56 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE E 7 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL E 53 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL E 88 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE E 55 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET E 127 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE E 124 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU E 145 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR E 126 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 34 Processing sheet with id=AB6, first strand: chain 'E' and resid 205 through 208 removed outlier: 6.117A pdb=" N ILE E 167 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE E 192 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER E 169 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS E 194 " --> pdb=" O SER E 169 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR E 249 " --> pdb=" O ASP E 220 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET E 222 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY E 251 " --> pdb=" O MET E 222 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL E 244 " --> pdb=" O PHE E 266 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR E 272 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS E 250 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLN E 288 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL E 269 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE E 290 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 6.564A 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: 6.121A pdb=" N LYS F 5 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL F 56 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE F 7 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL F 53 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL F 88 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE F 55 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET F 127 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE F 124 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU F 145 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR F 126 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 30 through 34 Processing sheet with id=AB9, first strand: chain 'F' and resid 205 through 208 removed outlier: 6.117A pdb=" N ILE F 167 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE F 192 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER F 169 " --> pdb=" O ILE F 192 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS F 194 " --> pdb=" O SER F 169 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR F 249 " --> pdb=" O ASP F 220 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N MET F 222 " --> pdb=" O THR F 249 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLY F 251 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL F 244 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR F 272 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS F 250 " --> pdb=" O THR F 272 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLN F 288 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL F 269 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE F 290 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL F 271 " --> pdb=" O ILE F 290 " (cutoff:3.500A) 660 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: 2.81 Time building geometry restraints manager: 1.69 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: 4953 1.34 - 1.46: 1956 1.46 - 1.57: 7989 1.57 - 1.69: 36 1.69 - 1.81: 150 Bond restraints: 15084 Sorted by residual: bond pdb=" C4 ADP A 405 " pdb=" C5 ADP A 405 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C4 ADP B 405 " pdb=" C5 ADP B 405 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.80e+01 ... (remaining 15079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 20094 2.97 - 5.94: 234 5.94 - 8.91: 100 8.91 - 11.88: 32 11.88 - 14.85: 12 Bond angle restraints: 20472 Sorted by residual: angle pdb=" PA ADP F 403 " pdb=" O3A ADP F 403 " pdb=" PB ADP F 403 " ideal model delta sigma weight residual 120.50 135.35 -14.85 3.00e+00 1.11e-01 2.45e+01 angle pdb=" PA ADP E 403 " pdb=" O3A ADP E 403 " pdb=" PB ADP E 403 " ideal model delta sigma weight residual 120.50 135.35 -14.85 3.00e+00 1.11e-01 2.45e+01 angle pdb=" PA ADP C 403 " pdb=" O3A ADP C 403 " pdb=" PB ADP C 403 " ideal model delta sigma weight residual 120.50 135.34 -14.84 3.00e+00 1.11e-01 2.45e+01 angle pdb=" PA ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PB ADP B 402 " ideal model delta sigma weight residual 120.50 135.32 -14.82 3.00e+00 1.11e-01 2.44e+01 angle pdb=" PA ADP D 402 " pdb=" O3A ADP D 402 " pdb=" PB ADP D 402 " ideal model delta sigma weight residual 120.50 135.31 -14.81 3.00e+00 1.11e-01 2.44e+01 ... (remaining 20467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 8826 34.00 - 67.99: 297 67.99 - 101.99: 33 101.99 - 135.99: 15 135.99 - 169.99: 9 Dihedral angle restraints: 9180 sinusoidal: 3672 harmonic: 5508 Sorted by residual: dihedral pdb=" O2A ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PA ADP B 402 " pdb=" PB ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 109.99 -169.99 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP D 402 " pdb=" O3A ADP D 402 " pdb=" PA ADP D 402 " pdb=" PB ADP D 402 " ideal model delta sinusoidal sigma weight residual -60.00 109.97 -169.97 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP F 403 " pdb=" O3A ADP F 403 " pdb=" PA ADP F 403 " pdb=" PB ADP F 403 " ideal model delta sinusoidal sigma weight residual -60.00 109.95 -169.95 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 9177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1508 0.041 - 0.082: 600 0.082 - 0.123: 240 0.123 - 0.163: 46 0.163 - 0.204: 12 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CA VAL C 151 " pdb=" N VAL C 151 " pdb=" C VAL C 151 " pdb=" CB VAL C 151 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL B 151 " pdb=" N VAL B 151 " pdb=" C VAL B 151 " pdb=" CB VAL B 151 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL E 151 " pdb=" N VAL E 151 " pdb=" C VAL E 151 " pdb=" CB VAL E 151 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2403 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 65 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.47e+00 pdb=" CG ASP C 65 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP C 65 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP C 65 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP B 402 " 0.019 2.00e-02 2.50e+03 9.40e-03 2.43e+00 pdb=" C2 ADP B 402 " -0.005 2.00e-02 2.50e+03 pdb=" C4 ADP B 402 " -0.002 2.00e-02 2.50e+03 pdb=" C5 ADP B 402 " -0.003 2.00e-02 2.50e+03 pdb=" C6 ADP B 402 " -0.000 2.00e-02 2.50e+03 pdb=" C8 ADP B 402 " -0.009 2.00e-02 2.50e+03 pdb=" N1 ADP B 402 " -0.005 2.00e-02 2.50e+03 pdb=" N3 ADP B 402 " -0.003 2.00e-02 2.50e+03 pdb=" N6 ADP B 402 " 0.019 2.00e-02 2.50e+03 pdb=" N7 ADP B 402 " -0.009 2.00e-02 2.50e+03 pdb=" N9 ADP B 402 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 65 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" CG ASP A 65 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP A 65 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 65 " -0.010 2.00e-02 2.50e+03 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 96 2.47 - 3.08: 10623 3.08 - 3.69: 24138 3.69 - 4.29: 37203 4.29 - 4.90: 59181 Nonbonded interactions: 131241 Sorted by model distance: nonbonded pdb="MG MG B 403 " pdb=" O HOH B 503 " model vdw 1.866 2.170 nonbonded pdb="MG MG F 404 " pdb=" O HOH F 503 " model vdw 1.866 2.170 nonbonded pdb="MG MG A 403 " pdb=" O HOH A 503 " model vdw 1.866 2.170 nonbonded pdb="MG MG E 404 " pdb=" O HOH E 503 " model vdw 1.866 2.170 nonbonded pdb="MG MG D 403 " pdb=" O HOH D 503 " model vdw 1.867 2.170 ... (remaining 131236 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 317 or resid 404)) selection = (chain 'B' and (resid 2 through 317 or resid 404)) selection = (chain 'C' and (resid 2 through 317 or resid 404)) selection = (chain 'D' and (resid 2 through 317 or resid 404)) selection = (chain 'E' and (resid 2 through 317 or resid 404)) selection = (chain 'F' and (resid 2 through 317 or resid 404)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.320 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.020 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:9.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 15084 Z= 0.343 Angle : 1.022 14.848 20472 Z= 0.449 Chirality : 0.053 0.204 2406 Planarity : 0.003 0.020 2568 Dihedral : 18.642 169.985 5592 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.37 % Allowed : 14.23 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 1884 helix: 1.78 (0.20), residues: 702 sheet: -0.38 (0.24), residues: 450 loop : 0.24 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 214 TYR 0.011 0.002 TYR E 311 PHE 0.013 0.002 PHE F 138 TRP 0.011 0.003 TRP E 162 HIS 0.007 0.001 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00703 (15084) covalent geometry : angle 1.02227 (20472) hydrogen bonds : bond 0.14915 ( 660) hydrogen bonds : angle 5.25072 ( 1800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 555 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.7724 (tt) cc_final: 0.7510 (mm) REVERT: A 280 LYS cc_start: 0.7820 (mmtm) cc_final: 0.7457 (mmmt) REVERT: B 280 LYS cc_start: 0.7870 (mmtm) cc_final: 0.7540 (mmmt) REVERT: C 191 LEU cc_start: 0.7852 (tt) cc_final: 0.7588 (mm) REVERT: C 280 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7680 (mmmt) REVERT: D 191 LEU cc_start: 0.7854 (tt) cc_final: 0.7601 (mm) REVERT: D 280 LYS cc_start: 0.7943 (mmtm) cc_final: 0.7699 (mmmt) REVERT: E 280 LYS cc_start: 0.7873 (mmtm) cc_final: 0.7544 (mmmt) REVERT: F 280 LYS cc_start: 0.7829 (mmtm) cc_final: 0.7463 (mmmt) outliers start: 54 outliers final: 11 residues processed: 591 average time/residue: 0.6824 time to fit residues: 439.1432 Evaluate side-chains 382 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 371 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 196 ARG Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.4980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN B 97 GLN B 263 ASN E 97 GLN E 263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.271945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.257837 restraints weight = 13429.180| |-----------------------------------------------------------------------------| r_work (start): 0.4956 rms_B_bonded: 0.83 r_work: 0.4913 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.4831 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.4831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15084 Z= 0.142 Angle : 0.694 8.659 20472 Z= 0.324 Chirality : 0.049 0.157 2406 Planarity : 0.004 0.026 2568 Dihedral : 16.110 167.157 2170 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.37 % Allowed : 22.28 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.22 (0.19), residues: 1884 helix: 1.34 (0.19), residues: 756 sheet: -0.81 (0.23), residues: 492 loop : -0.31 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 214 TYR 0.011 0.002 TYR E 311 PHE 0.011 0.002 PHE A 313 TRP 0.008 0.002 TRP E 154 HIS 0.008 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00305 (15084) covalent geometry : angle 0.69367 (20472) hydrogen bonds : bond 0.03514 ( 660) hydrogen bonds : angle 4.55792 ( 1800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 355 time to evaluate : 0.577 Fit side-chains REVERT: A 29 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7579 (mtmt) REVERT: A 78 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.6771 (ttmt) REVERT: F 78 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6996 (tptp) outliers start: 70 outliers final: 33 residues processed: 398 average time/residue: 0.5558 time to fit residues: 245.4164 Evaluate side-chains 374 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 338 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 5 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 40 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN E 263 ASN E 283 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.269250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.254508 restraints weight = 13504.924| |-----------------------------------------------------------------------------| r_work (start): 0.4925 rms_B_bonded: 0.84 r_work: 0.4862 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.4766 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.4766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15084 Z= 0.150 Angle : 0.685 8.547 20472 Z= 0.316 Chirality : 0.048 0.173 2406 Planarity : 0.003 0.024 2568 Dihedral : 15.784 172.091 2152 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.87 % Allowed : 22.28 % Favored : 72.85 % 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 (0.19), residues: 1884 helix: 1.30 (0.19), residues: 750 sheet: -1.04 (0.22), residues: 492 loop : -0.20 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 184 TYR 0.010 0.002 TYR C 54 PHE 0.011 0.002 PHE B 313 TRP 0.008 0.002 TRP F 154 HIS 0.004 0.001 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00328 (15084) covalent geometry : angle 0.68543 (20472) hydrogen bonds : bond 0.03673 ( 660) hydrogen bonds : angle 4.45025 ( 1800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 348 time to evaluate : 0.563 Fit side-chains REVERT: A 78 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7111 (tptp) REVERT: C 176 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6831 (mttp) REVERT: D 176 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6816 (mttp) REVERT: F 78 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.6848 (ttmt) outliers start: 78 outliers final: 34 residues processed: 392 average time/residue: 0.5658 time to fit residues: 245.6088 Evaluate side-chains 371 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 333 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 40 optimal weight: 0.0980 chunk 25 optimal weight: 0.0060 chunk 73 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 283 HIS C 123 HIS C 283 HIS D 123 HIS D 283 HIS E 133 GLN E 263 ASN F 133 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.267900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.252966 restraints weight = 13535.509| |-----------------------------------------------------------------------------| r_work (start): 0.4912 rms_B_bonded: 0.85 r_work: 0.4842 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.4745 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.4745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15084 Z= 0.154 Angle : 0.688 8.575 20472 Z= 0.317 Chirality : 0.048 0.174 2406 Planarity : 0.003 0.026 2568 Dihedral : 15.462 172.942 2150 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.93 % Allowed : 23.22 % Favored : 71.85 % 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: -0.01 (0.19), residues: 1884 helix: 1.25 (0.19), residues: 750 sheet: -1.35 (0.22), residues: 456 loop : -0.26 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 49 TYR 0.010 0.002 TYR C 54 PHE 0.008 0.002 PHE B 313 TRP 0.008 0.002 TRP F 154 HIS 0.004 0.001 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00336 (15084) covalent geometry : angle 0.68803 (20472) hydrogen bonds : bond 0.03516 ( 660) hydrogen bonds : angle 4.44008 ( 1800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 328 time to evaluate : 0.607 Fit side-chains REVERT: A 78 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7162 (tptp) REVERT: B 231 HIS cc_start: 0.7500 (m90) cc_final: 0.7263 (m90) REVERT: C 73 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7772 (ttm) REVERT: C 176 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6931 (mttp) REVERT: D 176 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6860 (mttp) REVERT: F 26 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6937 (tp30) REVERT: F 78 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7122 (tptp) outliers start: 79 outliers final: 36 residues processed: 379 average time/residue: 0.5907 time to fit residues: 247.2775 Evaluate side-chains 373 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 332 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 100 optimal weight: 3.9990 chunk 89 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 283 HIS E 263 ASN E 283 HIS F 133 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.269202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.254762 restraints weight = 13543.871| |-----------------------------------------------------------------------------| r_work (start): 0.4926 rms_B_bonded: 0.78 r_work: 0.4874 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.4778 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.4778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15084 Z= 0.129 Angle : 0.668 8.342 20472 Z= 0.307 Chirality : 0.047 0.169 2406 Planarity : 0.003 0.026 2568 Dihedral : 15.141 175.233 2150 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.99 % Allowed : 22.72 % Favored : 72.28 % 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: 0.13 (0.19), residues: 1884 helix: 1.45 (0.19), residues: 750 sheet: -1.34 (0.23), residues: 456 loop : -0.23 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 49 TYR 0.008 0.001 TYR F 245 PHE 0.007 0.001 PHE E 313 TRP 0.008 0.002 TRP F 154 HIS 0.003 0.001 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00281 (15084) covalent geometry : angle 0.66753 (20472) hydrogen bonds : bond 0.03207 ( 660) hydrogen bonds : angle 4.33782 ( 1800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 338 time to evaluate : 0.596 Fit side-chains REVERT: A 5 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7609 (mptm) REVERT: A 288 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7356 (mt0) REVERT: A 302 ARG cc_start: 0.7262 (mpt180) cc_final: 0.6865 (mpt90) REVERT: B 231 HIS cc_start: 0.7449 (m90) cc_final: 0.7190 (m90) REVERT: B 302 ARG cc_start: 0.7080 (mpt180) cc_final: 0.6816 (mpt180) REVERT: C 176 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6861 (mttp) REVERT: C 281 MET cc_start: 0.8351 (mtp) cc_final: 0.8090 (mtm) REVERT: D 176 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6848 (mttp) REVERT: D 281 MET cc_start: 0.8382 (mtp) cc_final: 0.8117 (mtm) REVERT: E 302 ARG cc_start: 0.7086 (mpt180) cc_final: 0.6827 (mpt180) REVERT: F 5 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7684 (mptm) REVERT: F 283 HIS cc_start: 0.7682 (m170) cc_final: 0.7462 (m170) outliers start: 80 outliers final: 38 residues processed: 390 average time/residue: 0.6133 time to fit residues: 262.8619 Evaluate side-chains 361 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 318 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 263 ASN Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 4 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 75 ASN D 133 GLN E 283 HIS ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.265342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.250275 restraints weight = 13439.092| |-----------------------------------------------------------------------------| r_work (start): 0.4888 rms_B_bonded: 0.85 r_work: 0.4838 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.4748 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.4748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15084 Z= 0.183 Angle : 0.718 8.687 20472 Z= 0.335 Chirality : 0.049 0.177 2406 Planarity : 0.004 0.029 2568 Dihedral : 14.990 165.487 2150 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.93 % Allowed : 23.22 % Favored : 71.85 % 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: -0.37 (0.19), residues: 1884 helix: 0.88 (0.19), residues: 792 sheet: -1.50 (0.22), residues: 456 loop : -0.48 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 49 TYR 0.014 0.002 TYR D 54 PHE 0.009 0.002 PHE A 253 TRP 0.007 0.002 TRP F 154 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00406 (15084) covalent geometry : angle 0.71848 (20472) hydrogen bonds : bond 0.03710 ( 660) hydrogen bonds : angle 4.49632 ( 1800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 336 time to evaluate : 0.574 Fit side-chains REVERT: A 5 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7593 (mptm) REVERT: A 78 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7171 (tptp) REVERT: A 298 GLU cc_start: 0.6852 (mp0) cc_final: 0.6641 (mp0) REVERT: A 302 ARG cc_start: 0.7218 (mpt180) cc_final: 0.6946 (mpt90) REVERT: B 231 HIS cc_start: 0.7524 (m90) cc_final: 0.7321 (m90) REVERT: C 73 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7653 (ttm) REVERT: C 176 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6853 (mttp) REVERT: C 281 MET cc_start: 0.8427 (mtp) cc_final: 0.8031 (mtm) REVERT: C 302 ARG cc_start: 0.7169 (mpt180) cc_final: 0.6936 (mpt180) REVERT: D 73 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7751 (ttm) REVERT: D 176 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6883 (mttp) REVERT: D 281 MET cc_start: 0.8458 (mtp) cc_final: 0.8065 (mtm) REVERT: F 5 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7719 (mptm) REVERT: F 34 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6778 (tptp) REVERT: F 78 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7145 (tptp) REVERT: F 283 HIS cc_start: 0.7725 (m170) cc_final: 0.7514 (m170) REVERT: F 302 ARG cc_start: 0.7110 (mpt180) cc_final: 0.6858 (mpt180) outliers start: 79 outliers final: 36 residues processed: 385 average time/residue: 0.5761 time to fit residues: 244.8573 Evaluate side-chains 378 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 333 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 102 LYS Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 103 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 263 ASN A 283 HIS B 38 GLN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 263 ASN E 283 HIS ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 263 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.263878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.248742 restraints weight = 13455.655| |-----------------------------------------------------------------------------| r_work (start): 0.4875 rms_B_bonded: 0.85 r_work: 0.4825 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.4738 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.4738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15084 Z= 0.197 Angle : 0.730 8.758 20472 Z= 0.341 Chirality : 0.049 0.179 2406 Planarity : 0.004 0.033 2568 Dihedral : 14.825 163.154 2150 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.87 % Allowed : 23.28 % Favored : 71.85 % 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: -0.57 (0.19), residues: 1884 helix: 0.72 (0.19), residues: 792 sheet: -1.66 (0.22), residues: 456 loop : -0.52 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 49 TYR 0.014 0.002 TYR D 54 PHE 0.010 0.002 PHE A 253 TRP 0.008 0.002 TRP F 154 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00437 (15084) covalent geometry : angle 0.72960 (20472) hydrogen bonds : bond 0.03859 ( 660) hydrogen bonds : angle 4.53044 ( 1800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 328 time to evaluate : 0.566 Fit side-chains REVERT: A 78 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7184 (tptp) REVERT: C 176 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6845 (mttp) REVERT: C 281 MET cc_start: 0.8446 (mtp) cc_final: 0.8003 (mtm) REVERT: D 73 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7715 (ttm) REVERT: D 176 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6813 (mttp) REVERT: D 281 MET cc_start: 0.8459 (mtp) cc_final: 0.8049 (mtm) REVERT: D 302 ARG cc_start: 0.7078 (mpt180) cc_final: 0.6851 (mpt180) REVERT: F 5 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7593 (mptm) REVERT: F 34 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6830 (tptp) REVERT: F 78 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7191 (tptp) REVERT: F 302 ARG cc_start: 0.7358 (mpt180) cc_final: 0.7114 (mpt180) outliers start: 78 outliers final: 46 residues processed: 376 average time/residue: 0.5482 time to fit residues: 227.9926 Evaluate side-chains 372 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 319 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 127 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 180 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN A 158 ASN A 263 ASN A 283 HIS ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS D 133 GLN E 283 HIS ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 283 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.265210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.251259 restraints weight = 13617.877| |-----------------------------------------------------------------------------| r_work (start): 0.4900 rms_B_bonded: 0.77 r_work: 0.4851 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.4763 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.4763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15084 Z= 0.173 Angle : 0.716 8.585 20472 Z= 0.333 Chirality : 0.049 0.175 2406 Planarity : 0.004 0.034 2568 Dihedral : 14.658 163.895 2150 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.81 % Allowed : 23.16 % Favored : 72.03 % 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: -0.59 (0.19), residues: 1884 helix: 0.76 (0.19), residues: 792 sheet: -1.73 (0.22), residues: 456 loop : -0.56 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 49 TYR 0.014 0.002 TYR A 94 PHE 0.009 0.002 PHE B 313 TRP 0.008 0.002 TRP E 154 HIS 0.004 0.001 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00383 (15084) covalent geometry : angle 0.71621 (20472) hydrogen bonds : bond 0.03663 ( 660) hydrogen bonds : angle 4.45059 ( 1800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 324 time to evaluate : 0.596 Fit side-chains REVERT: A 78 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7172 (tptp) REVERT: C 176 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6925 (mttp) REVERT: C 281 MET cc_start: 0.8474 (mtp) cc_final: 0.8114 (mtm) REVERT: D 73 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7698 (ttm) REVERT: D 176 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6875 (mttp) REVERT: D 281 MET cc_start: 0.8484 (mtp) cc_final: 0.8128 (mtm) REVERT: F 5 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7612 (mptm) REVERT: F 34 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6799 (tptp) REVERT: F 78 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7176 (tptp) REVERT: F 302 ARG cc_start: 0.7284 (mpt180) cc_final: 0.7074 (mpt180) outliers start: 77 outliers final: 47 residues processed: 372 average time/residue: 0.5901 time to fit residues: 241.7057 Evaluate side-chains 369 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 315 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN A 263 ASN A 283 HIS B 158 ASN B 283 HIS E 133 GLN E 283 HIS F 133 GLN F 283 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.264822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.249873 restraints weight = 13541.848| |-----------------------------------------------------------------------------| r_work (start): 0.4887 rms_B_bonded: 0.85 r_work: 0.4838 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.4750 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.4750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15084 Z= 0.167 Angle : 0.719 8.489 20472 Z= 0.334 Chirality : 0.049 0.174 2406 Planarity : 0.004 0.033 2568 Dihedral : 14.529 163.855 2150 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.37 % Allowed : 23.85 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.19), residues: 1884 helix: 0.77 (0.19), residues: 792 sheet: -1.73 (0.22), residues: 456 loop : -0.56 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 49 TYR 0.018 0.002 TYR A 94 PHE 0.008 0.002 PHE E 313 TRP 0.010 0.002 TRP B 154 HIS 0.004 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00370 (15084) covalent geometry : angle 0.71880 (20472) hydrogen bonds : bond 0.03600 ( 660) hydrogen bonds : angle 4.43219 ( 1800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 323 time to evaluate : 0.587 Fit side-chains REVERT: A 78 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7181 (tptp) REVERT: C 73 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7682 (ttm) REVERT: C 176 LYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6885 (mttp) REVERT: C 281 MET cc_start: 0.8452 (mtp) cc_final: 0.8089 (mtm) REVERT: C 302 ARG cc_start: 0.7293 (mpt180) cc_final: 0.7066 (mpt180) REVERT: D 73 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7738 (ttm) REVERT: D 176 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6867 (mttp) REVERT: D 281 MET cc_start: 0.8457 (mtp) cc_final: 0.8098 (mtm) REVERT: F 5 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7595 (mptm) REVERT: F 34 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6752 (tptp) REVERT: F 78 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7145 (tptp) outliers start: 70 outliers final: 43 residues processed: 368 average time/residue: 0.5603 time to fit residues: 227.9182 Evaluate side-chains 361 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 310 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 152 optimal weight: 0.7980 chunk 173 optimal weight: 0.0070 chunk 157 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 165 optimal weight: 0.0570 chunk 101 optimal weight: 0.4980 chunk 168 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 283 HIS B 158 ASN B 283 HIS C 263 ASN E 283 HIS F 283 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.270138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.255606 restraints weight = 13487.522| |-----------------------------------------------------------------------------| r_work (start): 0.4933 rms_B_bonded: 0.85 r_work: 0.4885 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.4796 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.4796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15084 Z= 0.114 Angle : 0.675 8.006 20472 Z= 0.307 Chirality : 0.047 0.160 2406 Planarity : 0.003 0.032 2568 Dihedral : 14.161 175.144 2150 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.43 % Allowed : 24.78 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.20), residues: 1884 helix: 1.46 (0.20), residues: 750 sheet: -1.55 (0.23), residues: 456 loop : -0.31 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 184 TYR 0.019 0.002 TYR F 94 PHE 0.006 0.001 PHE A 138 TRP 0.010 0.002 TRP E 154 HIS 0.003 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00255 (15084) covalent geometry : angle 0.67518 (20472) hydrogen bonds : bond 0.02965 ( 660) hydrogen bonds : angle 4.25466 ( 1800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 321 time to evaluate : 0.596 Fit side-chains REVERT: A 78 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7173 (tptp) REVERT: A 302 ARG cc_start: 0.7135 (mpt180) cc_final: 0.6855 (mpt90) REVERT: C 281 MET cc_start: 0.8373 (mtp) cc_final: 0.8115 (mtm) REVERT: D 281 MET cc_start: 0.8428 (mtp) cc_final: 0.8167 (mtm) REVERT: E 26 GLU cc_start: 0.6952 (tp30) cc_final: 0.6741 (tp30) REVERT: E 302 ARG cc_start: 0.7150 (mpt180) cc_final: 0.6881 (mmt180) REVERT: F 5 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7348 (mptm) REVERT: F 78 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7132 (tptp) outliers start: 55 outliers final: 32 residues processed: 357 average time/residue: 0.6030 time to fit residues: 237.2421 Evaluate side-chains 358 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 323 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 283 HIS Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 237 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 231 HIS A 263 ASN A 283 HIS B 231 HIS B 283 HIS E 75 ASN E 158 ASN E 231 HIS E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 HIS F 283 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.266242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.251391 restraints weight = 13351.848| |-----------------------------------------------------------------------------| r_work (start): 0.4900 rms_B_bonded: 0.86 r_work: 0.4851 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.4763 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.4763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15084 Z= 0.155 Angle : 0.718 8.191 20472 Z= 0.333 Chirality : 0.048 0.169 2406 Planarity : 0.004 0.033 2568 Dihedral : 14.073 166.893 2148 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.87 % Allowed : 26.28 % Favored : 70.85 % 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 (0.20), residues: 1884 helix: 1.26 (0.19), residues: 750 sheet: -1.59 (0.23), residues: 456 loop : -0.34 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 49 TYR 0.021 0.002 TYR A 94 PHE 0.008 0.001 PHE E 313 TRP 0.011 0.002 TRP E 154 HIS 0.011 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00349 (15084) covalent geometry : angle 0.71752 (20472) hydrogen bonds : bond 0.03435 ( 660) hydrogen bonds : angle 4.37855 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6687.85 seconds wall clock time: 114 minutes 42.15 seconds (6882.15 seconds total)