Starting phenix.real_space_refine on Wed Mar 4 16:43:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbo_27293/03_2026/8dbo_27293.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbo_27293/03_2026/8dbo_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_27293/03_2026/8dbo_27293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbo_27293/03_2026/8dbo_27293.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dbo_27293/03_2026/8dbo_27293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbo_27293/03_2026/8dbo_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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14880 Number of models: 1 Model: "" Number of chains: 18 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: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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} Time building chain proxies: 3.44, per 1000 atoms: 0.23 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: 1.19 Conformation dependent library (CDL) restraints added in 470.1 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: 0.53 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: 2.52 Time building geometry restraints manager: 1.60 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: 2.080 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.790 Find NCS groups from input model: 0.350 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.950 ------------------------------------------------------------------------------- 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 : 0.540 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: 0.7853 (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: 0.6360 time to fit residues: 408.8963 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 : 0.387 ------------------------------------------------------------------------------- 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: 0.4832 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.4832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 : 0.573 Fit side-chains REVERT: A 29 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7584 (mtmt) REVERT: A 78 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6771 (ttmt) REVERT: F 78 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.6996 (tptp) outliers start: 70 outliers final: 33 residues processed: 398 average time/residue: 0.5228 time to fit residues: 231.0242 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 : 0.722 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.8782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.269547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.254794 restraints weight = 13526.105| |-----------------------------------------------------------------------------| r_work (start): 0.4926 rms_B_bonded: 0.84 r_work: 0.4864 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.4770 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.4770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3189 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= 0.145 Angle : 0.682 8.514 20472 Z= 0.314 Chirality : 0.048 0.172 2406 Planarity : 0.003 0.025 2568 Dihedral : 15.797 172.336 2152 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.12 % Allowed : 22.16 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.17 (0.19), residues: 1884 helix: 1.33 (0.19), residues: 750 sheet: -1.02 (0.22), residues: 492 loop : -0.19 (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 D 54 PHE 0.011 0.002 PHE B 313 TRP 0.008 0.002 TRP F 154 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00317 (15084) covalent geometry : angle 0.68209 (20472) hydrogen bonds : bond 0.03637 ( 660) hydrogen bonds : angle 4.44166 ( 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: 82 poor density : 344 time to evaluate : 0.587 Fit side-chains REVERT: A 78 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.6953 (ttmt) REVERT: C 176 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6866 (mttp) REVERT: D 176 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6896 (mttp) REVERT: F 78 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.6882 (ttmt) outliers start: 82 outliers final: 38 residues processed: 391 average time/residue: 0.5165 time to fit residues: 224.1042 Evaluate side-chains 375 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 333 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 102 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 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 58 SER 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 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 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: 0.9980 chunk 25 optimal weight: 0.9980 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: 0.0980 chunk 157 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 283 HIS C 283 HIS D 123 HIS D 283 HIS E 133 GLN E 263 ASN E 283 HIS F 133 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.267697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.252777 restraints weight = 13534.074| |-----------------------------------------------------------------------------| r_work (start): 0.4908 rms_B_bonded: 0.85 r_work: 0.4854 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.4759 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.4759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15084 Z= 0.155 Angle : 0.690 8.581 20472 Z= 0.318 Chirality : 0.048 0.175 2406 Planarity : 0.003 0.026 2568 Dihedral : 15.482 172.489 2150 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.99 % Allowed : 23.35 % Favored : 71.66 % 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 (0.19), residues: 1884 helix: 1.24 (0.19), residues: 750 sheet: -1.33 (0.22), residues: 456 loop : -0.27 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 49 TYR 0.010 0.002 TYR C 54 PHE 0.008 0.002 PHE D 313 TRP 0.008 0.002 TRP F 154 HIS 0.003 0.001 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00340 (15084) covalent geometry : angle 0.69031 (20472) hydrogen bonds : bond 0.03539 ( 660) hydrogen bonds : angle 4.45064 ( 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 414 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 334 time to evaluate : 0.546 Fit side-chains REVERT: A 78 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7159 (tptp) REVERT: A 84 ARG cc_start: 0.7936 (ttp-110) cc_final: 0.7582 (ttp80) REVERT: B 231 HIS cc_start: 0.7476 (m90) cc_final: 0.7258 (m90) REVERT: C 73 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7726 (ttm) REVERT: C 176 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6895 (mttp) REVERT: D 73 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7738 (ttm) REVERT: D 176 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6825 (mttp) REVERT: F 26 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6878 (tp30) REVERT: F 78 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7118 (tptp) outliers start: 80 outliers final: 36 residues processed: 383 average time/residue: 0.5486 time to fit residues: 231.6742 Evaluate side-chains 378 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 336 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 102 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 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 47 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 73 MET 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 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: 2.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 C 75 ASN C 123 HIS D 75 ASN E 263 ASN E 283 HIS F 133 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.264551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.249340 restraints weight = 13505.464| |-----------------------------------------------------------------------------| r_work (start): 0.4880 rms_B_bonded: 0.85 r_work: 0.4832 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.4744 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.4744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3677 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= 0.202 Angle : 0.731 8.935 20472 Z= 0.343 Chirality : 0.050 0.180 2406 Planarity : 0.004 0.032 2568 Dihedral : 15.224 161.153 2150 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.74 % Allowed : 22.85 % Favored : 72.41 % 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: -0.51 (0.19), residues: 1884 helix: 0.72 (0.19), residues: 792 sheet: -1.58 (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 D 49 TYR 0.013 0.002 TYR D 54 PHE 0.011 0.002 PHE A 253 TRP 0.008 0.002 TRP F 154 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00444 (15084) covalent geometry : angle 0.73076 (20472) hydrogen bonds : bond 0.03914 ( 660) hydrogen bonds : angle 4.58304 ( 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 426 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 350 time to evaluate : 0.419 Fit side-chains REVERT: A 5 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7695 (mptm) REVERT: A 78 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7203 (tptp) REVERT: A 84 ARG cc_start: 0.7972 (ttp-110) cc_final: 0.7629 (ttp80) REVERT: A 298 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: A 302 ARG cc_start: 0.7213 (mpt180) cc_final: 0.6919 (mpt90) REVERT: B 231 HIS cc_start: 0.7492 (m90) cc_final: 0.7262 (m90) REVERT: C 73 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7664 (ttm) REVERT: C 176 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6858 (mttp) REVERT: D 73 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7698 (ttm) REVERT: D 176 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6816 (mttp) REVERT: F 5 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7752 (mptm) REVERT: F 34 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6857 (tptp) REVERT: F 78 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7178 (tptp) outliers start: 76 outliers final: 39 residues processed: 394 average time/residue: 0.5753 time to fit residues: 248.7513 Evaluate side-chains 386 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 337 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 102 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 A residue 298 GLU 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 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 47 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 4 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 92 optimal weight: 0.2980 chunk 170 optimal weight: 0.9980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 263 ASN A 283 HIS ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS D 133 GLN D 263 ASN 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 = 0.4973 r_free = 0.4973 target = 0.264101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.248963 restraints weight = 13436.746| |-----------------------------------------------------------------------------| r_work (start): 0.4876 rms_B_bonded: 0.85 r_work: 0.4825 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.4734 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.4734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15084 Z= 0.192 Angle : 0.731 8.739 20472 Z= 0.343 Chirality : 0.049 0.178 2406 Planarity : 0.004 0.035 2568 Dihedral : 15.047 162.693 2150 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.24 % Allowed : 22.60 % Favored : 72.16 % 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: -0.62 (0.19), residues: 1884 helix: 0.65 (0.19), residues: 792 sheet: -1.71 (0.22), residues: 456 loop : -0.49 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 49 TYR 0.013 0.002 TYR D 54 PHE 0.010 0.002 PHE F 253 TRP 0.008 0.002 TRP F 154 HIS 0.003 0.001 HIS F 283 Details of bonding type rmsd covalent geometry : bond 0.00426 (15084) covalent geometry : angle 0.73124 (20472) hydrogen bonds : bond 0.03830 ( 660) hydrogen bonds : angle 4.56486 ( 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 410 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 326 time to evaluate : 0.522 Fit side-chains REVERT: A 5 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7552 (mptm) REVERT: A 78 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7185 (tptp) REVERT: A 84 ARG cc_start: 0.7960 (ttp-110) cc_final: 0.7599 (ttp80) REVERT: C 73 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7673 (ttm) REVERT: C 176 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6823 (mttp) REVERT: C 302 ARG cc_start: 0.7167 (mpt180) cc_final: 0.6923 (mpt180) REVERT: D 73 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7714 (ttm) REVERT: D 176 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6914 (mttp) REVERT: D 302 ARG cc_start: 0.7137 (mpt180) cc_final: 0.6826 (mpt180) REVERT: F 5 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7592 (mptm) REVERT: F 34 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6883 (tptp) REVERT: F 78 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7198 (tptp) REVERT: F 302 ARG cc_start: 0.7272 (mpt180) cc_final: 0.7055 (mpt180) outliers start: 84 outliers final: 47 residues processed: 378 average time/residue: 0.5610 time to fit residues: 234.0453 Evaluate side-chains 374 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 318 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 102 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 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 298 GLU 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 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 C residue 301 ARG Chi-restraints excluded: chain D residue 47 SER 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 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 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 E residue 301 ARG 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 62 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 103 optimal weight: 1.9990 chunk 157 optimal weight: 0.2980 chunk 131 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 159 optimal weight: 4.9990 chunk 102 optimal weight: 0.3980 chunk 185 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 133 GLN B 283 HIS C 263 ASN E 283 HIS F 133 GLN 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 = 0.5013 r_free = 0.5013 target = 0.268703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.253986 restraints weight = 13476.320| |-----------------------------------------------------------------------------| r_work (start): 0.4918 rms_B_bonded: 0.83 r_work: 0.4870 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.4779 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.4779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15084 Z= 0.120 Angle : 0.671 8.168 20472 Z= 0.306 Chirality : 0.047 0.166 2406 Planarity : 0.003 0.027 2568 Dihedral : 14.710 174.437 2150 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.56 % Allowed : 23.72 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.28 (0.20), residues: 1884 helix: 1.06 (0.19), residues: 792 sheet: -1.60 (0.22), residues: 456 loop : -0.46 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 49 TYR 0.008 0.001 TYR A 245 PHE 0.007 0.001 PHE C 138 TRP 0.010 0.002 TRP B 154 HIS 0.005 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00262 (15084) covalent geometry : angle 0.67115 (20472) hydrogen bonds : bond 0.03088 ( 660) hydrogen bonds : angle 4.31412 ( 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 405 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 332 time to evaluate : 0.398 Fit side-chains REVERT: A 84 ARG cc_start: 0.7913 (ttp-110) cc_final: 0.7606 (ttp80) REVERT: A 260 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7774 (mtt180) REVERT: A 302 ARG cc_start: 0.7220 (mpt180) cc_final: 0.6793 (mpt90) REVERT: B 176 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6650 (mttp) REVERT: B 302 ARG cc_start: 0.7063 (mpt180) cc_final: 0.6793 (mpt180) REVERT: C 176 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6861 (mttp) REVERT: C 281 MET cc_start: 0.8389 (mtp) cc_final: 0.8098 (mtm) REVERT: D 176 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6857 (mttp) REVERT: D 281 MET cc_start: 0.8405 (mtp) cc_final: 0.8118 (mtm) REVERT: E 26 GLU cc_start: 0.6972 (tp30) cc_final: 0.6768 (tp30) REVERT: F 5 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7507 (mptm) outliers start: 73 outliers final: 34 residues processed: 377 average time/residue: 0.5887 time to fit residues: 243.5965 Evaluate side-chains 360 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 322 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 263 ASN 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 176 LYS 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 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 301 ARG Chi-restraints excluded: chain D residue 47 SER 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 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 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 298 GLU Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 34 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 127 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 180 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN A 283 HIS B 133 GLN B 283 HIS D 133 GLN E 283 HIS F 158 ASN F 283 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.266858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.251998 restraints weight = 13489.961| |-----------------------------------------------------------------------------| r_work (start): 0.4906 rms_B_bonded: 0.85 r_work: 0.4857 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.4770 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.4770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15084 Z= 0.140 Angle : 0.692 8.293 20472 Z= 0.318 Chirality : 0.047 0.170 2406 Planarity : 0.003 0.028 2568 Dihedral : 14.560 172.234 2148 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.00 % Allowed : 24.84 % Favored : 71.16 % 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: -0.07 (0.20), residues: 1884 helix: 1.33 (0.19), residues: 750 sheet: -1.58 (0.23), residues: 456 loop : -0.30 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 49 TYR 0.012 0.002 TYR A 94 PHE 0.008 0.001 PHE B 313 TRP 0.008 0.002 TRP A 162 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00308 (15084) covalent geometry : angle 0.69180 (20472) hydrogen bonds : bond 0.03290 ( 660) hydrogen bonds : angle 4.33767 ( 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 387 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 323 time to evaluate : 0.520 Fit side-chains REVERT: A 84 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7610 (ttp80) REVERT: A 260 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7785 (mtt180) REVERT: C 176 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6811 (mttp) REVERT: C 281 MET cc_start: 0.8432 (mtp) cc_final: 0.8026 (mtm) REVERT: D 176 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6811 (mttp) REVERT: D 281 MET cc_start: 0.8443 (mtp) cc_final: 0.8010 (mtm) REVERT: E 26 GLU cc_start: 0.6911 (tp30) cc_final: 0.6701 (tp30) REVERT: F 5 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7649 (mptm) outliers start: 64 outliers final: 40 residues processed: 364 average time/residue: 0.5590 time to fit residues: 224.1384 Evaluate side-chains 362 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 319 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 160 SER 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 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 C residue 301 ARG Chi-restraints excluded: chain D residue 47 SER 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 132 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 D residue 301 ARG 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 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 284 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.9980 chunk 159 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 133 GLN A 263 ASN A 283 HIS B 133 GLN B 283 HIS ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 283 HIS F 283 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5000 r_free = 0.5000 target = 0.267041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.252229 restraints weight = 13511.237| |-----------------------------------------------------------------------------| r_work (start): 0.4908 rms_B_bonded: 0.86 r_work: 0.4858 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.4770 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.4770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15084 Z= 0.139 Angle : 0.690 8.274 20472 Z= 0.317 Chirality : 0.048 0.172 2406 Planarity : 0.003 0.028 2568 Dihedral : 14.280 172.096 2148 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.43 % Allowed : 25.03 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.97 (0.19), residues: 792 sheet: -1.61 (0.23), residues: 456 loop : -0.52 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 49 TYR 0.016 0.002 TYR A 94 PHE 0.007 0.001 PHE E 313 TRP 0.008 0.002 TRP B 154 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00306 (15084) covalent geometry : angle 0.68986 (20472) hydrogen bonds : bond 0.03286 ( 660) hydrogen bonds : angle 4.33081 ( 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 376 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 321 time to evaluate : 0.464 Fit side-chains REVERT: A 84 ARG cc_start: 0.7913 (ttp-110) cc_final: 0.7599 (ttp80) REVERT: A 260 ARG cc_start: 0.8114 (mtt180) cc_final: 0.7805 (mtt180) REVERT: C 176 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6788 (mttp) REVERT: C 281 MET cc_start: 0.8444 (mtp) cc_final: 0.8126 (mtm) REVERT: D 176 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6846 (mttp) REVERT: D 281 MET cc_start: 0.8450 (mtp) cc_final: 0.8109 (mtm) REVERT: F 5 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7553 (mptm) outliers start: 55 outliers final: 37 residues processed: 357 average time/residue: 0.5557 time to fit residues: 218.7850 Evaluate side-chains 355 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 315 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 47 SER 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 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 D residue 301 ARG 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 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 152 optimal weight: 0.0470 chunk 173 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 168 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 133 GLN A 263 ASN A 283 HIS B 133 GLN B 158 ASN B 283 HIS C 133 GLN E 231 HIS E 283 HIS F 283 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.268010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.253348 restraints weight = 13449.096| |-----------------------------------------------------------------------------| r_work (start): 0.4913 rms_B_bonded: 0.84 r_work: 0.4865 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.4776 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.4776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15084 Z= 0.130 Angle : 0.690 8.008 20472 Z= 0.317 Chirality : 0.047 0.170 2406 Planarity : 0.003 0.033 2568 Dihedral : 14.059 174.688 2148 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.31 % Allowed : 25.16 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.04 (0.20), residues: 1884 helix: 1.36 (0.19), residues: 750 sheet: -1.58 (0.23), residues: 456 loop : -0.28 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 302 TYR 0.016 0.002 TYR A 94 PHE 0.007 0.001 PHE B 313 TRP 0.010 0.002 TRP B 154 HIS 0.011 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00290 (15084) covalent geometry : angle 0.69012 (20472) hydrogen bonds : bond 0.03174 ( 660) hydrogen bonds : angle 4.29491 ( 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 377 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 324 time to evaluate : 0.542 Fit side-chains REVERT: A 26 GLU cc_start: 0.6829 (tp30) cc_final: 0.6624 (tp30) REVERT: A 84 ARG cc_start: 0.7901 (ttp-110) cc_final: 0.7591 (ttp80) REVERT: A 260 ARG cc_start: 0.8105 (mtt180) cc_final: 0.7797 (mtt180) REVERT: B 176 LYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6647 (mttp) REVERT: C 176 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6781 (mttp) REVERT: C 281 MET cc_start: 0.8391 (mtp) cc_final: 0.8095 (mtm) REVERT: D 99 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7922 (ptpt) REVERT: D 176 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6817 (mttp) REVERT: D 281 MET cc_start: 0.8414 (mtp) cc_final: 0.8109 (mtm) REVERT: E 26 GLU cc_start: 0.6984 (tp30) cc_final: 0.6731 (tp30) REVERT: E 78 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7156 (tptp) REVERT: F 5 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7533 (mptm) REVERT: F 78 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7133 (tptp) outliers start: 53 outliers final: 32 residues processed: 356 average time/residue: 0.5513 time to fit residues: 216.6392 Evaluate side-chains 357 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 318 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 263 ASN 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 176 LYS 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 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 47 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 102 LYS 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 78 LYS Chi-restraints excluded: chain E residue 140 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 154 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 185 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 133 GLN A 263 ASN A 283 HIS B 38 GLN B 133 GLN B 231 HIS B 283 HIS C 263 ASN D 12 HIS E 283 HIS 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 = 0.5008 r_free = 0.5008 target = 0.267704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.253127 restraints weight = 13499.815| |-----------------------------------------------------------------------------| r_work (start): 0.4918 rms_B_bonded: 0.81 r_work: 0.4870 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.4785 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.4785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15084 Z= 0.143 Angle : 0.708 8.041 20472 Z= 0.328 Chirality : 0.048 0.171 2406 Planarity : 0.003 0.036 2568 Dihedral : 13.963 172.841 2148 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.50 % Allowed : 25.34 % Favored : 71.16 % 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: 1.25 (0.19), residues: 750 sheet: -1.60 (0.23), residues: 456 loop : -0.32 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 302 TYR 0.018 0.002 TYR F 94 PHE 0.007 0.001 PHE E 313 TRP 0.009 0.002 TRP B 154 HIS 0.011 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00318 (15084) covalent geometry : angle 0.70756 (20472) hydrogen bonds : bond 0.03298 ( 660) hydrogen bonds : angle 4.35588 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6195.98 seconds wall clock time: 106 minutes 4.76 seconds (6364.76 seconds total)