Starting phenix.real_space_refine on Fri May 16 22:36:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbo_27293/05_2025/8dbo_27293.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbo_27293/05_2025/8dbo_27293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dbo_27293/05_2025/8dbo_27293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbo_27293/05_2025/8dbo_27293.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbo_27293/05_2025/8dbo_27293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbo_27293/05_2025/8dbo_27293.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.347 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14880 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2416 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 2, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 6.19, per 1000 atoms: 0.42 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: 3.71 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 2.22 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: 4.47 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4953 1.34 - 1.46: 1956 1.46 - 1.57: 7989 1.57 - 1.69: 36 1.69 - 1.81: 150 Bond restraints: 15084 Sorted by residual: bond pdb=" C4 ADP A 405 " pdb=" C5 ADP A 405 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C4 ADP B 405 " pdb=" C5 ADP B 405 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.80e+01 ... (remaining 15079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 20094 2.97 - 5.94: 234 5.94 - 8.91: 100 8.91 - 11.88: 32 11.88 - 14.85: 12 Bond angle restraints: 20472 Sorted by residual: angle pdb=" PA ADP F 403 " pdb=" O3A ADP F 403 " pdb=" PB ADP F 403 " ideal model delta sigma weight residual 120.50 135.35 -14.85 3.00e+00 1.11e-01 2.45e+01 angle pdb=" PA ADP E 403 " pdb=" O3A ADP E 403 " pdb=" PB ADP E 403 " ideal model delta sigma weight residual 120.50 135.35 -14.85 3.00e+00 1.11e-01 2.45e+01 angle pdb=" PA ADP C 403 " pdb=" O3A ADP C 403 " pdb=" PB ADP C 403 " ideal model delta sigma weight residual 120.50 135.34 -14.84 3.00e+00 1.11e-01 2.45e+01 angle pdb=" PA ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PB ADP B 402 " ideal model delta sigma weight residual 120.50 135.32 -14.82 3.00e+00 1.11e-01 2.44e+01 angle pdb=" PA ADP D 402 " pdb=" O3A ADP D 402 " pdb=" PB ADP D 402 " ideal model delta sigma weight residual 120.50 135.31 -14.81 3.00e+00 1.11e-01 2.44e+01 ... (remaining 20467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 8826 34.00 - 67.99: 297 67.99 - 101.99: 33 101.99 - 135.99: 15 135.99 - 169.99: 9 Dihedral angle restraints: 9180 sinusoidal: 3672 harmonic: 5508 Sorted by residual: dihedral pdb=" O2A ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PA ADP B 402 " pdb=" PB ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 109.99 -169.99 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP D 402 " pdb=" O3A ADP D 402 " pdb=" PA ADP D 402 " pdb=" PB ADP D 402 " ideal model delta sinusoidal sigma weight residual -60.00 109.97 -169.97 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP F 403 " pdb=" O3A ADP F 403 " pdb=" PA ADP F 403 " pdb=" PB ADP F 403 " ideal model delta sinusoidal sigma weight residual -60.00 109.95 -169.95 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 9177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1508 0.041 - 0.082: 600 0.082 - 0.123: 240 0.123 - 0.163: 46 0.163 - 0.204: 12 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CA VAL C 151 " pdb=" N VAL C 151 " pdb=" C VAL C 151 " pdb=" CB VAL C 151 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL B 151 " pdb=" N VAL B 151 " pdb=" C VAL B 151 " pdb=" CB VAL B 151 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL E 151 " pdb=" N VAL E 151 " pdb=" C VAL E 151 " pdb=" CB VAL E 151 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2403 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 65 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.47e+00 pdb=" CG ASP C 65 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP C 65 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP C 65 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP B 402 " 0.019 2.00e-02 2.50e+03 9.40e-03 2.43e+00 pdb=" C2 ADP B 402 " -0.005 2.00e-02 2.50e+03 pdb=" C4 ADP B 402 " -0.002 2.00e-02 2.50e+03 pdb=" C5 ADP B 402 " -0.003 2.00e-02 2.50e+03 pdb=" C6 ADP B 402 " -0.000 2.00e-02 2.50e+03 pdb=" C8 ADP B 402 " -0.009 2.00e-02 2.50e+03 pdb=" N1 ADP B 402 " -0.005 2.00e-02 2.50e+03 pdb=" N3 ADP B 402 " -0.003 2.00e-02 2.50e+03 pdb=" N6 ADP B 402 " 0.019 2.00e-02 2.50e+03 pdb=" N7 ADP B 402 " -0.009 2.00e-02 2.50e+03 pdb=" N9 ADP B 402 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 65 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" CG ASP A 65 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP A 65 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 65 " -0.010 2.00e-02 2.50e+03 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 96 2.47 - 3.08: 10623 3.08 - 3.69: 24138 3.69 - 4.29: 37203 4.29 - 4.90: 59181 Nonbonded interactions: 131241 Sorted by model distance: nonbonded pdb="MG MG B 403 " pdb=" O HOH B 503 " model vdw 1.866 2.170 nonbonded pdb="MG MG F 404 " pdb=" O HOH F 503 " model vdw 1.866 2.170 nonbonded pdb="MG MG A 403 " pdb=" O HOH A 503 " model vdw 1.866 2.170 nonbonded pdb="MG MG E 404 " pdb=" O HOH E 503 " model vdw 1.866 2.170 nonbonded pdb="MG MG D 403 " pdb=" O HOH D 503 " model vdw 1.867 2.170 ... (remaining 131236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 317 or resid 404)) selection = (chain 'B' and (resid 2 through 317 or resid 404)) selection = (chain 'C' and (resid 2 through 317 or resid 404)) selection = (chain 'D' and (resid 2 through 317 or resid 404)) selection = (chain 'E' and (resid 2 through 317 or resid 404)) selection = (chain 'F' and (resid 2 through 317 or resid 404)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.450 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.040 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:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.770 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.19), 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 TRP 0.011 0.003 TRP E 162 HIS 0.007 0.001 HIS F 12 PHE 0.013 0.002 PHE F 138 TYR 0.011 0.002 TYR E 311 ARG 0.008 0.001 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.14915 ( 660) hydrogen bonds : angle 5.25072 ( 1800) covalent geometry : bond 0.00703 (15084) covalent geometry : angle 1.02227 (20472) *********************** 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 : 1.595 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: 0.7458 (mmmt) REVERT: B 280 LYS cc_start: 0.7870 (mmtm) cc_final: 0.7539 (mmmt) REVERT: C 191 LEU cc_start: 0.7852 (tt) cc_final: 0.7590 (mm) REVERT: C 280 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7680 (mmmt) REVERT: D 191 LEU cc_start: 0.7854 (tt) cc_final: 0.7601 (mm) REVERT: D 280 LYS cc_start: 0.7943 (mmtm) cc_final: 0.7698 (mmmt) REVERT: E 280 LYS cc_start: 0.7873 (mmtm) cc_final: 0.7543 (mmmt) REVERT: F 280 LYS cc_start: 0.7829 (mmtm) cc_final: 0.7464 (mmmt) outliers start: 54 outliers final: 11 residues processed: 591 average time/residue: 1.2986 time to fit residues: 837.7877 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 : 1.501 ------------------------------------------------------------------------------- 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 157 optimal weight: 0.5980 chunk 140 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN B 263 ASN C 133 GLN C 283 HIS D 133 GLN D 283 HIS E 97 GLN E 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5060 r_free = 0.5060 target = 0.271749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.257905 restraints weight = 13364.731| |-----------------------------------------------------------------------------| r_work (start): 0.4956 rms_B_bonded: 0.88 r_work: 0.4905 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.4818 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.4818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15084 Z= 0.137 Angle : 0.687 8.715 20472 Z= 0.321 Chirality : 0.048 0.154 2406 Planarity : 0.004 0.027 2568 Dihedral : 16.114 166.865 2170 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.00 % Allowed : 22.72 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.19), residues: 1884 helix: 1.42 (0.19), residues: 756 sheet: -0.77 (0.23), residues: 492 loop : -0.31 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 154 HIS 0.008 0.001 HIS C 12 PHE 0.011 0.002 PHE A 313 TYR 0.011 0.002 TYR E 311 ARG 0.004 0.001 ARG C 184 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 660) hydrogen bonds : angle 4.54840 ( 1800) covalent geometry : bond 0.00299 (15084) covalent geometry : angle 0.68710 (20472) *********************** 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 417 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 353 time to evaluate : 1.539 Fit side-chains REVERT: A 78 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.6777 (ttmt) REVERT: F 78 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6705 (ttmt) REVERT: F 288 GLN cc_start: 0.7943 (mt0) cc_final: 0.7150 (mt0) outliers start: 64 outliers final: 31 residues processed: 395 average time/residue: 1.1008 time to fit residues: 482.8336 Evaluate side-chains 374 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 341 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 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 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 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 120 optimal weight: 0.8980 chunk 185 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 34 optimal weight: 0.0770 chunk 145 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 25 optimal weight: 0.0570 overall best weight: 0.5256 ------------------------------------------------------------------------------- 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 283 HIS E 133 GLN E 263 ASN E 283 HIS F 133 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.273038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.258591 restraints weight = 13481.968| |-----------------------------------------------------------------------------| r_work (start): 0.4968 rms_B_bonded: 0.83 r_work: 0.4882 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.4786 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.4786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15084 Z= 0.120 Angle : 0.656 8.137 20472 Z= 0.300 Chirality : 0.047 0.160 2406 Planarity : 0.003 0.022 2568 Dihedral : 15.765 174.212 2152 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.31 % Allowed : 23.22 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1884 helix: 1.56 (0.19), residues: 750 sheet: -0.84 (0.23), residues: 492 loop : -0.18 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 154 HIS 0.003 0.001 HIS A 12 PHE 0.009 0.001 PHE B 313 TYR 0.007 0.001 TYR E 245 ARG 0.003 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 660) hydrogen bonds : angle 4.34049 ( 1800) covalent geometry : bond 0.00261 (15084) covalent geometry : angle 0.65608 (20472) *********************** 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 401 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 332 time to evaluate : 1.526 Fit side-chains REVERT: A 302 ARG cc_start: 0.7089 (mpt180) cc_final: 0.6818 (mpt180) REVERT: C 176 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6877 (mttp) REVERT: D 176 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6860 (mttp) REVERT: F 302 ARG cc_start: 0.7119 (mpt180) cc_final: 0.6853 (mpt180) outliers start: 69 outliers final: 33 residues processed: 378 average time/residue: 1.1203 time to fit residues: 470.0248 Evaluate side-chains 359 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 324 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain 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 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 248 LEU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 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 248 LEU 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 62 GLU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 176 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 142 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 12 HIS C 283 HIS D 12 HIS D 283 HIS E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN F 283 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.268215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.253897 restraints weight = 13225.576| |-----------------------------------------------------------------------------| r_work (start): 0.4923 rms_B_bonded: 0.87 r_work: 0.4875 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.4787 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.4787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3416 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= 0.141 Angle : 0.674 8.408 20472 Z= 0.309 Chirality : 0.047 0.171 2406 Planarity : 0.003 0.024 2568 Dihedral : 15.512 176.081 2150 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.56 % Allowed : 23.22 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 1884 helix: 1.40 (0.19), residues: 750 sheet: -1.17 (0.23), residues: 456 loop : -0.22 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 154 HIS 0.003 0.001 HIS C 123 PHE 0.008 0.002 PHE C 313 TYR 0.009 0.001 TYR D 54 ARG 0.007 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 660) hydrogen bonds : angle 4.35477 ( 1800) covalent geometry : bond 0.00308 (15084) covalent geometry : angle 0.67372 (20472) *********************** 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 427 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 354 time to evaluate : 1.570 Fit side-chains REVERT: A 78 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7103 (tptp) REVERT: A 302 ARG cc_start: 0.7139 (mpt180) cc_final: 0.6917 (mpt180) REVERT: B 231 HIS cc_start: 0.7447 (m90) cc_final: 0.7225 (m90) REVERT: C 176 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6916 (mttp) REVERT: D 176 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6832 (mttp) REVERT: E 231 HIS cc_start: 0.7454 (m90) cc_final: 0.7243 (m90) REVERT: F 78 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7131 (tptp) outliers start: 73 outliers final: 33 residues processed: 394 average time/residue: 1.1876 time to fit residues: 518.1381 Evaluate side-chains 366 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 329 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 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 301 ARG Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 0.0170 chunk 41 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 167 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.267126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.252177 restraints weight = 13543.550| |-----------------------------------------------------------------------------| r_work (start): 0.4902 rms_B_bonded: 0.84 r_work: 0.4850 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.4754 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.4754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15084 Z= 0.169 Angle : 0.701 8.650 20472 Z= 0.325 Chirality : 0.049 0.180 2406 Planarity : 0.003 0.027 2568 Dihedral : 15.236 171.593 2150 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.93 % Allowed : 23.16 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 1884 helix: 1.23 (0.19), residues: 750 sheet: -1.44 (0.22), residues: 456 loop : -0.24 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 154 HIS 0.003 0.001 HIS A 123 PHE 0.009 0.002 PHE A 253 TYR 0.012 0.002 TYR D 54 ARG 0.005 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 660) hydrogen bonds : angle 4.48570 ( 1800) covalent geometry : bond 0.00373 (15084) covalent geometry : angle 0.70110 (20472) *********************** 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 416 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 337 time to evaluate : 1.642 Fit side-chains REVERT: B 231 HIS cc_start: 0.7505 (m90) cc_final: 0.7269 (m90) REVERT: C 73 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7720 (ttm) REVERT: C 176 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6906 (mttp) REVERT: C 302 ARG cc_start: 0.7173 (mpt180) cc_final: 0.6929 (mpt180) REVERT: D 73 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7695 (ttm) REVERT: D 176 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6883 (mttp) REVERT: E 231 HIS cc_start: 0.7505 (m90) cc_final: 0.7279 (m90) outliers start: 79 outliers final: 36 residues processed: 384 average time/residue: 1.1025 time to fit residues: 470.4249 Evaluate side-chains 374 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 334 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 249 THR Chi-restraints excluded: chain B residue 58 SER 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 248 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 127 MET Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 127 MET 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 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 248 LEU Chi-restraints excluded: chain E residue 263 ASN Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 284 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN A 263 ASN B 75 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN D 75 ASN D 133 GLN E 75 ASN E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 133 GLN F 283 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.263415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.251184 restraints weight = 13676.581| |-----------------------------------------------------------------------------| r_work (start): 0.4890 rms_B_bonded: 0.69 r_work: 0.4853 rms_B_bonded: 0.83 restraints_weight: 0.5000 r_work: 0.4768 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work (final): 0.4768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15084 Z= 0.281 Angle : 0.807 9.022 20472 Z= 0.388 Chirality : 0.053 0.187 2406 Planarity : 0.005 0.038 2568 Dihedral : 15.068 152.697 2150 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.18 % Allowed : 22.47 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.19), residues: 1884 helix: 0.33 (0.19), residues: 792 sheet: -1.71 (0.22), residues: 456 loop : -0.56 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 154 HIS 0.004 0.001 HIS F 283 PHE 0.016 0.003 PHE F 253 TYR 0.019 0.003 TYR D 54 ARG 0.005 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 660) hydrogen bonds : angle 4.76181 ( 1800) covalent geometry : bond 0.00624 (15084) covalent geometry : angle 0.80734 (20472) *********************** 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 422 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 339 time to evaluate : 1.547 Fit side-chains REVERT: A 5 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7784 (mptm) REVERT: A 262 ASN cc_start: 0.7444 (m-40) cc_final: 0.7103 (m-40) REVERT: C 73 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7590 (ttm) REVERT: C 176 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6814 (mttp) REVERT: D 73 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7609 (ttm) REVERT: D 176 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6772 (mttp) REVERT: D 302 ARG cc_start: 0.7081 (mpt180) cc_final: 0.6817 (mpt180) REVERT: E 231 HIS cc_start: 0.7493 (m90) cc_final: 0.7289 (m90) REVERT: F 78 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7161 (tptp) outliers start: 83 outliers final: 46 residues processed: 383 average time/residue: 1.1574 time to fit residues: 489.8340 Evaluate side-chains 381 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 329 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 192 ILE 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 127 MET 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 237 LEU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 127 MET 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 237 LEU Chi-restraints excluded: chain D residue 284 CYS Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 192 ILE 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 248 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 151 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 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 75 ASN A 158 ASN A 263 ASN A 283 HIS B 75 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN 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 = 0.267492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.251856 restraints weight = 13395.841| |-----------------------------------------------------------------------------| r_work (start): 0.4912 rms_B_bonded: 0.85 r_work: 0.4790 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.4684 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.4684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15084 Z= 0.144 Angle : 0.702 8.472 20472 Z= 0.326 Chirality : 0.048 0.174 2406 Planarity : 0.004 0.032 2568 Dihedral : 14.748 162.661 2150 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.37 % Allowed : 23.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.19), residues: 1884 helix: 0.78 (0.19), residues: 792 sheet: -1.71 (0.22), residues: 456 loop : -0.44 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 154 HIS 0.003 0.001 HIS A 123 PHE 0.007 0.001 PHE C 138 TYR 0.010 0.002 TYR D 54 ARG 0.006 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 660) hydrogen bonds : angle 4.45985 ( 1800) covalent geometry : bond 0.00319 (15084) covalent geometry : angle 0.70227 (20472) *********************** 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 408 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 338 time to evaluate : 1.730 Fit side-chains REVERT: A 5 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7532 (mptm) REVERT: B 221 ASP cc_start: 0.8232 (p0) cc_final: 0.8007 (p0) REVERT: C 176 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6965 (mttp) REVERT: C 281 MET cc_start: 0.8414 (mtp) cc_final: 0.8006 (mtm) REVERT: D 176 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6946 (mttp) REVERT: D 302 ARG cc_start: 0.7165 (mpt180) cc_final: 0.6908 (mpt180) REVERT: E 46 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7218 (mt-10) REVERT: E 221 ASP cc_start: 0.8268 (p0) cc_final: 0.8053 (p0) REVERT: E 231 HIS cc_start: 0.7601 (m90) cc_final: 0.7393 (m90) REVERT: F 78 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7131 (tptp) REVERT: F 302 ARG cc_start: 0.7481 (mpt180) cc_final: 0.7199 (mpt180) outliers start: 70 outliers final: 41 residues processed: 383 average time/residue: 1.1681 time to fit residues: 494.9039 Evaluate side-chains 375 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 330 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 115 MET 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 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 284 CYS 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 85 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 127 MET 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 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 284 CYS Chi-restraints excluded: chain E residue 301 ARG 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 284 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 85 optimal weight: 3.9990 chunk 165 optimal weight: 0.3980 chunk 168 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 133 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN A 158 ASN A 263 ASN A 283 HIS B 75 ASN B 97 GLN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN E 97 GLN E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 158 ASN F 283 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.265534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.250317 restraints weight = 13522.884| |-----------------------------------------------------------------------------| r_work (start): 0.4893 rms_B_bonded: 0.83 r_work: 0.4828 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.4735 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.4735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15084 Z= 0.168 Angle : 0.720 8.545 20472 Z= 0.336 Chirality : 0.048 0.176 2406 Planarity : 0.004 0.032 2568 Dihedral : 14.425 158.253 2148 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.49 % Allowed : 23.60 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.19), residues: 1884 helix: 0.79 (0.19), residues: 792 sheet: -1.73 (0.22), residues: 456 loop : -0.51 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 154 HIS 0.003 0.001 HIS D 123 PHE 0.009 0.002 PHE B 313 TYR 0.014 0.002 TYR C 54 ARG 0.006 0.001 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 660) hydrogen bonds : angle 4.47159 ( 1800) covalent geometry : bond 0.00373 (15084) covalent geometry : angle 0.71962 (20472) *********************** 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 410 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 338 time to evaluate : 1.610 Fit side-chains REVERT: A 5 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7527 (mptm) REVERT: C 73 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7796 (ttm) REVERT: C 176 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6840 (mttp) REVERT: D 73 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7859 (ttm) REVERT: D 176 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6839 (mttp) REVERT: D 281 MET cc_start: 0.8460 (mtp) cc_final: 0.8016 (mtm) REVERT: D 302 ARG cc_start: 0.7153 (mpt180) cc_final: 0.6911 (mpt180) REVERT: E 26 GLU cc_start: 0.7099 (tp30) cc_final: 0.6840 (tp30) REVERT: E 46 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7127 (mt-10) REVERT: F 78 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7155 (tptp) outliers start: 72 outliers final: 43 residues processed: 380 average time/residue: 1.2480 time to fit residues: 522.7855 Evaluate side-chains 369 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 320 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 115 MET 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 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 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 127 MET 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 C residue 301 ARG Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 127 MET 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 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 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 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 248 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 139 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 68 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN A 263 ASN A 283 HIS B 75 ASN B 158 ASN B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN E 97 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.263867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.248735 restraints weight = 12831.948| |-----------------------------------------------------------------------------| r_work (start): 0.4897 rms_B_bonded: 0.95 r_work: 0.4781 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.4669 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.4669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15084 Z= 0.153 Angle : 0.714 8.448 20472 Z= 0.332 Chirality : 0.048 0.175 2406 Planarity : 0.004 0.043 2568 Dihedral : 14.235 160.621 2148 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.56 % Allowed : 24.47 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1884 helix: 1.14 (0.19), residues: 750 sheet: -1.73 (0.22), residues: 456 loop : -0.29 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 154 HIS 0.003 0.001 HIS F 283 PHE 0.006 0.001 PHE A 138 TYR 0.016 0.002 TYR A 94 ARG 0.009 0.001 ARG E 302 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 660) hydrogen bonds : angle 4.43283 ( 1800) covalent geometry : bond 0.00340 (15084) covalent geometry : angle 0.71374 (20472) *********************** 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 382 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 325 time to evaluate : 1.753 Fit side-chains REVERT: A 5 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7476 (mptm) REVERT: B 302 ARG cc_start: 0.7061 (mpt180) cc_final: 0.6787 (mmt180) REVERT: C 176 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6942 (mttp) REVERT: C 281 MET cc_start: 0.8425 (mtp) cc_final: 0.7985 (mtm) REVERT: D 176 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6957 (mttp) REVERT: D 281 MET cc_start: 0.8421 (mtp) cc_final: 0.7980 (mtm) REVERT: D 302 ARG cc_start: 0.7200 (mpt180) cc_final: 0.6914 (mpt180) REVERT: E 26 GLU cc_start: 0.7238 (tp30) cc_final: 0.6990 (tp30) REVERT: E 46 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7196 (mt-10) REVERT: F 78 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7139 (tptp) outliers start: 57 outliers final: 42 residues processed: 362 average time/residue: 1.1572 time to fit residues: 463.7417 Evaluate side-chains 368 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 322 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 115 MET 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 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 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 102 LYS Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 127 MET 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 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 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 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 284 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 77 optimal weight: 3.9990 chunk 78 optimal weight: 0.0970 chunk 149 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 50 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 75 ASN B 97 GLN B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.269036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.254080 restraints weight = 13623.585| |-----------------------------------------------------------------------------| r_work (start): 0.4927 rms_B_bonded: 0.83 r_work: 0.4882 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.4799 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.4799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4102 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= 0.126 Angle : 0.693 8.055 20472 Z= 0.319 Chirality : 0.047 0.166 2406 Planarity : 0.003 0.043 2568 Dihedral : 13.947 167.614 2148 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.43 % Allowed : 24.72 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1884 helix: 1.34 (0.19), residues: 750 sheet: -1.66 (0.23), residues: 456 loop : -0.28 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 154 HIS 0.004 0.001 HIS F 283 PHE 0.007 0.001 PHE B 313 TYR 0.021 0.002 TYR A 94 ARG 0.010 0.001 ARG C 302 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 660) hydrogen bonds : angle 4.33579 ( 1800) covalent geometry : bond 0.00281 (15084) covalent geometry : angle 0.69293 (20472) ********************** 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 385 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 330 time to evaluate : 1.481 Fit side-chains REVERT: A 5 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7470 (mptm) REVERT: C 176 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6783 (mttp) REVERT: C 281 MET cc_start: 0.8351 (mtp) cc_final: 0.7962 (mtm) REVERT: D 73 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7729 (ttm) REVERT: D 176 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6781 (mttp) REVERT: D 281 MET cc_start: 0.8360 (mtp) cc_final: 0.7983 (mtm) REVERT: E 26 GLU cc_start: 0.6954 (tp30) cc_final: 0.6750 (tp30) REVERT: F 78 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7131 (tptp) outliers start: 55 outliers final: 35 residues processed: 363 average time/residue: 1.1727 time to fit residues: 470.8010 Evaluate side-chains 361 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 321 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 47 SER 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 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 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 58 SER Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 85 VAL 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 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 47 SER Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 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 75 ASN A 263 ASN A 283 HIS B 75 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS B 283 HIS C 12 HIS C 75 ASN E 75 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5007 r_free = 0.5007 target = 0.267756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.252780 restraints weight = 13533.695| |-----------------------------------------------------------------------------| r_work (start): 0.4916 rms_B_bonded: 0.83 r_work: 0.4871 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.4786 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.4786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15084 Z= 0.144 Angle : 0.711 8.189 20472 Z= 0.331 Chirality : 0.048 0.172 2406 Planarity : 0.004 0.038 2568 Dihedral : 13.828 167.192 2148 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.06 % Allowed : 25.53 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1884 helix: 1.28 (0.19), residues: 750 sheet: -1.66 (0.23), residues: 456 loop : -0.30 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 154 HIS 0.011 0.001 HIS B 231 PHE 0.006 0.001 PHE B 253 TYR 0.022 0.002 TYR A 94 ARG 0.010 0.001 ARG C 302 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 660) hydrogen bonds : angle 4.37115 ( 1800) covalent geometry : bond 0.00325 (15084) covalent geometry : angle 0.71105 (20472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13087.75 seconds wall clock time: 225 minutes 35.01 seconds (13535.01 seconds total)