Starting phenix.real_space_refine on Thu Aug 6 12:59:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qna_53241/08_2026/9qna_53241.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qna_53241/08_2026/9qna_53241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qna_53241/08_2026/9qna_53241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qna_53241/08_2026/9qna_53241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qna_53241/08_2026/9qna_53241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qna_53241/08_2026/9qna_53241.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.121 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: 7 Type Number sf(0) Gaussians K 6 8.98 5 P 41 5.49 5 Mg 6 5.21 5 S 78 5.16 5 C 9217 2.51 5 N 2646 2.21 5 O 2937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14931 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "C" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "E" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "G" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "I" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "K" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "Z" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.65, per 1000 atoms: 0.24 Number of scatterers: 14931 At special positions: 0 Unit cell: (117.72, 116.64, 164.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 6 19.00 S 78 16.00 P 41 15.00 Mg 6 11.99 O 2937 8.00 N 2646 7.00 C 9217 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: 0.87 Conformation dependent library (CDL) restraints added in 649.3 milliseconds 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3406 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 18 sheets defined 52.5% alpha, 16.3% beta 0 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.760A pdb=" N GLU A 29 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 25 through 31' Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 89 through 98 Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.751A pdb=" N ILE A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 169 through 179 Processing helix chain 'A' and resid 181 through 188 removed outlier: 3.664A pdb=" N ASN A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 214 removed outlier: 3.571A pdb=" N GLN A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.863A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.896A pdb=" N GLU C 29 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 25 through 30' Processing helix chain 'C' and resid 35 through 45 Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 67 through 82 Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.802A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 188 Processing helix chain 'C' and resid 196 through 212 removed outlier: 4.236A pdb=" N VAL C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 232 removed outlier: 4.338A pdb=" N THR C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 260 Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.811A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 32 removed outlier: 3.882A pdb=" N GLY E 32 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 45 Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 56 through 63 removed outlier: 3.551A pdb=" N LEU E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 82 Processing helix chain 'E' and resid 89 through 97 Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 132 through 144 Processing helix chain 'E' and resid 145 through 146 No H-bonds generated for 'chain 'E' and resid 145 through 146' Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 179 removed outlier: 4.004A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'E' and resid 196 through 211 Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.589A pdb=" N TYR E 232 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 260 Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'G' and resid 25 through 30 removed outlier: 3.856A pdb=" N GLU G 29 " --> pdb=" O ILE G 25 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN G 30 " --> pdb=" O SER G 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 25 through 30' Processing helix chain 'G' and resid 34 through 45 Processing helix chain 'G' and resid 48 through 55 Processing helix chain 'G' and resid 56 through 63 removed outlier: 3.886A pdb=" N ILE G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 82 removed outlier: 3.738A pdb=" N LYS G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 97 Processing helix chain 'G' and resid 106 through 114 Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 145 through 146 No H-bonds generated for 'chain 'G' and resid 145 through 146' Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.927A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 188 Processing helix chain 'G' and resid 196 through 212 removed outlier: 4.009A pdb=" N VAL G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 232 removed outlier: 3.938A pdb=" N ARG G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR G 230 " --> pdb=" O ALA G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 260 Processing helix chain 'G' and resid 288 through 296 removed outlier: 3.880A pdb=" N ILE G 292 " --> pdb=" O GLY G 288 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA G 293 " --> pdb=" O GLY G 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 32 removed outlier: 3.749A pdb=" N GLN I 30 " --> pdb=" O ARG I 27 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY I 32 " --> pdb=" O GLU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 45 Processing helix chain 'I' and resid 48 through 54 Processing helix chain 'I' and resid 56 through 63 removed outlier: 4.116A pdb=" N ILE I 63 " --> pdb=" O GLU I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 Processing helix chain 'I' and resid 88 through 98 removed outlier: 3.563A pdb=" N PHE I 92 " --> pdb=" O THR I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 113 Processing helix chain 'I' and resid 132 through 144 Processing helix chain 'I' and resid 145 through 146 No H-bonds generated for 'chain 'I' and resid 145 through 146' Processing helix chain 'I' and resid 147 through 151 removed outlier: 3.544A pdb=" N GLY I 151 " --> pdb=" O ILE I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 178 removed outlier: 3.866A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 188 Processing helix chain 'I' and resid 196 through 214 removed outlier: 3.995A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN I 206 " --> pdb=" O GLN I 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU I 213 " --> pdb=" O ALA I 209 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER I 214 " --> pdb=" O MET I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 232 Processing helix chain 'I' and resid 237 through 260 Processing helix chain 'I' and resid 289 through 296 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.781A pdb=" N GLY K 32 " --> pdb=" O GLU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 45 Processing helix chain 'K' and resid 48 through 55 Processing helix chain 'K' and resid 56 through 62 removed outlier: 3.516A pdb=" N ASN K 62 " --> pdb=" O LYS K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 Processing helix chain 'K' and resid 88 through 97 Processing helix chain 'K' and resid 106 through 114 Processing helix chain 'K' and resid 133 through 144 Processing helix chain 'K' and resid 145 through 146 No H-bonds generated for 'chain 'K' and resid 145 through 146' Processing helix chain 'K' and resid 147 through 151 Processing helix chain 'K' and resid 167 through 179 removed outlier: 3.984A pdb=" N LEU K 171 " --> pdb=" O ARG K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 187 Processing helix chain 'K' and resid 196 through 212 removed outlier: 3.948A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR K 205 " --> pdb=" O THR K 201 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN K 206 " --> pdb=" O GLN K 202 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL K 212 " --> pdb=" O SER K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 232 removed outlier: 3.879A pdb=" N ARG K 229 " --> pdb=" O THR K 225 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR K 230 " --> pdb=" O ALA K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 288 through 296 removed outlier: 3.942A pdb=" N ILE K 292 " --> pdb=" O GLY K 288 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA K 293 " --> pdb=" O GLY K 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.965A pdb=" N ALA C 157 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ALA C 192 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TYR C 159 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS C 156 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C 218 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 220 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR C 123 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASN C 267 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET C 125 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG C 299 " --> pdb=" O TYR C 315 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 193 removed outlier: 5.577A pdb=" N LYS A 156 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 218 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 264 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASP A 222 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR A 266 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 127 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG A 299 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 88 removed outlier: 7.427A pdb=" N LYS E 156 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU E 219 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N MET E 158 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL E 221 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ILE E 160 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA E 217 " --> pdb=" O ALA E 262 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL E 264 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU E 219 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR E 266 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL E 221 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR E 123 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASN E 267 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET E 125 " --> pdb=" O ASN E 267 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE E 122 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU E 300 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU E 124 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU E 302 " --> pdb=" O GLU E 124 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE E 126 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N LYS E 304 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG E 299 " --> pdb=" O TYR E 315 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY E 333 " --> pdb=" O ASN E 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 269 through 271 Processing sheet with id=AA7, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.560A pdb=" N ALA G 157 " --> pdb=" O ALA G 190 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ALA G 192 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR G 159 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LYS G 156 " --> pdb=" O TYR G 216 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU G 218 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP G 222 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA G 217 " --> pdb=" O ALA G 262 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL G 264 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU G 219 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N THR G 266 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL G 221 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY G 127 " --> pdb=" O ASN G 267 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE G 122 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LEU G 300 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU G 124 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU G 302 " --> pdb=" O GLU G 124 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE G 126 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LYS G 304 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG G 299 " --> pdb=" O TYR G 315 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY G 333 " --> pdb=" O ASN G 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AB1, first strand: chain 'G' and resid 87 through 88 removed outlier: 6.278A pdb=" N THR I 123 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ASN I 267 " --> pdb=" O THR I 123 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N MET I 125 " --> pdb=" O ASN I 267 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE I 122 " --> pdb=" O THR I 298 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU I 300 " --> pdb=" O ILE I 122 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU I 124 " --> pdb=" O LEU I 300 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU I 302 " --> pdb=" O GLU I 124 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE I 126 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N LYS I 304 " --> pdb=" O PHE I 126 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AB3, first strand: chain 'G' and resid 269 through 271 Processing sheet with id=AB4, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AB5, first strand: chain 'I' and resid 269 through 271 Processing sheet with id=AB6, first strand: chain 'K' and resid 101 through 102 Processing sheet with id=AB7, first strand: chain 'K' and resid 263 through 267 removed outlier: 6.672A pdb=" N ILE K 122 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU K 300 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU K 124 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU K 302 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE K 126 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N LYS K 304 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG K 299 " --> pdb=" O TYR K 315 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY K 333 " --> pdb=" O ASN K 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 191 through 193 removed outlier: 8.469A pdb=" N ALA K 192 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR K 159 " --> pdb=" O ALA K 192 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LYS K 156 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU K 218 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE K 220 " --> pdb=" O MET K 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 269 through 271 725 hydrogen bonds defined for protein. 2079 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5002 1.34 - 1.46: 2889 1.46 - 1.58: 7098 1.58 - 1.69: 74 1.69 - 1.81: 126 Bond restraints: 15189 Sorted by residual: bond pdb=" C3' DC Z 19 " pdb=" C2' DC Z 19 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.40e+00 bond pdb=" C3' DC Z 7 " pdb=" C2' DC Z 7 " ideal model delta sigma weight residual 1.516 1.531 -0.015 8.00e-03 1.56e+04 3.34e+00 bond pdb=" C3' DC Z 10 " pdb=" C2' DC Z 10 " ideal model delta sigma weight residual 1.516 1.530 -0.014 8.00e-03 1.56e+04 3.25e+00 bond pdb=" C2' DC Z 19 " pdb=" C1' DC Z 19 " ideal model delta sigma weight residual 1.518 1.536 -0.018 1.00e-02 1.00e+04 3.19e+00 bond pdb=" C1' DC Z 16 " pdb=" N1 DC Z 16 " ideal model delta sigma weight residual 1.468 1.492 -0.024 1.40e-02 5.10e+03 2.93e+00 ... (remaining 15184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 20296 1.42 - 2.84: 271 2.84 - 4.25: 40 4.25 - 5.67: 5 5.67 - 7.09: 2 Bond angle restraints: 20614 Sorted by residual: angle pdb=" O4' DC Z 4 " pdb=" C4' DC Z 4 " pdb=" C3' DC Z 4 " ideal model delta sigma weight residual 106.00 104.45 1.55 6.00e-01 2.78e+00 6.68e+00 angle pdb=" CB GLU A 77 " pdb=" CG GLU A 77 " pdb=" CD GLU A 77 " ideal model delta sigma weight residual 112.60 116.93 -4.33 1.70e+00 3.46e-01 6.47e+00 angle pdb=" O4' DC Z 19 " pdb=" C4' DC Z 19 " pdb=" C3' DC Z 19 " ideal model delta sigma weight residual 106.00 104.51 1.49 6.00e-01 2.78e+00 6.16e+00 angle pdb=" O5' DA Z 15 " pdb=" C5' DA Z 15 " pdb=" C4' DA Z 15 " ideal model delta sigma weight residual 109.40 111.37 -1.97 8.00e-01 1.56e+00 6.08e+00 angle pdb=" O5' DA Z 12 " pdb=" C5' DA Z 12 " pdb=" C4' DA Z 12 " ideal model delta sigma weight residual 109.40 111.36 -1.96 8.00e-01 1.56e+00 6.03e+00 ... (remaining 20609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7781 17.95 - 35.91: 1102 35.91 - 53.86: 351 53.86 - 71.82: 84 71.82 - 89.77: 20 Dihedral angle restraints: 9338 sinusoidal: 4019 harmonic: 5319 Sorted by residual: dihedral pdb=" CA THR A 197 " pdb=" C THR A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA ASP E 184 " pdb=" CB ASP E 184 " pdb=" CG ASP E 184 " pdb=" OD1 ASP E 184 " ideal model delta sinusoidal sigma weight residual -30.00 -87.66 57.66 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CB GLU I 43 " pdb=" CG GLU I 43 " pdb=" CD GLU I 43 " pdb=" OE1 GLU I 43 " ideal model delta sinusoidal sigma weight residual 0.00 89.36 -89.36 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 9335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2027 0.054 - 0.107: 276 0.107 - 0.161: 41 0.161 - 0.214: 0 0.214 - 0.268: 1 Chirality restraints: 2345 Sorted by residual: chirality pdb=" CG LEU E 75 " pdb=" CB LEU E 75 " pdb=" CD1 LEU E 75 " pdb=" CD2 LEU E 75 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB THR A 165 " pdb=" CA THR A 165 " pdb=" OG1 THR A 165 " pdb=" CG2 THR A 165 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CG LEU K 75 " pdb=" CB LEU K 75 " pdb=" CD1 LEU K 75 " pdb=" CD2 LEU K 75 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 2342 not shown) Planarity restraints: 2575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP K 332 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" CG ASP K 332 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASP K 332 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP K 332 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP K 332 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C ASP K 332 " -0.032 2.00e-02 2.50e+03 pdb=" O ASP K 332 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY K 333 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 167 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO A 168 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " -0.019 5.00e-02 4.00e+02 ... (remaining 2572 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.58: 31 2.58 - 3.22: 13170 3.22 - 3.86: 27962 3.86 - 4.50: 38082 4.50 - 5.14: 62754 Nonbonded interactions: 141999 Sorted by model distance: nonbonded pdb=" OG1 THR I 134 " pdb="MG MG I 402 " model vdw 1.940 2.170 nonbonded pdb=" OG1 THR E 134 " pdb="MG MG E 402 " model vdw 1.954 2.170 nonbonded pdb=" OG1 THR A 134 " pdb="MG MG A 402 " model vdw 1.957 2.170 nonbonded pdb=" O1G ATP I 401 " pdb="MG MG I 402 " model vdw 1.965 2.170 nonbonded pdb=" OG1 THR K 134 " pdb="MG MG K 403 " model vdw 1.976 2.170 ... (remaining 141994 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 21 through 401) selection = (chain 'C' and (resid 21 through 273 or resid 283 through 401)) selection = (chain 'E' and (resid 21 through 273 or resid 283 through 401)) selection = (chain 'G' and (resid 21 through 273 or resid 283 through 401)) selection = (chain 'I' and (resid 21 through 273 or resid 283 through 401)) selection = (chain 'K' and (resid 21 through 273 or resid 283 through 401)) } 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: 1.750 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.050 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.002 0.031 15189 Z= 0.148 Angle : 0.429 7.091 20614 Z= 0.250 Chirality : 0.038 0.268 2345 Planarity : 0.003 0.035 2575 Dihedral : 18.633 89.772 5932 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.68 % Favored : 98.26 % Rotamer: Outliers : 0.54 % Allowed : 29.54 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1841 helix: 1.45 (0.19), residues: 837 sheet: 0.96 (0.38), residues: 210 loop : -1.08 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.007 0.001 TYR K 191 PHE 0.014 0.001 PHE I 129 HIS 0.001 0.000 HIS K 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.15 (15189) covalent geometry : angle 0.42883 / 0.25 (20614) hydrogen bonds : bond 0.13699 / 9.12 ( 725) hydrogen bonds : angle 5.83608 / 4.23 ( 2079) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.347 Fit side-chains REVERT: I 87 THR cc_start: 0.8906 (m) cc_final: 0.8634 (p) REVERT: K 285 LYS cc_start: 0.7519 (tppt) cc_final: 0.7269 (tptp) outliers start: 8 outliers final: 8 residues processed: 128 average time/residue: 0.0850 time to fit residues: 17.5938 Evaluate side-chains 131 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 165 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.0370 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.137643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.107559 restraints weight = 22340.146| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.70 r_work: 0.3265 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.0381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15189 Z= 0.106 Angle : 0.408 5.166 20614 Z= 0.226 Chirality : 0.038 0.186 2345 Planarity : 0.003 0.039 2575 Dihedral : 12.178 89.768 2538 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.52 % Favored : 98.42 % Rotamer: Outliers : 3.01 % Allowed : 27.66 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.20), residues: 1841 helix: 1.68 (0.19), residues: 836 sheet: 0.36 (0.35), residues: 270 loop : -0.86 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.007 0.001 TYR K 191 PHE 0.013 0.001 PHE I 129 HIS 0.001 0.000 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (15189) covalent geometry : angle 0.40838 / 0.23 (20614) hydrogen bonds : bond 0.03487 / 2.33 ( 725) hydrogen bonds : angle 4.63212 / 3.30 ( 2079) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7399 (p0) REVERT: E 237 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7524 (pt0) REVERT: I 87 THR cc_start: 0.8870 (m) cc_final: 0.8566 (p) outliers start: 45 outliers final: 29 residues processed: 164 average time/residue: 0.0775 time to fit residues: 20.4905 Evaluate side-chains 149 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 311 ILE Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 101 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.105598 restraints weight = 22670.043| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.76 r_work: 0.3238 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.0558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15189 Z= 0.125 Angle : 0.414 5.051 20614 Z= 0.228 Chirality : 0.038 0.187 2345 Planarity : 0.003 0.039 2575 Dihedral : 12.181 89.827 2532 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.17 % Favored : 97.77 % Rotamer: Outliers : 4.22 % Allowed : 27.06 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.20), residues: 1841 helix: 1.71 (0.19), residues: 836 sheet: 0.28 (0.35), residues: 271 loop : -0.89 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27 TYR 0.008 0.001 TYR I 315 PHE 0.012 0.001 PHE I 129 HIS 0.001 0.000 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (15189) covalent geometry : angle 0.41407 / 0.23 (20614) hydrogen bonds : bond 0.03443 / 2.28 ( 725) hydrogen bonds : angle 4.41044 / 3.14 ( 2079) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 123 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7713 (OUTLIER) cc_final: 0.7417 (p0) REVERT: E 237 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7475 (pt0) REVERT: I 81 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8045 (mt) REVERT: I 87 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8577 (p) REVERT: K 332 ASP cc_start: 0.6686 (t0) cc_final: 0.6393 (t0) outliers start: 63 outliers final: 49 residues processed: 170 average time/residue: 0.0736 time to fit residues: 21.0093 Evaluate side-chains 172 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 119 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 311 ILE Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 21 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 123 optimal weight: 9.9990 chunk 120 optimal weight: 0.5980 chunk 36 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 chunk 149 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.137932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.106941 restraints weight = 22434.636| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.78 r_work: 0.3263 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15189 Z= 0.089 Angle : 0.386 4.782 20614 Z= 0.212 Chirality : 0.038 0.181 2345 Planarity : 0.003 0.038 2575 Dihedral : 12.163 89.929 2532 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.30 % Favored : 98.64 % Rotamer: Outliers : 4.02 % Allowed : 27.06 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.20), residues: 1841 helix: 1.80 (0.19), residues: 835 sheet: 0.37 (0.35), residues: 270 loop : -0.88 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 95 TYR 0.007 0.001 TYR C 205 PHE 0.009 0.001 PHE I 129 HIS 0.001 0.000 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.09 (15189) covalent geometry : angle 0.38582 / 0.21 (20614) hydrogen bonds : bond 0.02796 / 1.86 ( 725) hydrogen bonds : angle 4.18771 / 2.99 ( 2079) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 128 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7413 (p0) REVERT: C 43 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7600 (pt0) REVERT: E 237 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7384 (pt0) REVERT: I 87 THR cc_start: 0.8872 (m) cc_final: 0.8563 (p) outliers start: 60 outliers final: 41 residues processed: 176 average time/residue: 0.0808 time to fit residues: 22.9406 Evaluate side-chains 165 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 34 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.133511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104498 restraints weight = 22044.898| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.51 r_work: 0.3240 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15189 Z= 0.148 Angle : 0.432 5.917 20614 Z= 0.234 Chirality : 0.039 0.181 2345 Planarity : 0.003 0.040 2575 Dihedral : 12.221 89.404 2531 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.88 % Favored : 97.07 % Rotamer: Outliers : 4.82 % Allowed : 26.39 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1841 helix: 1.72 (0.19), residues: 835 sheet: 0.16 (0.34), residues: 282 loop : -0.88 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 27 TYR 0.011 0.001 TYR I 228 PHE 0.012 0.001 PHE I 129 HIS 0.001 0.000 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (15189) covalent geometry : angle 0.43152 / 0.23 (20614) hydrogen bonds : bond 0.03379 / 2.24 ( 725) hydrogen bonds : angle 4.23536 / 3.02 ( 2079) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 125 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7484 (p0) REVERT: E 237 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: I 81 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8099 (mt) REVERT: I 87 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8568 (p) REVERT: K 332 ASP cc_start: 0.6717 (t0) cc_final: 0.6441 (t0) outliers start: 72 outliers final: 50 residues processed: 184 average time/residue: 0.0785 time to fit residues: 23.6281 Evaluate side-chains 177 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 123 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 311 ILE Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain I residue 330 ASN Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 67 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 169 optimal weight: 0.0020 chunk 138 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.131993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.102892 restraints weight = 21992.074| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.49 r_work: 0.3212 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15189 Z= 0.186 Angle : 0.471 5.983 20614 Z= 0.255 Chirality : 0.040 0.184 2345 Planarity : 0.004 0.040 2575 Dihedral : 12.317 89.245 2531 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 5.49 % Allowed : 26.32 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 1841 helix: 1.56 (0.19), residues: 836 sheet: -0.19 (0.33), residues: 292 loop : -0.95 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 177 TYR 0.013 0.002 TYR I 228 PHE 0.013 0.002 PHE I 129 HIS 0.002 0.001 HIS E 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (15189) covalent geometry : angle 0.47062 / 0.25 (20614) hydrogen bonds : bond 0.03778 / 2.49 ( 725) hydrogen bonds : angle 4.31698 / 3.07 ( 2079) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 122 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7371 (p0) REVERT: C 96 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7832 (ttm-80) REVERT: E 237 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7493 (pt0) REVERT: I 81 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8124 (mt) outliers start: 82 outliers final: 61 residues processed: 189 average time/residue: 0.0860 time to fit residues: 26.5617 Evaluate side-chains 183 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 118 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 311 ILE Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain I residue 330 ASN Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 23 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.135345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.103236 restraints weight = 22612.961| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.76 r_work: 0.3192 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15189 Z= 0.196 Angle : 0.484 6.162 20614 Z= 0.261 Chirality : 0.041 0.184 2345 Planarity : 0.004 0.040 2575 Dihedral : 12.383 88.868 2531 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.26 % Favored : 96.69 % Rotamer: Outliers : 5.29 % Allowed : 26.12 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.20), residues: 1841 helix: 1.46 (0.19), residues: 836 sheet: -0.31 (0.33), residues: 291 loop : -1.00 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 193 TYR 0.013 0.002 TYR I 228 PHE 0.013 0.002 PHE I 129 HIS 0.002 0.001 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (15189) covalent geometry : angle 0.48358 / 0.26 (20614) hydrogen bonds : bond 0.03846 / 2.54 ( 725) hydrogen bonds : angle 4.37363 / 3.12 ( 2079) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 120 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7536 (OUTLIER) cc_final: 0.7220 (p0) REVERT: C 96 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7777 (ttm-80) REVERT: E 237 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7553 (pt0) REVERT: G 184 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8146 (m-30) REVERT: I 81 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8051 (mt) REVERT: K 332 ASP cc_start: 0.6964 (t0) cc_final: 0.6750 (t0) outliers start: 79 outliers final: 65 residues processed: 184 average time/residue: 0.0901 time to fit residues: 26.8727 Evaluate side-chains 189 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 119 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 311 ILE Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain I residue 330 ASN Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 67 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 187 optimal weight: 20.0000 chunk 133 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.130577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.098016 restraints weight = 22858.126| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.91 r_work: 0.3118 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 15189 Z= 0.283 Angle : 0.570 7.145 20614 Z= 0.306 Chirality : 0.044 0.190 2345 Planarity : 0.004 0.040 2575 Dihedral : 12.564 88.152 2531 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.24 % Favored : 95.71 % Rotamer: Outliers : 5.56 % Allowed : 26.05 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.20), residues: 1841 helix: 1.17 (0.18), residues: 836 sheet: -0.61 (0.32), residues: 291 loop : -1.11 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 306 TYR 0.020 0.002 TYR I 228 PHE 0.015 0.002 PHE G 327 HIS 0.003 0.001 HIS E 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.28 (15189) covalent geometry : angle 0.57030 / 0.31 (20614) hydrogen bonds : bond 0.04678 / 3.08 ( 725) hydrogen bonds : angle 4.63024 / 3.30 ( 2079) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 118 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.7237 (p0) REVERT: C 96 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7803 (ttm-80) REVERT: C 180 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8021 (mp) REVERT: E 237 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7737 (pt0) REVERT: G 184 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8257 (m-30) REVERT: I 81 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8089 (mt) REVERT: K 251 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8183 (ttp) outliers start: 83 outliers final: 60 residues processed: 186 average time/residue: 0.0910 time to fit residues: 26.9475 Evaluate side-chains 185 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 118 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 311 ILE Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain I residue 330 ASN Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 136 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 187 optimal weight: 20.0000 chunk 114 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN I 268 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.132565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101003 restraints weight = 22380.070| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.74 r_work: 0.3181 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15189 Z= 0.107 Angle : 0.444 5.773 20614 Z= 0.241 Chirality : 0.039 0.182 2345 Planarity : 0.003 0.037 2575 Dihedral : 12.430 89.124 2531 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.17 % Favored : 97.77 % Rotamer: Outliers : 3.48 % Allowed : 27.86 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1841 helix: 1.48 (0.19), residues: 835 sheet: -0.36 (0.34), residues: 281 loop : -1.04 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 306 TYR 0.011 0.001 TYR C 205 PHE 0.008 0.001 PHE A 126 HIS 0.001 0.000 HIS K 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (15189) covalent geometry : angle 0.44384 / 0.24 (20614) hydrogen bonds : bond 0.03191 / 2.11 ( 725) hydrogen bonds : angle 4.27874 / 3.06 ( 2079) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 124 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7505 (OUTLIER) cc_final: 0.7180 (p0) REVERT: C 96 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7734 (ttm-80) REVERT: C 180 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7895 (mp) REVERT: E 237 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7468 (pt0) REVERT: G 184 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8245 (m-30) REVERT: I 61 ILE cc_start: 0.7311 (OUTLIER) cc_final: 0.7050 (mt) REVERT: I 81 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8053 (mt) REVERT: I 87 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8615 (p) outliers start: 52 outliers final: 37 residues processed: 168 average time/residue: 0.0900 time to fit residues: 24.5583 Evaluate side-chains 168 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.128796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.097937 restraints weight = 22272.917| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.61 r_work: 0.3140 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15189 Z= 0.224 Angle : 0.515 6.552 20614 Z= 0.277 Chirality : 0.042 0.185 2345 Planarity : 0.004 0.038 2575 Dihedral : 12.502 88.478 2531 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.14 % Rotamer: Outliers : 3.35 % Allowed : 28.20 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.20), residues: 1841 helix: 1.32 (0.18), residues: 835 sheet: -0.62 (0.32), residues: 291 loop : -1.07 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 306 TYR 0.016 0.002 TYR I 228 PHE 0.012 0.002 PHE G 129 HIS 0.002 0.001 HIS E 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (15189) covalent geometry : angle 0.51543 / 0.28 (20614) hydrogen bonds : bond 0.04068 / 2.68 ( 725) hydrogen bonds : angle 4.43043 / 3.16 ( 2079) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 120 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7595 (OUTLIER) cc_final: 0.7269 (p0) REVERT: C 96 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7830 (ttm-80) REVERT: C 180 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7991 (mp) REVERT: E 237 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7593 (pt0) REVERT: G 184 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8189 (m-30) REVERT: I 61 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7146 (mt) REVERT: I 81 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8145 (mt) REVERT: I 87 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8621 (p) outliers start: 50 outliers final: 39 residues processed: 164 average time/residue: 0.0912 time to fit residues: 23.7489 Evaluate side-chains 166 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain I residue 330 ASN Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 223 SER Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 326 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 22 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.133274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.103751 restraints weight = 21860.002| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.46 r_work: 0.3243 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15189 Z= 0.098 Angle : 0.433 6.132 20614 Z= 0.235 Chirality : 0.038 0.180 2345 Planarity : 0.003 0.036 2575 Dihedral : 12.360 89.253 2530 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.85 % Favored : 98.10 % Rotamer: Outliers : 2.75 % Allowed : 28.73 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.20), residues: 1841 helix: 1.55 (0.19), residues: 835 sheet: -0.34 (0.34), residues: 281 loop : -1.02 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 306 TYR 0.010 0.001 TYR C 205 PHE 0.007 0.001 PHE A 126 HIS 0.001 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (15189) covalent geometry : angle 0.43270 / 0.23 (20614) hydrogen bonds : bond 0.02926 / 1.94 ( 725) hydrogen bonds : angle 4.17987 / 2.99 ( 2079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2625.83 seconds wall clock time: 45 minutes 45.42 seconds (2745.42 seconds total)