Starting phenix.real_space_refine on Fri Jul 3 17:49:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qna_53241/07_2026/9qna_53241.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qna_53241/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9qna_53241/07_2026/9qna_53241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qna_53241/07_2026/9qna_53241.map" model { file = "/net/cci-nas-00/data/ceres_data/9qna_53241/07_2026/9qna_53241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qna_53241/07_2026/9qna_53241.cif" } 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-dev-6108/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, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "K" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Time building chain proxies: 3.79, per 1000 atoms: 0.25 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: 1.26 Conformation dependent library (CDL) restraints added in 782.8 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: 1.77 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: 2.81 Time building geometry restraints manager: 1.71 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.650 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.160 ------------------------------------------------------------------------------- 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 : 0.428 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 0.42830 / 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 : 0.556 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: 0.1018 time to fit residues: 21.1366 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 : 0.548 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.137404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108384 restraints weight = 22232.515| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.36 r_work: 0.3262 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.0395 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 5.259 20614 Z= 0.226 Chirality : 0.038 0.195 2345 Planarity : 0.003 0.039 2575 Dihedral : 12.148 85.197 2538 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.47 % Favored : 98.48 % Rotamer: Outliers : 3.22 % Allowed : 27.39 % Favored : 69.39 % 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: 0.72 (0.20), residues: 1841 helix: 1.68 (0.19), residues: 836 sheet: 0.35 (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 I 315 PHE 0.013 0.001 PHE I 129 HIS 0.001 0.000 HIS E 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (15189) covalent geometry : angle 0.40846 / 0.23 (20614) hydrogen bonds : bond 0.03491 / 2.33 ( 725) hydrogen bonds : angle 4.63339 / 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 177 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 129 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7419 (p0) REVERT: E 237 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7512 (pt0) REVERT: I 87 THR cc_start: 0.8862 (m) cc_final: 0.8565 (p) outliers start: 48 outliers final: 31 residues processed: 167 average time/residue: 0.0983 time to fit residues: 26.5853 Evaluate side-chains 151 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 82 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 314 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 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 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 269 VAL 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: 4.9990 chunk 67 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 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: 8.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.133670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.103368 restraints weight = 22753.395| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.70 r_work: 0.3196 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15189 Z= 0.200 Angle : 0.484 6.185 20614 Z= 0.263 Chirality : 0.041 0.191 2345 Planarity : 0.004 0.039 2575 Dihedral : 12.313 86.103 2532 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.26 % Favored : 96.69 % Rotamer: Outliers : 5.63 % Allowed : 25.72 % 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: 0.46 (0.20), residues: 1841 helix: 1.52 (0.19), residues: 836 sheet: -0.17 (0.33), residues: 292 loop : -0.93 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 177 TYR 0.014 0.002 TYR I 228 PHE 0.015 0.002 PHE I 129 HIS 0.002 0.001 HIS E 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (15189) covalent geometry : angle 0.48379 / 0.26 (20614) hydrogen bonds : bond 0.04192 / 2.77 ( 725) hydrogen bonds : angle 4.56201 / 3.24 ( 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 205 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 121 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.7320 (p0) REVERT: C 125 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8405 (mtp) REVERT: E 237 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7545 (pt0) REVERT: I 81 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8090 (mt) outliers start: 84 outliers final: 62 residues processed: 186 average time/residue: 0.0994 time to fit residues: 30.0911 Evaluate side-chains 186 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 120 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 82 VAL 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 125 MET Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 314 ILE 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 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 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 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 104 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 269 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 21 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.129503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098831 restraints weight = 22230.530| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.51 r_work: 0.3149 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15189 Z= 0.210 Angle : 0.494 6.364 20614 Z= 0.267 Chirality : 0.041 0.187 2345 Planarity : 0.004 0.040 2575 Dihedral : 12.450 85.423 2532 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.18 % Rotamer: Outliers : 5.63 % Allowed : 26.32 % Favored : 68.05 % 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: 0.27 (0.20), residues: 1841 helix: 1.36 (0.19), residues: 836 sheet: -0.31 (0.33), residues: 291 loop : -0.99 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 306 TYR 0.013 0.002 TYR I 228 PHE 0.014 0.002 PHE I 129 HIS 0.002 0.001 HIS E 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (15189) covalent geometry : angle 0.49398 / 0.27 (20614) hydrogen bonds : bond 0.04101 / 2.71 ( 725) hydrogen bonds : angle 4.55570 / 3.23 ( 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 208 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 124 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7592 (OUTLIER) cc_final: 0.7231 (p0) REVERT: C 96 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7800 (ttm-80) REVERT: E 237 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7559 (pt0) REVERT: I 81 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8101 (mt) REVERT: K 332 ASP cc_start: 0.7034 (t0) cc_final: 0.6779 (t0) outliers start: 84 outliers final: 60 residues processed: 189 average time/residue: 0.0945 time to fit residues: 28.2408 Evaluate side-chains 180 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 116 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 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 255 LEU 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 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 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 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 104 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 34 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.134599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.103403 restraints weight = 22445.338| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.74 r_work: 0.3215 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15189 Z= 0.125 Angle : 0.432 6.583 20614 Z= 0.235 Chirality : 0.039 0.184 2345 Planarity : 0.003 0.037 2575 Dihedral : 12.394 85.545 2532 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.56 % Rotamer: Outliers : 4.62 % Allowed : 27.39 % Favored : 67.98 % 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: 0.41 (0.20), residues: 1841 helix: 1.53 (0.19), residues: 835 sheet: -0.20 (0.34), residues: 281 loop : -0.99 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 306 TYR 0.010 0.001 TYR C 205 PHE 0.010 0.001 PHE I 129 HIS 0.002 0.000 HIS E 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (15189) covalent geometry : angle 0.43183 / 0.23 (20614) hydrogen bonds : bond 0.03295 / 2.18 ( 725) hydrogen bonds : angle 4.33603 / 3.09 ( 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 194 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 125 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7505 (OUTLIER) cc_final: 0.7161 (p0) REVERT: C 96 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7705 (ttm-80) REVERT: E 237 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7494 (pt0) REVERT: G 184 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8157 (m-30) REVERT: G 193 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8390 (ttp-170) REVERT: I 81 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8052 (mt) REVERT: I 87 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8616 (p) REVERT: K 332 ASP cc_start: 0.6791 (t0) cc_final: 0.6481 (t0) outliers start: 69 outliers final: 47 residues processed: 182 average time/residue: 0.0922 time to fit residues: 26.5606 Evaluate side-chains 174 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 120 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 158 MET 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 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 125 MET Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 314 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 204 LEU Chi-restraints excluded: chain E residue 237 GLU 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 184 ASP Chi-restraints excluded: chain G residue 193 ARG 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 chunk 169 optimal weight: 2.9990 chunk 138 optimal weight: 0.0980 chunk 13 optimal weight: 8.9990 chunk 9 optimal weight: 0.0770 chunk 40 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN C 145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.106038 restraints weight = 22259.324| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.72 r_work: 0.3253 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15189 Z= 0.087 Angle : 0.401 4.846 20614 Z= 0.218 Chirality : 0.038 0.179 2345 Planarity : 0.003 0.035 2575 Dihedral : 12.286 85.830 2532 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.41 % Favored : 98.53 % Rotamer: Outliers : 3.08 % Allowed : 28.47 % 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: 0.59 (0.20), residues: 1841 helix: 1.66 (0.19), residues: 836 sheet: 0.03 (0.35), residues: 280 loop : -0.96 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 306 TYR 0.009 0.001 TYR C 205 PHE 0.008 0.001 PHE I 129 HIS 0.001 0.000 HIS E 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00171 / 0.09 (15189) covalent geometry : angle 0.40087 / 0.22 (20614) hydrogen bonds : bond 0.02662 / 1.77 ( 725) hydrogen bonds : angle 4.10959 / 2.93 ( 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 177 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.7176 (p0) REVERT: E 237 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: G 184 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8130 (m-30) REVERT: G 193 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8313 (ttp-170) REVERT: I 87 THR cc_start: 0.8881 (m) cc_final: 0.8609 (p) REVERT: I 178 TYR cc_start: 0.7718 (m-10) cc_final: 0.7490 (m-10) outliers start: 46 outliers final: 36 residues processed: 167 average time/residue: 0.0818 time to fit residues: 22.0957 Evaluate side-chains 161 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 158 MET 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 103 THR Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 185 VAL 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 172 LEU 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 123 THR Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 193 ARG Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 223 SER 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 211 MET 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 165 THR Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 184 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 23 optimal weight: 7.9990 chunk 118 optimal weight: 0.0870 chunk 169 optimal weight: 0.4980 chunk 75 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 2.3162 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.136204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104083 restraints weight = 22590.144| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.83 r_work: 0.3198 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15189 Z= 0.171 Angle : 0.464 5.680 20614 Z= 0.251 Chirality : 0.040 0.182 2345 Planarity : 0.003 0.039 2575 Dihedral : 12.346 86.730 2531 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 4.42 % Allowed : 27.06 % 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: 0.43 (0.20), residues: 1841 helix: 1.54 (0.19), residues: 836 sheet: -0.23 (0.33), residues: 291 loop : -0.98 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 306 TYR 0.014 0.002 TYR I 228 PHE 0.012 0.002 PHE I 129 HIS 0.002 0.001 HIS E 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (15189) covalent geometry : angle 0.46433 / 0.25 (20614) hydrogen bonds : bond 0.03609 / 2.39 ( 725) hydrogen bonds : angle 4.22491 / 3.01 ( 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 185 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 119 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7210 (p0) REVERT: E 237 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7522 (pt0) REVERT: G 184 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8162 (m-30) REVERT: G 193 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8491 (ttp-170) REVERT: I 81 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8049 (mt) REVERT: I 87 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8603 (p) REVERT: K 332 ASP cc_start: 0.6942 (t0) cc_final: 0.6716 (t0) outliers start: 66 outliers final: 49 residues processed: 173 average time/residue: 0.0845 time to fit residues: 23.5071 Evaluate side-chains 172 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 117 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 158 MET 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 103 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 185 VAL 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 99 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 109 LEU 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 311 ILE Chi-restraints excluded: chain G residue 61 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 184 ASP Chi-restraints excluded: chain G residue 193 ARG 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 77 GLU 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 K residue 72 ASP Chi-restraints excluded: chain K residue 82 VAL 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 172 LEU Chi-restraints excluded: chain K residue 184 ASP 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: 3.9990 chunk 71 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 187 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.129281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098722 restraints weight = 22169.963| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.51 r_work: 0.3149 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15189 Z= 0.208 Angle : 0.496 6.200 20614 Z= 0.268 Chirality : 0.041 0.189 2345 Planarity : 0.004 0.039 2575 Dihedral : 12.442 86.886 2530 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 4.76 % Allowed : 27.13 % Favored : 68.12 % 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: 0.24 (0.20), residues: 1841 helix: 1.40 (0.19), residues: 836 sheet: -0.42 (0.33), residues: 291 loop : -1.04 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 306 TYR 0.014 0.002 TYR I 228 PHE 0.012 0.002 PHE I 129 HIS 0.002 0.001 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (15189) covalent geometry : angle 0.49615 / 0.27 (20614) hydrogen bonds : bond 0.03984 / 2.63 ( 725) hydrogen bonds : angle 4.37158 / 3.12 ( 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 190 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 119 time to evaluate : 0.587 Fit side-chains REVERT: A 188 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7284 (p0) REVERT: C 96 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7819 (ttm-80) REVERT: E 237 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7573 (pt0) REVERT: G 193 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8568 (ttp-170) REVERT: I 81 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8165 (mt) REVERT: I 87 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8580 (p) outliers start: 71 outliers final: 54 residues processed: 178 average time/residue: 0.1018 time to fit residues: 28.8113 Evaluate side-chains 177 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 117 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 158 MET 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 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 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 99 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 125 MET 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 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 193 ARG 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 81 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 104 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 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 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: 2.9990 chunk 146 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 187 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 268 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.131442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.100824 restraints weight = 22077.413| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.61 r_work: 0.3183 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1143 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= 0.118 Angle : 0.441 5.210 20614 Z= 0.240 Chirality : 0.039 0.184 2345 Planarity : 0.003 0.037 2575 Dihedral : 12.389 86.751 2530 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 3.42 % Allowed : 28.87 % Favored : 67.72 % 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: 0.35 (0.20), residues: 1841 helix: 1.49 (0.19), residues: 835 sheet: -0.35 (0.33), residues: 291 loop : -0.99 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 306 TYR 0.009 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 0.00261 / 0.12 (15189) covalent geometry : angle 0.44053 / 0.24 (20614) hydrogen bonds : bond 0.03296 / 2.19 ( 725) hydrogen bonds : angle 4.23680 / 3.03 ( 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 172 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 0.562 Fit side-chains REVERT: A 188 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.7263 (p0) REVERT: C 96 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7797 (ttm-80) REVERT: C 180 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7940 (mp) REVERT: E 237 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7507 (pt0) REVERT: G 184 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8157 (m-30) REVERT: G 193 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8470 (ttp-170) REVERT: I 87 THR cc_start: 0.8896 (m) cc_final: 0.8626 (p) outliers start: 51 outliers final: 42 residues processed: 164 average time/residue: 0.0842 time to fit residues: 22.4744 Evaluate side-chains 166 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 118 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 158 MET 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 72 ASP 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 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 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 61 ILE Chi-restraints excluded: chain G residue 63 ILE 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 184 ASP Chi-restraints excluded: chain G residue 193 ARG Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 211 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 165 THR Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 184 ASP 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 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.133722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.101393 restraints weight = 22659.466| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.81 r_work: 0.3165 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15189 Z= 0.153 Angle : 0.459 5.804 20614 Z= 0.249 Chirality : 0.040 0.184 2345 Planarity : 0.003 0.037 2575 Dihedral : 12.393 87.092 2530 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 3.48 % Allowed : 28.87 % Favored : 67.65 % 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: 0.30 (0.20), residues: 1841 helix: 1.46 (0.19), residues: 835 sheet: -0.40 (0.33), residues: 291 loop : -1.01 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 306 TYR 0.010 0.001 TYR I 228 PHE 0.011 0.001 PHE I 129 HIS 0.001 0.000 HIS E 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (15189) covalent geometry : angle 0.45854 / 0.25 (20614) hydrogen bonds : bond 0.03483 / 2.31 ( 725) hydrogen bonds : angle 4.25270 / 3.04 ( 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 174 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 0.501 Fit side-chains REVERT: A 188 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7250 (p0) REVERT: C 96 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7773 (ttm-80) REVERT: C 180 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7924 (mp) REVERT: E 237 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7541 (pt0) REVERT: G 184 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8202 (m-30) REVERT: G 193 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8451 (ttp-170) REVERT: I 87 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8625 (p) outliers start: 52 outliers final: 42 residues processed: 165 average time/residue: 0.0966 time to fit residues: 25.5972 Evaluate side-chains 168 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 119 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 158 MET 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 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 180 LEU Chi-restraints excluded: chain C residue 185 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 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 61 ILE Chi-restraints excluded: chain G residue 63 ILE 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 184 ASP Chi-restraints excluded: chain G residue 193 ARG Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 123 THR 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 165 THR Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 184 ASP 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: 3.9990 chunk 69 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 130 optimal weight: 0.1980 chunk 103 optimal weight: 0.0270 chunk 114 optimal weight: 5.9990 overall best weight: 0.5842 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.136519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.105777 restraints weight = 22320.241| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.70 r_work: 0.3250 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15189 Z= 0.089 Angle : 0.416 5.860 20614 Z= 0.227 Chirality : 0.038 0.181 2345 Planarity : 0.003 0.035 2575 Dihedral : 12.296 87.292 2530 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.79 % Favored : 98.15 % Rotamer: Outliers : 3.08 % Allowed : 29.34 % Favored : 67.58 % 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: 0.49 (0.20), residues: 1841 helix: 1.63 (0.19), residues: 835 sheet: -0.17 (0.35), residues: 275 loop : -1.00 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 306 TYR 0.009 0.001 TYR C 205 PHE 0.007 0.001 PHE C 126 HIS 0.001 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.09 (15189) covalent geometry : angle 0.41594 / 0.23 (20614) hydrogen bonds : bond 0.02734 / 1.83 ( 725) hydrogen bonds : angle 4.08317 / 2.92 ( 2079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2987.11 seconds wall clock time: 52 minutes 1.68 seconds (3121.68 seconds total)