Starting phenix.real_space_refine on Sun Aug 24 07:46:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gyk_34372/08_2025/8gyk_34372.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gyk_34372/08_2025/8gyk_34372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gyk_34372/08_2025/8gyk_34372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gyk_34372/08_2025/8gyk_34372.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gyk_34372/08_2025/8gyk_34372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gyk_34372/08_2025/8gyk_34372.map" } resolution = 3.14 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= 0.004 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 96 5.16 5 C 11290 2.51 5 N 3211 2.21 5 O 3482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18103 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2233 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 6, 'TRANS': 283} Chain breaks: 2 Chain: "B" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2249 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 6, 'TRANS': 286} Chain breaks: 2 Chain: "C" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2241 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 6, 'TRANS': 285} Chain breaks: 2 Chain: "D" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2225 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 6, 'TRANS': 282} Chain breaks: 2 Chain: "E" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2232 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 283} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2233 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 6, 'TRANS': 283} Chain breaks: 2 Chain: "G" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2241 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 6, 'TRANS': 285} Chain breaks: 2 Chain: "H" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2225 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 6, 'TRANS': 282} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.49, per 1000 atoms: 0.25 Number of scatterers: 18103 At special positions: 0 Unit cell: (124.5, 122.84, 146.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 16 15.00 Mg 8 11.99 O 3482 8.00 N 3211 7.00 C 11290 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: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4238 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 14 sheets defined 50.7% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.821A pdb=" N GLU A 29 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.636A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 132 through 144 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 167 through 179 Processing helix chain 'A' and resid 183 through 189 removed outlier: 3.508A pdb=" N ASP A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 212 removed outlier: 3.605A pdb=" N THR A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.570A pdb=" N ASP A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.909A pdb=" N GLU B 29 " --> pdb=" O SER B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 45 Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.514A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 80 Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.646A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 187 Processing helix chain 'B' and resid 197 through 214 removed outlier: 3.793A pdb=" N THR B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 3.584A pdb=" N TYR B 232 " --> pdb=" O TYR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 260 Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.916A pdb=" N HIS B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 29 removed outlier: 3.933A pdb=" N GLU C 29 " --> pdb=" O SER C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 45 Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 56 through 62 removed outlier: 3.724A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) 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 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.653A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 189 removed outlier: 3.698A pdb=" N LEU C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 214 removed outlier: 3.711A pdb=" N THR C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET C 210 " --> pdb=" O GLN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 237 through 260 Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.551A pdb=" N ARG D 27 " --> pdb=" O PRO D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 43 removed outlier: 3.832A pdb=" N GLU D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 56 through 62 removed outlier: 3.709A pdb=" N LEU D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 88 through 97 Processing helix chain 'D' and resid 132 through 144 removed outlier: 3.531A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.669A pdb=" N LEU D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 189 removed outlier: 3.628A pdb=" N ASN D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 211 removed outlier: 3.820A pdb=" N THR D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 removed outlier: 3.507A pdb=" N THR D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR D 232 " --> pdb=" O TYR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 260 Processing helix chain 'E' and resid 24 through 29 Processing helix chain 'E' and resid 37 through 45 Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 56 through 62 removed outlier: 3.794A pdb=" N LEU E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 82 removed outlier: 3.612A pdb=" N LEU E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) 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 removed outlier: 3.577A pdb=" N CYS E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) 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 178 removed outlier: 4.065A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 189 removed outlier: 3.703A pdb=" N VAL E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 212 removed outlier: 3.623A pdb=" N THR E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 232 removed outlier: 3.566A pdb=" N THR E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 260 removed outlier: 4.490A pdb=" N GLU E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.817A pdb=" N GLU F 29 " --> pdb=" O SER F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 43 removed outlier: 3.741A pdb=" N LYS F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS F 40 " --> pdb=" O ASN F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 56 through 62 removed outlier: 3.521A pdb=" N LEU F 60 " --> pdb=" O PRO F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 80 removed outlier: 3.691A pdb=" N LYS F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 95 Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.512A pdb=" N CYS F 137 " --> pdb=" O LYS F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 167 through 179 removed outlier: 3.848A pdb=" N LEU F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR F 178 " --> pdb=" O VAL F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 187 removed outlier: 3.819A pdb=" N LEU F 186 " --> pdb=" O GLY F 182 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 214 removed outlier: 3.855A pdb=" N ALA F 209 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER F 214 " --> pdb=" O MET F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 232 removed outlier: 3.608A pdb=" N TYR F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 260 removed outlier: 3.606A pdb=" N MET F 243 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS F 244 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE F 259 " --> pdb=" O LEU F 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 29 removed outlier: 3.536A pdb=" N GLU G 29 " --> pdb=" O SER G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 43 Processing helix chain 'G' and resid 48 through 54 Processing helix chain 'G' and resid 56 through 62 Processing helix chain 'G' and resid 67 through 82 Processing helix chain 'G' and resid 89 through 97 Processing helix chain 'G' and resid 106 through 113 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 178 removed outlier: 3.836A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR G 178 " --> pdb=" O VAL G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 189 removed outlier: 3.516A pdb=" N VAL G 185 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU G 186 " --> pdb=" O GLY G 182 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP G 187 " --> pdb=" O SER G 183 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 189 " --> pdb=" O VAL G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 214 removed outlier: 3.973A pdb=" N THR G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA G 209 " --> pdb=" O TYR G 205 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 231 removed outlier: 3.503A pdb=" N ASP G 231 " --> pdb=" O LEU G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 237 through 260 removed outlier: 3.758A pdb=" N PHE G 259 " --> pdb=" O LEU G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 296 removed outlier: 3.716A pdb=" N HIS G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA G 295 " --> pdb=" O ILE G 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 29 Processing helix chain 'H' and resid 34 through 43 removed outlier: 3.752A pdb=" N GLU H 43 " --> pdb=" O LYS H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 54 Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 67 through 82 removed outlier: 3.512A pdb=" N LEU H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 97 Processing helix chain 'H' and resid 132 through 144 Processing helix chain 'H' and resid 167 through 178 removed outlier: 3.647A pdb=" N LEU H 171 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 172 " --> pdb=" O PRO H 168 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR H 178 " --> pdb=" O VAL H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 189 removed outlier: 3.673A pdb=" N ASN H 188 " --> pdb=" O ASP H 184 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL H 189 " --> pdb=" O VAL H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 211 removed outlier: 3.809A pdb=" N THR H 201 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 232 removed outlier: 3.594A pdb=" N THR H 230 " --> pdb=" O ALA H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 260 removed outlier: 3.838A pdb=" N MET H 243 " --> pdb=" O SER H 239 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS H 244 " --> pdb=" O ALA H 240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA2, first strand: chain 'A' and resid 123 through 125 removed outlier: 3.648A pdb=" N ILE A 265 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'B' and resid 301 through 306 removed outlier: 3.567A pdb=" N ILE B 311 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY B 305 " --> pdb=" O THR B 309 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N THR B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.309A pdb=" N MET D 158 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU D 219 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR D 266 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL D 221 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE D 122 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU D 300 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU D 124 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU D 302 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 311 " --> pdb=" O ARG D 303 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY D 305 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR D 309 " --> pdb=" O GLY D 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 264 through 266 removed outlier: 6.133A pdb=" N THR C 123 " --> pdb=" O ILE C 265 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 302 through 303 removed outlier: 3.502A pdb=" N ILE C 311 " --> pdb=" O ARG C 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.667A pdb=" N MET F 158 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE F 327 " --> pdb=" O ARG F 310 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS F 312 " --> pdb=" O ALA F 325 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 190 through 191 removed outlier: 6.873A pdb=" N ALA E 157 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS E 156 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU E 219 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N MET E 158 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA E 217 " --> pdb=" O ALA E 262 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL E 264 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU E 219 " --> pdb=" O VAL E 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AB3, first strand: chain 'G' and resid 87 through 88 removed outlier: 6.294A pdb=" N MET H 158 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR H 266 " --> pdb=" O VAL H 221 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE H 122 " --> pdb=" O THR H 298 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 264 through 266 removed outlier: 6.158A pdb=" N THR G 123 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE G 126 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG G 303 " --> pdb=" O ILE G 311 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE G 311 " --> pdb=" O ARG G 303 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 301 through 303 727 hydrogen bonds defined for protein. 2049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6086 1.34 - 1.46: 3112 1.46 - 1.58: 8960 1.58 - 1.69: 25 1.69 - 1.81: 160 Bond restraints: 18343 Sorted by residual: bond pdb=" CG PRO C 83 " pdb=" CD PRO C 83 " ideal model delta sigma weight residual 1.503 1.286 0.217 3.40e-02 8.65e+02 4.06e+01 bond pdb=" CB PRO C 83 " pdb=" CG PRO C 83 " ideal model delta sigma weight residual 1.492 1.688 -0.196 5.00e-02 4.00e+02 1.53e+01 bond pdb=" N PRO C 83 " pdb=" CD PRO C 83 " ideal model delta sigma weight residual 1.473 1.515 -0.042 1.40e-02 5.10e+03 9.02e+00 bond pdb=" N PRO C 83 " pdb=" CA PRO C 83 " ideal model delta sigma weight residual 1.469 1.450 0.019 1.28e-02 6.10e+03 2.22e+00 bond pdb=" C4 ADP B 600 " pdb=" C5 ADP B 600 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.15e+00 ... (remaining 18338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 24505 3.10 - 6.21: 225 6.21 - 9.31: 12 9.31 - 12.42: 2 12.42 - 15.52: 2 Bond angle restraints: 24746 Sorted by residual: angle pdb=" CA PRO C 83 " pdb=" N PRO C 83 " pdb=" CD PRO C 83 " ideal model delta sigma weight residual 112.00 96.48 15.52 1.40e+00 5.10e-01 1.23e+02 angle pdb=" N PRO C 83 " pdb=" CD PRO C 83 " pdb=" CG PRO C 83 " ideal model delta sigma weight residual 103.20 89.22 13.98 1.50e+00 4.44e-01 8.69e+01 angle pdb=" CA PRO C 83 " pdb=" CB PRO C 83 " pdb=" CG PRO C 83 " ideal model delta sigma weight residual 104.50 93.55 10.95 1.90e+00 2.77e-01 3.32e+01 angle pdb=" N ILE A 314 " pdb=" CA ILE A 314 " pdb=" C ILE A 314 " ideal model delta sigma weight residual 113.10 107.75 5.35 9.70e-01 1.06e+00 3.04e+01 angle pdb=" N MET H 326 " pdb=" CA MET H 326 " pdb=" C MET H 326 " ideal model delta sigma weight residual 109.85 115.92 -6.07 1.58e+00 4.01e-01 1.48e+01 ... (remaining 24741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.42: 10579 28.42 - 56.84: 419 56.84 - 85.25: 45 85.25 - 113.67: 8 113.67 - 142.09: 13 Dihedral angle restraints: 11064 sinusoidal: 4445 harmonic: 6619 Sorted by residual: dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 82.09 -142.09 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" O1B ADP B 600 " pdb=" O3A ADP B 600 " pdb=" PB ADP B 600 " pdb=" PA ADP B 600 " ideal model delta sinusoidal sigma weight residual 300.00 162.60 137.40 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" C5' ADP B 600 " pdb=" O5' ADP B 600 " pdb=" PA ADP B 600 " pdb=" O2A ADP B 600 " ideal model delta sinusoidal sigma weight residual -60.00 76.96 -136.96 1 2.00e+01 2.50e-03 4.15e+01 ... (remaining 11061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2213 0.046 - 0.092: 477 0.092 - 0.138: 141 0.138 - 0.184: 8 0.184 - 0.230: 1 Chirality restraints: 2840 Sorted by residual: chirality pdb=" CB ILE G 314 " pdb=" CA ILE G 314 " pdb=" CG1 ILE G 314 " pdb=" CG2 ILE G 314 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE C 314 " pdb=" CA ILE C 314 " pdb=" CG1 ILE C 314 " pdb=" CG2 ILE C 314 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.26e-01 chirality pdb=" CB ILE E 314 " pdb=" CA ILE E 314 " pdb=" CG1 ILE E 314 " pdb=" CG2 ILE E 314 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.91e-01 ... (remaining 2837 not shown) Planarity restraints: 3163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 82 " 0.061 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO C 83 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 83 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 83 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 23 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO F 24 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO F 24 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 24 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 21 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO B 22 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 22 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 22 " -0.034 5.00e-02 4.00e+02 ... (remaining 3160 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 221 2.58 - 3.16: 15718 3.16 - 3.74: 28301 3.74 - 4.32: 38684 4.32 - 4.90: 63197 Nonbonded interactions: 146121 Sorted by model distance: nonbonded pdb=" O2A ADP G 600 " pdb="MG MG G 601 " model vdw 2.003 2.170 nonbonded pdb=" O1A ADP E 600 " pdb="MG MG E 601 " model vdw 2.004 2.170 nonbonded pdb=" O3B ADP B 600 " pdb="MG MG B 601 " model vdw 2.016 2.170 nonbonded pdb=" O3A ADP H 600 " pdb="MG MG H 601 " model vdw 2.025 2.170 nonbonded pdb=" O3A ADP B 600 " pdb="MG MG B 601 " model vdw 2.030 2.170 ... (remaining 146116 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 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 270 or resid 291 through 601)) selection = (chain 'B' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 270 or resid 291 through 601)) selection = (chain 'C' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 270 or resid 291 through 601)) selection = (chain 'D' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 601)) selection = (chain 'E' and (resid 21 through 270 or resid 291 through 601)) selection = (chain 'F' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 270 or resid 291 through 601)) selection = (chain 'G' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 270 or resid 291 through 601)) selection = (chain 'H' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 601)) } 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: 5.050 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.690 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 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 : 0.003 0.217 18343 Z= 0.144 Angle : 0.733 15.524 24746 Z= 0.383 Chirality : 0.042 0.230 2840 Planarity : 0.005 0.082 3163 Dihedral : 15.842 142.089 6826 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.41 % Favored : 92.89 % Rotamer: Outliers : 0.05 % Allowed : 0.22 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.17), residues: 2277 helix: -0.62 (0.16), residues: 1067 sheet: -1.65 (0.31), residues: 309 loop : -2.09 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 27 TYR 0.022 0.001 TYR C 315 PHE 0.020 0.001 PHE A 126 HIS 0.003 0.001 HIS E 244 Details of bonding type rmsd covalent geometry : bond 0.00339 (18343) covalent geometry : angle 0.73300 (24746) hydrogen bonds : bond 0.24048 ( 727) hydrogen bonds : angle 7.50611 ( 2049) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 473 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.7678 (p) cc_final: 0.7349 (t) REVERT: B 50 GLU cc_start: 0.6821 (mt-10) cc_final: 0.5238 (pt0) REVERT: B 130 ARG cc_start: 0.6629 (mmp-170) cc_final: 0.6375 (ttm-80) REVERT: B 253 LEU cc_start: 0.7411 (mm) cc_final: 0.7060 (mt) REVERT: B 313 LYS cc_start: 0.6027 (mttp) cc_final: 0.5557 (pttp) REVERT: C 97 SER cc_start: 0.6994 (m) cc_final: 0.6657 (p) REVERT: C 111 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7671 (mttm) REVERT: C 118 GLU cc_start: 0.7204 (pt0) cc_final: 0.6915 (tt0) REVERT: C 124 GLU cc_start: 0.7603 (mt-10) cc_final: 0.6971 (tt0) REVERT: C 126 PHE cc_start: 0.7481 (m-10) cc_final: 0.6979 (m-80) REVERT: C 242 GLN cc_start: 0.8005 (mm110) cc_final: 0.7525 (mm-40) REVERT: C 250 ARG cc_start: 0.7751 (ttp-110) cc_final: 0.7317 (mtp-110) REVERT: C 255 LEU cc_start: 0.7774 (tt) cc_final: 0.7572 (tp) REVERT: C 315 TYR cc_start: 0.7331 (t80) cc_final: 0.6962 (t80) REVERT: D 97 SER cc_start: 0.7961 (t) cc_final: 0.7711 (p) REVERT: D 170 ARG cc_start: 0.7558 (tpp-160) cc_final: 0.7247 (tpp80) REVERT: D 178 TYR cc_start: 0.8020 (m-10) cc_final: 0.7812 (m-10) REVERT: D 208 SER cc_start: 0.8620 (t) cc_final: 0.8362 (t) REVERT: D 267 ASN cc_start: 0.7747 (t0) cc_final: 0.7541 (t0) REVERT: D 326 MET cc_start: 0.6806 (mmp) cc_final: 0.6589 (tmm) REVERT: E 140 LEU cc_start: 0.7384 (tp) cc_final: 0.6726 (mt) REVERT: F 124 GLU cc_start: 0.7391 (tt0) cc_final: 0.6950 (tt0) REVERT: F 301 TYR cc_start: 0.7670 (t80) cc_final: 0.7279 (t80) REVERT: G 68 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7317 (mm-30) REVERT: G 126 PHE cc_start: 0.6690 (m-80) cc_final: 0.5868 (m-10) REVERT: G 130 ARG cc_start: 0.6596 (mtt90) cc_final: 0.6177 (mmm160) REVERT: G 154 GLU cc_start: 0.7181 (pt0) cc_final: 0.6339 (tp30) REVERT: G 326 MET cc_start: 0.5126 (mmp) cc_final: 0.4495 (mmp) REVERT: H 210 MET cc_start: 0.8613 (ptm) cc_final: 0.8276 (ptp) REVERT: H 250 ARG cc_start: 0.7418 (ttp-110) cc_final: 0.7162 (ttp-110) REVERT: H 267 ASN cc_start: 0.7491 (t0) cc_final: 0.7143 (t0) outliers start: 1 outliers final: 0 residues processed: 473 average time/residue: 0.1783 time to fit residues: 119.9012 Evaluate side-chains 322 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 138 HIS ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 101 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 23 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN D 62 ASN D 200 GLN D 206 GLN E 188 ASN E 206 GLN F 135 GLN ** F 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 GLN H 200 GLN H 294 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.188211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144299 restraints weight = 19017.815| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.57 r_work: 0.3519 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 18343 Z= 0.234 Angle : 0.793 8.235 24746 Z= 0.387 Chirality : 0.048 0.195 2840 Planarity : 0.005 0.062 3163 Dihedral : 10.313 133.975 2629 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.20 % Favored : 92.14 % Rotamer: Outliers : 1.73 % Allowed : 12.03 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.16), residues: 2277 helix: -0.63 (0.15), residues: 1111 sheet: -2.13 (0.29), residues: 306 loop : -2.30 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 303 TYR 0.023 0.002 TYR G 159 PHE 0.031 0.002 PHE A 327 HIS 0.006 0.001 HIS F 47 Details of bonding type rmsd covalent geometry : bond 0.00553 (18343) covalent geometry : angle 0.79311 (24746) hydrogen bonds : bond 0.04349 ( 727) hydrogen bonds : angle 5.27219 ( 2049) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 358 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.8202 (p) cc_final: 0.7980 (t) REVERT: A 229 ARG cc_start: 0.4608 (mmt180) cc_final: 0.4184 (mmp-170) REVERT: A 251 MET cc_start: 0.7906 (ttm) cc_final: 0.7644 (ttm) REVERT: B 39 LYS cc_start: 0.7578 (mtmm) cc_final: 0.6775 (ttpp) REVERT: B 84 MET cc_start: 0.8082 (mtp) cc_final: 0.7817 (mmm) REVERT: B 130 ARG cc_start: 0.7058 (mmp-170) cc_final: 0.6393 (mtp85) REVERT: B 154 GLU cc_start: 0.7386 (tt0) cc_final: 0.7134 (tm-30) REVERT: B 229 ARG cc_start: 0.7998 (ttm-80) cc_final: 0.7504 (mtt90) REVERT: C 163 GLU cc_start: 0.6972 (tp30) cc_final: 0.6265 (tp30) REVERT: C 205 TYR cc_start: 0.8823 (m-10) cc_final: 0.8547 (m-10) REVERT: C 242 GLN cc_start: 0.8274 (mm110) cc_final: 0.7773 (mm-40) REVERT: C 315 TYR cc_start: 0.8040 (t80) cc_final: 0.7745 (t80) REVERT: D 170 ARG cc_start: 0.8365 (tpp-160) cc_final: 0.7885 (tpp80) REVERT: D 315 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6142 (m-80) REVERT: D 326 MET cc_start: 0.7269 (mmp) cc_final: 0.6620 (tmm) REVERT: E 176 GLU cc_start: 0.6747 (pt0) cc_final: 0.6497 (tp30) REVERT: E 250 ARG cc_start: 0.7545 (ttp-110) cc_final: 0.7098 (tpp-160) REVERT: E 251 MET cc_start: 0.7720 (mtm) cc_final: 0.7496 (tpt) REVERT: F 251 MET cc_start: 0.7839 (mtp) cc_final: 0.7584 (mtp) REVERT: G 130 ARG cc_start: 0.7346 (mtt90) cc_final: 0.6834 (mmm160) REVERT: G 205 TYR cc_start: 0.8154 (m-10) cc_final: 0.7868 (m-10) REVERT: G 210 MET cc_start: 0.8699 (mtm) cc_final: 0.8465 (mtp) REVERT: G 326 MET cc_start: 0.5755 (mmp) cc_final: 0.4694 (mtm) REVERT: H 100 ILE cc_start: 0.7713 (mm) cc_final: 0.7308 (mm) REVERT: H 118 GLU cc_start: 0.7655 (tt0) cc_final: 0.7201 (pt0) REVERT: H 148 ILE cc_start: 0.7755 (tp) cc_final: 0.7443 (tp) REVERT: H 154 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7419 (mm-30) REVERT: H 202 GLN cc_start: 0.7711 (tp40) cc_final: 0.7508 (tm-30) REVERT: H 243 MET cc_start: 0.7819 (ptt) cc_final: 0.7429 (mmp) REVERT: H 250 ARG cc_start: 0.7905 (ttp-110) cc_final: 0.7641 (ttp-110) REVERT: H 267 ASN cc_start: 0.8115 (t0) cc_final: 0.7741 (t0) outliers start: 32 outliers final: 16 residues processed: 376 average time/residue: 0.1652 time to fit residues: 90.2762 Evaluate side-chains 322 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 305 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 169 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 159 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 89 optimal weight: 0.1980 chunk 200 optimal weight: 0.9980 chunk 179 optimal weight: 0.7980 chunk 223 optimal weight: 0.0670 chunk 224 optimal weight: 0.5980 chunk 136 optimal weight: 10.0000 chunk 57 optimal weight: 0.0270 chunk 30 optimal weight: 8.9990 chunk 209 optimal weight: 0.0000 overall best weight: 0.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 23 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 23 GLN C 93 HIS C 135 GLN C 206 GLN C 330 ASN D 200 GLN E 188 ASN E 206 GLN ** F 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 HIS ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.196647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.150770 restraints weight = 18388.525| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.60 r_work: 0.3595 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18343 Z= 0.112 Angle : 0.642 7.226 24746 Z= 0.307 Chirality : 0.041 0.164 2840 Planarity : 0.004 0.062 3163 Dihedral : 9.408 125.349 2629 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.71 % Favored : 93.63 % Rotamer: Outliers : 2.05 % Allowed : 14.83 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.17), residues: 2277 helix: -0.02 (0.16), residues: 1087 sheet: -1.69 (0.29), residues: 326 loop : -2.04 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 254 TYR 0.019 0.001 TYR E 315 PHE 0.026 0.001 PHE A 327 HIS 0.005 0.001 HIS E 244 Details of bonding type rmsd covalent geometry : bond 0.00229 (18343) covalent geometry : angle 0.64220 (24746) hydrogen bonds : bond 0.03283 ( 727) hydrogen bonds : angle 4.66032 ( 2049) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 328 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.8167 (p) cc_final: 0.7930 (t) REVERT: A 158 MET cc_start: 0.8152 (ttm) cc_final: 0.7918 (ttm) REVERT: A 251 MET cc_start: 0.7871 (ttm) cc_final: 0.7639 (ttm) REVERT: B 23 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7899 (tp40) REVERT: B 130 ARG cc_start: 0.6410 (mmp-170) cc_final: 0.5819 (mtp85) REVERT: B 154 GLU cc_start: 0.7416 (tt0) cc_final: 0.7073 (tm-30) REVERT: B 250 ARG cc_start: 0.7260 (ttp-110) cc_final: 0.7009 (ttp-110) REVERT: B 253 LEU cc_start: 0.7458 (mm) cc_final: 0.7022 (mt) REVERT: C 80 LYS cc_start: 0.8365 (mtmm) cc_final: 0.8040 (mtmm) REVERT: C 111 LYS cc_start: 0.8322 (ttpp) cc_final: 0.7773 (mttm) REVERT: C 163 GLU cc_start: 0.6711 (tp30) cc_final: 0.5939 (tp30) REVERT: C 242 GLN cc_start: 0.8235 (mm110) cc_final: 0.7685 (mm-40) REVERT: C 243 MET cc_start: 0.7542 (mmt) cc_final: 0.7240 (mpp) REVERT: C 315 TYR cc_start: 0.7482 (t80) cc_final: 0.7074 (t80) REVERT: D 95 ARG cc_start: 0.7177 (ptt90) cc_final: 0.6537 (mmp80) REVERT: D 170 ARG cc_start: 0.8147 (tpp-160) cc_final: 0.7783 (mmm-85) REVERT: D 249 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7818 (mm) REVERT: D 250 ARG cc_start: 0.7912 (tpt170) cc_final: 0.7497 (ttm110) REVERT: D 315 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6021 (m-80) REVERT: D 326 MET cc_start: 0.7286 (mmp) cc_final: 0.6538 (tmm) REVERT: E 176 GLU cc_start: 0.6674 (pt0) cc_final: 0.6319 (tp30) REVERT: E 251 MET cc_start: 0.7758 (mtm) cc_final: 0.7438 (tpp) REVERT: F 43 GLU cc_start: 0.7051 (mp0) cc_final: 0.6760 (mp0) REVERT: F 64 LYS cc_start: 0.7848 (mmmt) cc_final: 0.7449 (mtpp) REVERT: F 107 LYS cc_start: 0.5460 (tttm) cc_final: 0.5223 (ttpt) REVERT: F 251 MET cc_start: 0.7654 (mtp) cc_final: 0.7291 (mtp) REVERT: G 59 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7224 (mt-10) REVERT: G 130 ARG cc_start: 0.6943 (mtt90) cc_final: 0.6443 (mmm160) REVERT: G 205 TYR cc_start: 0.7916 (m-10) cc_final: 0.7530 (m-10) REVERT: G 210 MET cc_start: 0.8632 (mtm) cc_final: 0.8394 (mtp) REVERT: G 326 MET cc_start: 0.5548 (mmp) cc_final: 0.4616 (mtm) REVERT: H 100 ILE cc_start: 0.7574 (mm) cc_final: 0.7137 (mm) REVERT: H 118 GLU cc_start: 0.7650 (tt0) cc_final: 0.7167 (pt0) REVERT: H 148 ILE cc_start: 0.7650 (tp) cc_final: 0.7433 (tp) REVERT: H 154 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7437 (mm-30) REVERT: H 170 ARG cc_start: 0.7968 (tpp-160) cc_final: 0.7565 (tpt170) REVERT: H 202 GLN cc_start: 0.7517 (tp40) cc_final: 0.7246 (tm-30) REVERT: H 250 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7541 (ttp-110) REVERT: H 257 ASP cc_start: 0.7848 (t70) cc_final: 0.7585 (t0) outliers start: 38 outliers final: 20 residues processed: 347 average time/residue: 0.1657 time to fit residues: 83.6670 Evaluate side-chains 318 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 295 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 210 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 207 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 135 GLN C 330 ASN D 196 ASN D 206 GLN E 206 GLN F 135 GLN G 47 HIS G 206 GLN H 196 ASN H 200 GLN H 206 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.179309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127957 restraints weight = 19212.608| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.09 r_work: 0.3322 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 18343 Z= 0.299 Angle : 0.806 8.695 24746 Z= 0.389 Chirality : 0.049 0.215 2840 Planarity : 0.005 0.064 3163 Dihedral : 9.359 132.675 2629 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.95 % Favored : 91.39 % Rotamer: Outliers : 3.34 % Allowed : 16.94 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.17), residues: 2277 helix: -0.41 (0.15), residues: 1086 sheet: -2.27 (0.29), residues: 284 loop : -2.17 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 250 TYR 0.025 0.002 TYR C 159 PHE 0.025 0.002 PHE A 327 HIS 0.005 0.001 HIS H 294 Details of bonding type rmsd covalent geometry : bond 0.00714 (18343) covalent geometry : angle 0.80641 (24746) hydrogen bonds : bond 0.04302 ( 727) hydrogen bonds : angle 5.11769 ( 2049) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 333 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.8070 (ttm) cc_final: 0.7615 (ttm) REVERT: B 23 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7883 (tp40) REVERT: B 39 LYS cc_start: 0.7369 (mtmm) cc_final: 0.6564 (tmmt) REVERT: B 154 GLU cc_start: 0.7611 (tt0) cc_final: 0.6959 (tm-30) REVERT: B 237 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5731 (pm20) REVERT: B 253 LEU cc_start: 0.7535 (mm) cc_final: 0.7197 (mp) REVERT: C 94 GLN cc_start: 0.7270 (pp30) cc_final: 0.6631 (mt0) REVERT: C 101 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7477 (tp40) REVERT: C 202 GLN cc_start: 0.7863 (mp10) cc_final: 0.7260 (tt0) REVERT: C 242 GLN cc_start: 0.8145 (mm110) cc_final: 0.7512 (mm-40) REVERT: C 243 MET cc_start: 0.7456 (mmt) cc_final: 0.7151 (mpp) REVERT: C 315 TYR cc_start: 0.8066 (t80) cc_final: 0.7345 (t80) REVERT: D 170 ARG cc_start: 0.8379 (tpp-160) cc_final: 0.7671 (tpp80) REVERT: D 315 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.6495 (m-80) REVERT: D 326 MET cc_start: 0.7604 (mmp) cc_final: 0.7336 (mmt) REVERT: E 77 GLU cc_start: 0.7500 (tp30) cc_final: 0.7290 (tp30) REVERT: E 94 GLN cc_start: 0.7046 (mt0) cc_final: 0.6557 (mp10) REVERT: E 186 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7283 (mt) REVERT: E 250 ARG cc_start: 0.7391 (ttp-110) cc_final: 0.6779 (tpp-160) REVERT: E 251 MET cc_start: 0.7887 (mtm) cc_final: 0.7257 (tpp) REVERT: F 64 LYS cc_start: 0.7789 (mmmt) cc_final: 0.7422 (mtpp) REVERT: F 198 ASP cc_start: 0.8021 (p0) cc_final: 0.7744 (p0) REVERT: F 251 MET cc_start: 0.7784 (mtp) cc_final: 0.7400 (mtp) REVERT: G 59 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7252 (mt-10) REVERT: G 130 ARG cc_start: 0.7523 (mtt90) cc_final: 0.6722 (mmt180) REVERT: G 254 ARG cc_start: 0.7498 (ptm-80) cc_final: 0.6963 (ttp-170) REVERT: G 326 MET cc_start: 0.6438 (mmp) cc_final: 0.5657 (mtm) REVERT: H 64 LYS cc_start: 0.4629 (tmmt) cc_final: 0.3788 (mmtt) REVERT: H 100 ILE cc_start: 0.7921 (mm) cc_final: 0.7406 (mm) REVERT: H 118 GLU cc_start: 0.7918 (tt0) cc_final: 0.7170 (pt0) REVERT: H 148 ILE cc_start: 0.7658 (tp) cc_final: 0.7379 (tp) REVERT: H 154 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7532 (mm-30) REVERT: H 243 MET cc_start: 0.7615 (ptm) cc_final: 0.7310 (mmp) REVERT: H 250 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7523 (ttp-110) outliers start: 62 outliers final: 40 residues processed: 370 average time/residue: 0.1600 time to fit residues: 87.5840 Evaluate side-chains 352 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 307 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 266 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 211 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 223 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 135 GLN C 330 ASN D 206 GLN E 206 GLN G 330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.187346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.139651 restraints weight = 18739.347| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.73 r_work: 0.3457 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18343 Z= 0.136 Angle : 0.667 8.160 24746 Z= 0.316 Chirality : 0.042 0.196 2840 Planarity : 0.004 0.059 3163 Dihedral : 8.619 126.427 2629 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.41 % Favored : 92.93 % Rotamer: Outliers : 2.91 % Allowed : 19.58 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.17), residues: 2277 helix: -0.10 (0.16), residues: 1083 sheet: -1.98 (0.30), residues: 280 loop : -2.19 (0.18), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 250 TYR 0.013 0.001 TYR H 315 PHE 0.025 0.001 PHE A 327 HIS 0.004 0.001 HIS H 294 Details of bonding type rmsd covalent geometry : bond 0.00307 (18343) covalent geometry : angle 0.66650 (24746) hydrogen bonds : bond 0.03244 ( 727) hydrogen bonds : angle 4.65511 ( 2049) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 316 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7554 (t) REVERT: A 251 MET cc_start: 0.8051 (ttm) cc_final: 0.7706 (ttm) REVERT: A 292 ILE cc_start: 0.7027 (tp) cc_final: 0.6738 (mm) REVERT: B 154 GLU cc_start: 0.7600 (tt0) cc_final: 0.7070 (tm-30) REVERT: C 94 GLN cc_start: 0.7224 (pp30) cc_final: 0.6628 (mt0) REVERT: C 202 GLN cc_start: 0.7720 (mp10) cc_final: 0.7213 (tt0) REVERT: C 242 GLN cc_start: 0.8132 (mm110) cc_final: 0.7496 (mm-40) REVERT: C 315 TYR cc_start: 0.7971 (t80) cc_final: 0.7262 (t80) REVERT: C 324 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7599 (mm-30) REVERT: D 170 ARG cc_start: 0.8272 (tpp-160) cc_final: 0.7758 (mmm-85) REVERT: D 211 MET cc_start: 0.7731 (mmm) cc_final: 0.7339 (mtp) REVERT: D 315 TYR cc_start: 0.7302 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: D 326 MET cc_start: 0.7647 (mmp) cc_final: 0.7417 (mmt) REVERT: D 332 ASP cc_start: 0.8098 (p0) cc_final: 0.7772 (p0) REVERT: E 94 GLN cc_start: 0.7009 (mt0) cc_final: 0.6584 (mp10) REVERT: E 126 PHE cc_start: 0.7533 (m-80) cc_final: 0.7251 (m-80) REVERT: E 250 ARG cc_start: 0.7409 (ttp-110) cc_final: 0.6845 (tpp-160) REVERT: E 251 MET cc_start: 0.7782 (mtm) cc_final: 0.7399 (tpp) REVERT: F 64 LYS cc_start: 0.7852 (mmmt) cc_final: 0.7577 (mtpp) REVERT: F 107 LYS cc_start: 0.5542 (tttm) cc_final: 0.5152 (ttpt) REVERT: F 198 ASP cc_start: 0.7920 (p0) cc_final: 0.7677 (p0) REVERT: G 43 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8139 (pm20) REVERT: G 59 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7209 (mt-10) REVERT: G 125 MET cc_start: 0.8112 (mtt) cc_final: 0.7841 (mtt) REVERT: G 130 ARG cc_start: 0.7438 (mtt90) cc_final: 0.6823 (mmt180) REVERT: G 210 MET cc_start: 0.8632 (mtm) cc_final: 0.8225 (mtm) REVERT: G 254 ARG cc_start: 0.7374 (ptm-80) cc_final: 0.6528 (mtm180) REVERT: G 258 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: G 326 MET cc_start: 0.6159 (mmp) cc_final: 0.5426 (mtm) REVERT: H 100 ILE cc_start: 0.7781 (mm) cc_final: 0.7324 (mm) REVERT: H 118 GLU cc_start: 0.7734 (tt0) cc_final: 0.6973 (pt0) REVERT: H 148 ILE cc_start: 0.7725 (tp) cc_final: 0.7496 (tp) REVERT: H 154 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7377 (mm-30) REVERT: H 250 ARG cc_start: 0.7852 (ttp-110) cc_final: 0.7571 (ttp-110) REVERT: H 267 ASN cc_start: 0.8294 (t0) cc_final: 0.8035 (m-40) REVERT: H 303 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7853 (ttp-110) outliers start: 54 outliers final: 34 residues processed: 348 average time/residue: 0.1568 time to fit residues: 81.0400 Evaluate side-chains 330 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 292 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 266 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 223 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 91 optimal weight: 0.0070 chunk 228 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 217 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 227 optimal weight: 0.6980 chunk 226 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 135 GLN C 330 ASN E 93 HIS E 188 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.187087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.138921 restraints weight = 18911.933| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.80 r_work: 0.3440 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18343 Z= 0.125 Angle : 0.653 7.732 24746 Z= 0.307 Chirality : 0.041 0.164 2840 Planarity : 0.003 0.052 3163 Dihedral : 8.151 121.177 2629 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.54 % Favored : 92.93 % Rotamer: Outliers : 3.02 % Allowed : 20.33 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.17), residues: 2277 helix: 0.06 (0.16), residues: 1092 sheet: -1.96 (0.31), residues: 279 loop : -2.11 (0.18), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 250 TYR 0.015 0.001 TYR B 301 PHE 0.025 0.001 PHE A 327 HIS 0.004 0.001 HIS H 294 Details of bonding type rmsd covalent geometry : bond 0.00281 (18343) covalent geometry : angle 0.65334 (24746) hydrogen bonds : bond 0.03080 ( 727) hydrogen bonds : angle 4.49367 ( 2049) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 302 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.7899 (p) cc_final: 0.7546 (t) REVERT: A 251 MET cc_start: 0.8004 (ttm) cc_final: 0.7670 (ttm) REVERT: B 154 GLU cc_start: 0.7615 (tt0) cc_final: 0.7080 (tm-30) REVERT: B 178 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.6941 (m-10) REVERT: B 229 ARG cc_start: 0.7827 (ttm-80) cc_final: 0.7254 (mtt90) REVERT: C 94 GLN cc_start: 0.7245 (pp30) cc_final: 0.6632 (mt0) REVERT: C 242 GLN cc_start: 0.8071 (mm110) cc_final: 0.7452 (mm-40) REVERT: C 315 TYR cc_start: 0.7860 (t80) cc_final: 0.7131 (t80) REVERT: C 332 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8178 (p0) REVERT: D 170 ARG cc_start: 0.8283 (tpp-160) cc_final: 0.7756 (mmm-85) REVERT: D 211 MET cc_start: 0.7697 (mmm) cc_final: 0.7278 (mtp) REVERT: D 249 LEU cc_start: 0.7829 (mt) cc_final: 0.7548 (mm) REVERT: D 250 ARG cc_start: 0.7853 (tpt170) cc_final: 0.7448 (ttp-110) REVERT: D 315 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.6475 (m-80) REVERT: D 332 ASP cc_start: 0.8109 (p0) cc_final: 0.7905 (p0) REVERT: E 94 GLN cc_start: 0.7023 (mt0) cc_final: 0.6593 (mp10) REVERT: E 126 PHE cc_start: 0.7540 (m-80) cc_final: 0.7168 (m-80) REVERT: E 211 MET cc_start: 0.7484 (mmt) cc_final: 0.7278 (mmt) REVERT: E 250 ARG cc_start: 0.7494 (ttp-110) cc_final: 0.6933 (tpp-160) REVERT: E 251 MET cc_start: 0.7854 (mtm) cc_final: 0.7418 (tpp) REVERT: F 23 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8372 (tt0) REVERT: F 64 LYS cc_start: 0.7816 (mmmt) cc_final: 0.7503 (mtpp) REVERT: F 107 LYS cc_start: 0.5432 (tttm) cc_final: 0.5119 (ttpt) REVERT: G 43 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8109 (pm20) REVERT: G 59 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7201 (mt-10) REVERT: G 125 MET cc_start: 0.8079 (mtt) cc_final: 0.7802 (mtt) REVERT: G 130 ARG cc_start: 0.7463 (mtt90) cc_final: 0.6802 (mmm160) REVERT: G 254 ARG cc_start: 0.7317 (ptm-80) cc_final: 0.6380 (mtm180) REVERT: G 258 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: G 326 MET cc_start: 0.6189 (mmp) cc_final: 0.5518 (mtm) REVERT: H 100 ILE cc_start: 0.7764 (mm) cc_final: 0.7295 (mm) REVERT: H 118 GLU cc_start: 0.7739 (tt0) cc_final: 0.6989 (pt0) REVERT: H 148 ILE cc_start: 0.7675 (tp) cc_final: 0.7458 (tp) REVERT: H 154 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7398 (mm-30) REVERT: H 250 ARG cc_start: 0.7868 (ttp-110) cc_final: 0.7587 (ttp-110) REVERT: H 267 ASN cc_start: 0.8295 (t0) cc_final: 0.8074 (m-40) outliers start: 56 outliers final: 36 residues processed: 341 average time/residue: 0.1614 time to fit residues: 80.5905 Evaluate side-chains 321 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 279 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 266 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 226 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 135 GLN C 330 ASN E 244 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.184169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.133549 restraints weight = 18912.386| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.95 r_work: 0.3356 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 18343 Z= 0.233 Angle : 0.735 8.208 24746 Z= 0.350 Chirality : 0.046 0.175 2840 Planarity : 0.004 0.049 3163 Dihedral : 8.232 129.418 2629 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.69 % Favored : 91.79 % Rotamer: Outliers : 3.99 % Allowed : 20.39 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.17), residues: 2277 helix: -0.14 (0.16), residues: 1086 sheet: -2.30 (0.29), residues: 296 loop : -2.22 (0.18), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 250 TYR 0.018 0.002 TYR H 315 PHE 0.025 0.002 PHE A 327 HIS 0.004 0.001 HIS H 294 Details of bonding type rmsd covalent geometry : bond 0.00557 (18343) covalent geometry : angle 0.73506 (24746) hydrogen bonds : bond 0.03680 ( 727) hydrogen bonds : angle 4.79617 ( 2049) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 310 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 198 ASP cc_start: 0.7245 (p0) cc_final: 0.6993 (t70) REVERT: A 251 MET cc_start: 0.8088 (ttm) cc_final: 0.7717 (ttm) REVERT: B 39 LYS cc_start: 0.7436 (mtmm) cc_final: 0.6722 (tmmt) REVERT: B 154 GLU cc_start: 0.7618 (tt0) cc_final: 0.7020 (tm-30) REVERT: B 178 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7143 (m-10) REVERT: B 229 ARG cc_start: 0.7886 (ttm-80) cc_final: 0.7329 (mtt90) REVERT: C 94 GLN cc_start: 0.7253 (pp30) cc_final: 0.6582 (mt0) REVERT: C 202 GLN cc_start: 0.7790 (mp10) cc_final: 0.7222 (tt0) REVERT: C 242 GLN cc_start: 0.8001 (mm110) cc_final: 0.7371 (mm-40) REVERT: C 315 TYR cc_start: 0.8057 (t80) cc_final: 0.7297 (t80) REVERT: D 27 ARG cc_start: 0.6872 (OUTLIER) cc_final: 0.6382 (ttp-110) REVERT: D 170 ARG cc_start: 0.8385 (tpp-160) cc_final: 0.7572 (tpp80) REVERT: D 332 ASP cc_start: 0.8072 (p0) cc_final: 0.7616 (p0) REVERT: E 77 GLU cc_start: 0.7520 (tp30) cc_final: 0.7298 (tp30) REVERT: E 94 GLN cc_start: 0.6974 (mt0) cc_final: 0.6520 (mp10) REVERT: E 126 PHE cc_start: 0.7526 (m-80) cc_final: 0.7173 (m-80) REVERT: E 136 ILE cc_start: 0.7721 (pt) cc_final: 0.6922 (mm) REVERT: E 143 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7173 (p) REVERT: E 211 MET cc_start: 0.7584 (mmt) cc_final: 0.7334 (mmt) REVERT: E 250 ARG cc_start: 0.7424 (ttp-110) cc_final: 0.6838 (tpp-160) REVERT: E 251 MET cc_start: 0.7938 (mtm) cc_final: 0.7349 (tpp) REVERT: F 23 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8245 (mt0) REVERT: F 107 LYS cc_start: 0.5409 (tttm) cc_final: 0.5057 (ttpt) REVERT: F 198 ASP cc_start: 0.8017 (p0) cc_final: 0.7736 (p0) REVERT: G 43 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: G 59 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7268 (mt-10) REVERT: G 130 ARG cc_start: 0.7575 (mtt90) cc_final: 0.6838 (mmm160) REVERT: G 254 ARG cc_start: 0.7356 (ptm-80) cc_final: 0.6446 (mtm180) REVERT: G 258 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: G 326 MET cc_start: 0.6321 (mmp) cc_final: 0.5573 (mtm) REVERT: H 100 ILE cc_start: 0.7892 (mm) cc_final: 0.7357 (mm) REVERT: H 118 GLU cc_start: 0.7920 (tt0) cc_final: 0.7154 (pt0) REVERT: H 148 ILE cc_start: 0.7586 (tp) cc_final: 0.7351 (tp) REVERT: H 154 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7437 (mm-30) REVERT: H 250 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7599 (ttp-110) REVERT: H 267 ASN cc_start: 0.8523 (t0) cc_final: 0.8202 (m-40) REVERT: H 304 LYS cc_start: 0.7631 (ttpt) cc_final: 0.7393 (tttp) outliers start: 74 outliers final: 52 residues processed: 355 average time/residue: 0.1610 time to fit residues: 83.8749 Evaluate side-chains 348 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 290 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 261 VAL Chi-restraints excluded: chain H residue 266 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 107 optimal weight: 0.7980 chunk 205 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 158 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 135 GLN C 330 ASN F 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.191326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.139371 restraints weight = 18603.948| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.81 r_work: 0.3455 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18343 Z= 0.117 Angle : 0.665 9.130 24746 Z= 0.313 Chirality : 0.041 0.166 2840 Planarity : 0.003 0.047 3163 Dihedral : 7.497 119.732 2629 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.32 % Favored : 93.15 % Rotamer: Outliers : 3.07 % Allowed : 21.47 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.17), residues: 2277 helix: 0.15 (0.16), residues: 1088 sheet: -1.92 (0.31), residues: 269 loop : -2.22 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 250 TYR 0.016 0.001 TYR B 301 PHE 0.018 0.001 PHE G 126 HIS 0.004 0.001 HIS E 244 Details of bonding type rmsd covalent geometry : bond 0.00255 (18343) covalent geometry : angle 0.66452 (24746) hydrogen bonds : bond 0.02981 ( 727) hydrogen bonds : angle 4.43129 ( 2049) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 289 time to evaluate : 0.703 Fit side-chains REVERT: A 87 THR cc_start: 0.7897 (p) cc_final: 0.7569 (t) REVERT: A 251 MET cc_start: 0.8063 (ttm) cc_final: 0.7740 (ttm) REVERT: B 154 GLU cc_start: 0.7666 (tt0) cc_final: 0.7113 (tm-30) REVERT: B 178 TYR cc_start: 0.7649 (OUTLIER) cc_final: 0.7047 (m-10) REVERT: B 229 ARG cc_start: 0.7811 (ttm-80) cc_final: 0.7289 (mtt180) REVERT: C 94 GLN cc_start: 0.7239 (pp30) cc_final: 0.6635 (mt0) REVERT: C 242 GLN cc_start: 0.7974 (mm110) cc_final: 0.7356 (mm-40) REVERT: C 315 TYR cc_start: 0.7921 (t80) cc_final: 0.7195 (t80) REVERT: D 170 ARG cc_start: 0.8276 (tpp-160) cc_final: 0.7729 (mmm-85) REVERT: D 250 ARG cc_start: 0.7774 (tpt170) cc_final: 0.7420 (ttt-90) REVERT: D 332 ASP cc_start: 0.7959 (p0) cc_final: 0.7747 (p0) REVERT: E 77 GLU cc_start: 0.7449 (tp30) cc_final: 0.7236 (tp30) REVERT: E 94 GLN cc_start: 0.7009 (mt0) cc_final: 0.6578 (mp10) REVERT: E 126 PHE cc_start: 0.7508 (m-80) cc_final: 0.7153 (m-80) REVERT: E 136 ILE cc_start: 0.7620 (pt) cc_final: 0.6750 (mm) REVERT: E 143 THR cc_start: 0.7714 (OUTLIER) cc_final: 0.7307 (p) REVERT: E 250 ARG cc_start: 0.7479 (ttp-110) cc_final: 0.6899 (tpp-160) REVERT: E 251 MET cc_start: 0.7863 (mtm) cc_final: 0.7463 (tpp) REVERT: E 326 MET cc_start: 0.1491 (mmm) cc_final: 0.1289 (mmt) REVERT: F 43 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: F 64 LYS cc_start: 0.7730 (mmmt) cc_final: 0.7327 (mtpp) REVERT: G 43 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: G 59 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7149 (mt-10) REVERT: G 130 ARG cc_start: 0.7539 (mtt90) cc_final: 0.6875 (mmt180) REVERT: G 254 ARG cc_start: 0.7335 (ptm-80) cc_final: 0.6390 (mtm180) REVERT: G 258 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: G 326 MET cc_start: 0.6240 (mmp) cc_final: 0.5736 (mtm) REVERT: H 100 ILE cc_start: 0.7776 (mm) cc_final: 0.7292 (mm) REVERT: H 118 GLU cc_start: 0.7750 (tt0) cc_final: 0.6964 (pt0) REVERT: H 154 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7355 (mm-30) REVERT: H 211 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7276 (mtt) REVERT: H 250 ARG cc_start: 0.7878 (ttp-110) cc_final: 0.7610 (ttp-110) REVERT: H 267 ASN cc_start: 0.8319 (t0) cc_final: 0.8116 (m-40) outliers start: 57 outliers final: 39 residues processed: 322 average time/residue: 0.1628 time to fit residues: 77.1002 Evaluate side-chains 320 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 275 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain H residue 266 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 83 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 164 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 161 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 135 GLN C 330 ASN E 188 ASN F 268 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.189305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135031 restraints weight = 18806.898| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.94 r_work: 0.3427 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18343 Z= 0.130 Angle : 0.663 9.420 24746 Z= 0.311 Chirality : 0.041 0.160 2840 Planarity : 0.004 0.047 3163 Dihedral : 7.158 114.996 2629 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.07 % Favored : 92.40 % Rotamer: Outliers : 2.97 % Allowed : 22.22 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.17), residues: 2277 helix: 0.23 (0.16), residues: 1090 sheet: -1.88 (0.31), residues: 275 loop : -2.20 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 250 TYR 0.016 0.001 TYR E 301 PHE 0.014 0.001 PHE G 126 HIS 0.009 0.001 HIS H 294 Details of bonding type rmsd covalent geometry : bond 0.00296 (18343) covalent geometry : angle 0.66320 (24746) hydrogen bonds : bond 0.02996 ( 727) hydrogen bonds : angle 4.38412 ( 2049) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 287 time to evaluate : 0.661 Fit side-chains REVERT: A 87 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7429 (t) REVERT: A 251 MET cc_start: 0.7973 (ttm) cc_final: 0.7616 (ttm) REVERT: B 154 GLU cc_start: 0.7704 (tt0) cc_final: 0.7046 (tm-30) REVERT: B 178 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6969 (m-10) REVERT: B 229 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7152 (mtt180) REVERT: C 94 GLN cc_start: 0.6971 (pp30) cc_final: 0.6328 (mt0) REVERT: C 242 GLN cc_start: 0.7859 (mm110) cc_final: 0.7217 (mm-40) REVERT: C 315 TYR cc_start: 0.7967 (t80) cc_final: 0.7230 (t80) REVERT: D 27 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6609 (ttm110) REVERT: D 170 ARG cc_start: 0.8221 (tpp-160) cc_final: 0.7634 (mmm-85) REVERT: D 250 ARG cc_start: 0.7681 (tpt170) cc_final: 0.7291 (ttt-90) REVERT: D 332 ASP cc_start: 0.7898 (p0) cc_final: 0.7695 (p0) REVERT: E 77 GLU cc_start: 0.7266 (tp30) cc_final: 0.7028 (tp30) REVERT: E 94 GLN cc_start: 0.6847 (mt0) cc_final: 0.6359 (mp10) REVERT: E 126 PHE cc_start: 0.7453 (m-80) cc_final: 0.7124 (m-80) REVERT: E 136 ILE cc_start: 0.7499 (pt) cc_final: 0.6826 (mm) REVERT: E 143 THR cc_start: 0.7579 (OUTLIER) cc_final: 0.7154 (p) REVERT: E 211 MET cc_start: 0.7437 (mmt) cc_final: 0.7223 (mmt) REVERT: E 250 ARG cc_start: 0.7346 (ttp-110) cc_final: 0.6704 (tpp-160) REVERT: E 251 MET cc_start: 0.7896 (mtm) cc_final: 0.7255 (tpp) REVERT: F 43 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: F 64 LYS cc_start: 0.7687 (mmmt) cc_final: 0.7251 (mtpp) REVERT: F 198 ASP cc_start: 0.7798 (p0) cc_final: 0.7410 (t70) REVERT: G 43 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: G 59 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7046 (mt-10) REVERT: G 130 ARG cc_start: 0.7559 (mtt90) cc_final: 0.6711 (mmm160) REVERT: G 254 ARG cc_start: 0.7182 (ptm-80) cc_final: 0.6246 (mtm180) REVERT: G 258 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: G 326 MET cc_start: 0.6219 (mmp) cc_final: 0.5558 (mtm) REVERT: H 100 ILE cc_start: 0.7699 (mm) cc_final: 0.7378 (mm) REVERT: H 118 GLU cc_start: 0.7774 (tt0) cc_final: 0.6867 (pt0) REVERT: H 154 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7364 (mm-30) REVERT: H 211 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.7044 (mtt) REVERT: H 250 ARG cc_start: 0.7801 (ttp-110) cc_final: 0.7508 (ttp-110) REVERT: H 267 ASN cc_start: 0.8399 (t0) cc_final: 0.8163 (m-40) outliers start: 55 outliers final: 40 residues processed: 320 average time/residue: 0.1458 time to fit residues: 69.0831 Evaluate side-chains 328 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 280 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain H residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 67 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 160 optimal weight: 0.4980 chunk 195 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 135 GLN C 330 ASN D 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.189404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139161 restraints weight = 18836.602| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.82 r_work: 0.3448 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18343 Z= 0.132 Angle : 0.664 10.019 24746 Z= 0.312 Chirality : 0.042 0.167 2840 Planarity : 0.003 0.046 3163 Dihedral : 6.844 107.113 2629 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.54 % Favored : 92.93 % Rotamer: Outliers : 2.75 % Allowed : 22.71 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.17), residues: 2277 helix: 0.31 (0.16), residues: 1087 sheet: -1.74 (0.32), residues: 269 loop : -2.15 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 250 TYR 0.018 0.001 TYR G 301 PHE 0.015 0.001 PHE G 126 HIS 0.008 0.001 HIS H 294 Details of bonding type rmsd covalent geometry : bond 0.00303 (18343) covalent geometry : angle 0.66416 (24746) hydrogen bonds : bond 0.02971 ( 727) hydrogen bonds : angle 4.34423 ( 2049) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 282 time to evaluate : 0.678 Fit side-chains REVERT: A 87 THR cc_start: 0.7807 (p) cc_final: 0.7441 (t) REVERT: A 251 MET cc_start: 0.7972 (ttm) cc_final: 0.7643 (ttm) REVERT: B 154 GLU cc_start: 0.7662 (tt0) cc_final: 0.7086 (tm-30) REVERT: B 178 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.6896 (m-10) REVERT: B 229 ARG cc_start: 0.7722 (ttm-80) cc_final: 0.7147 (mtt180) REVERT: C 94 GLN cc_start: 0.7009 (pp30) cc_final: 0.6382 (mt0) REVERT: C 242 GLN cc_start: 0.7887 (mm110) cc_final: 0.7253 (mm-40) REVERT: C 315 TYR cc_start: 0.7852 (t80) cc_final: 0.7173 (t80) REVERT: D 27 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6638 (ttm110) REVERT: D 170 ARG cc_start: 0.8236 (tpp-160) cc_final: 0.7653 (mmm-85) REVERT: D 250 ARG cc_start: 0.7697 (tpt170) cc_final: 0.7329 (ttt-90) REVERT: E 77 GLU cc_start: 0.7292 (tp30) cc_final: 0.7071 (tp30) REVERT: E 94 GLN cc_start: 0.6895 (mt0) cc_final: 0.6413 (mp10) REVERT: E 126 PHE cc_start: 0.7495 (m-80) cc_final: 0.7143 (m-80) REVERT: E 136 ILE cc_start: 0.7538 (pt) cc_final: 0.6853 (mm) REVERT: E 143 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7211 (p) REVERT: E 250 ARG cc_start: 0.7380 (ttp-110) cc_final: 0.6768 (tpp-160) REVERT: E 251 MET cc_start: 0.7910 (mtm) cc_final: 0.7326 (tpp) REVERT: E 301 TYR cc_start: 0.7731 (t80) cc_final: 0.7388 (t80) REVERT: F 43 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: F 64 LYS cc_start: 0.7777 (mmmt) cc_final: 0.7276 (mtpp) REVERT: F 198 ASP cc_start: 0.7815 (p0) cc_final: 0.7418 (t0) REVERT: G 43 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7964 (pm20) REVERT: G 59 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7080 (mt-10) REVERT: G 130 ARG cc_start: 0.7567 (mtt90) cc_final: 0.6773 (mmm160) REVERT: G 205 TYR cc_start: 0.8102 (m-10) cc_final: 0.7659 (m-10) REVERT: G 254 ARG cc_start: 0.7244 (ptm-80) cc_final: 0.6431 (mtm180) REVERT: G 258 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: G 326 MET cc_start: 0.6206 (mmp) cc_final: 0.5603 (mtm) REVERT: H 84 MET cc_start: 0.2165 (tpt) cc_final: 0.1587 (tpt) REVERT: H 100 ILE cc_start: 0.7680 (mm) cc_final: 0.7346 (mm) REVERT: H 154 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7358 (mm-30) REVERT: H 211 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.7076 (mtp) REVERT: H 250 ARG cc_start: 0.7808 (ttp-110) cc_final: 0.7511 (ttp-110) REVERT: H 267 ASN cc_start: 0.8385 (t0) cc_final: 0.8183 (m-40) outliers start: 51 outliers final: 39 residues processed: 312 average time/residue: 0.1500 time to fit residues: 68.6893 Evaluate side-chains 319 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 273 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain H residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 88 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 177 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 135 GLN C 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.189707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136275 restraints weight = 18532.658| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.82 r_work: 0.3380 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18343 Z= 0.215 Angle : 0.729 10.298 24746 Z= 0.348 Chirality : 0.045 0.175 2840 Planarity : 0.004 0.044 3163 Dihedral : 7.080 102.626 2629 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.91 % Favored : 91.57 % Rotamer: Outliers : 2.97 % Allowed : 22.55 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.17), residues: 2277 helix: 0.07 (0.16), residues: 1086 sheet: -2.10 (0.30), residues: 286 loop : -2.27 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 250 TYR 0.022 0.002 TYR G 301 PHE 0.016 0.002 PHE C 126 HIS 0.008 0.001 HIS H 294 Details of bonding type rmsd covalent geometry : bond 0.00512 (18343) covalent geometry : angle 0.72907 (24746) hydrogen bonds : bond 0.03516 ( 727) hydrogen bonds : angle 4.66335 ( 2049) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5112.13 seconds wall clock time: 88 minutes 32.83 seconds (5312.83 seconds total)