Starting phenix.real_space_refine on Mon Jun 16 03:50:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gyk_34372/06_2025/8gyk_34372.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gyk_34372/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gyk_34372/06_2025/8gyk_34372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gyk_34372/06_2025/8gyk_34372.map" model { file = "/net/cci-nas-00/data/ceres_data/8gyk_34372/06_2025/8gyk_34372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gyk_34372/06_2025/8gyk_34372.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.48, per 1000 atoms: 0.63 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: 4.05 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.00 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: 4.77 Time building geometry restraints manager: 4.83 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 336 or \ resid 600 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 336 or \ resid 600 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 336 or \ resid 600 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 336 or resid 600 through 601)) selection = (chain 'E' and (resid 21 through 270 or resid 291 through 336 or resid 600 throu \ gh 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 336 or \ resid 600 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 336 or \ resid 600 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 336 or resid 600 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: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.800 Check model and map are aligned: 0.120 Set scattering table: 0.190 Process input model: 39.180 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.080 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.580 ------------------------------------------------------------------------------- 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 : 13.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.003 0.001 HIS E 244 PHE 0.020 0.001 PHE A 126 TYR 0.022 0.001 TYR C 315 ARG 0.014 0.001 ARG B 27 Details of bonding type rmsd hydrogen bonds : bond 0.24048 ( 727) hydrogen bonds : angle 7.50611 ( 2049) covalent geometry : bond 0.00339 (18343) covalent geometry : angle 0.73300 (24746) *********************** 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 : 2.030 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: 0.3496 time to fit residues: 235.5236 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 : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 244 HIS B 23 GLN B 101 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 330 ASN D 62 ASN D 206 GLN E 188 ASN E 206 GLN F 135 GLN G 135 GLN H 200 GLN H 294 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.194299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.153649 restraints weight = 18721.232| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.36 r_work: 0.3586 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 18343 Z= 0.163 Angle : 0.729 7.765 24746 Z= 0.352 Chirality : 0.045 0.218 2840 Planarity : 0.005 0.059 3163 Dihedral : 10.104 130.597 2629 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.68 % Favored : 92.67 % Rotamer: Outliers : 1.62 % Allowed : 10.63 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.17), residues: 2277 helix: -0.36 (0.15), residues: 1087 sheet: -1.91 (0.28), residues: 330 loop : -2.11 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 47 PHE 0.031 0.002 PHE A 327 TYR 0.018 0.002 TYR E 315 ARG 0.007 0.001 ARG H 254 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 727) hydrogen bonds : angle 5.08579 ( 2049) covalent geometry : bond 0.00372 (18343) covalent geometry : angle 0.72947 (24746) *********************** 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 368 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 338 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.6610 (mmt) cc_final: 0.6276 (tpp) REVERT: A 229 ARG cc_start: 0.4408 (mmt180) cc_final: 0.4106 (mmt180) REVERT: A 243 MET cc_start: 0.7769 (ttm) cc_final: 0.7550 (ttp) REVERT: A 251 MET cc_start: 0.7897 (ttm) cc_final: 0.7692 (ttm) REVERT: B 130 ARG cc_start: 0.6825 (mmp-170) cc_final: 0.6250 (mtp85) REVERT: B 154 GLU cc_start: 0.7346 (tt0) cc_final: 0.7126 (tm-30) REVERT: B 229 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7583 (mtt90) REVERT: C 80 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8087 (mtmm) REVERT: C 163 GLU cc_start: 0.6771 (tp30) cc_final: 0.6087 (tp30) REVERT: C 205 TYR cc_start: 0.8761 (m-10) cc_final: 0.8479 (m-10) REVERT: C 242 GLN cc_start: 0.8210 (mm110) cc_final: 0.7723 (mm-40) REVERT: C 250 ARG cc_start: 0.8097 (ttp-110) cc_final: 0.7680 (mtp-110) REVERT: C 267 ASN cc_start: 0.8124 (t0) cc_final: 0.7924 (t0) REVERT: C 315 TYR cc_start: 0.7841 (t80) cc_final: 0.7317 (t80) REVERT: D 95 ARG cc_start: 0.7175 (ptt90) cc_final: 0.6691 (mmp80) REVERT: D 170 ARG cc_start: 0.8277 (tpp-160) cc_final: 0.7943 (mmm-85) REVERT: D 178 TYR cc_start: 0.7936 (m-80) cc_final: 0.7682 (m-80) REVERT: D 208 SER cc_start: 0.8742 (t) cc_final: 0.8475 (t) REVERT: D 243 MET cc_start: 0.7856 (tmm) cc_final: 0.7450 (tmm) REVERT: D 250 ARG cc_start: 0.8003 (tpt170) cc_final: 0.7655 (ttm110) REVERT: D 315 TYR cc_start: 0.7266 (OUTLIER) cc_final: 0.6176 (m-80) REVERT: D 326 MET cc_start: 0.7105 (mmp) cc_final: 0.6459 (tmm) REVERT: E 140 LEU cc_start: 0.7338 (tp) cc_final: 0.7052 (mt) REVERT: E 176 GLU cc_start: 0.6583 (pt0) cc_final: 0.6280 (tp30) REVERT: E 251 MET cc_start: 0.7718 (mtm) cc_final: 0.7504 (tpt) REVERT: G 59 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7091 (mt-10) REVERT: G 68 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7616 (tp30) REVERT: G 130 ARG cc_start: 0.7211 (mtt90) cc_final: 0.6722 (mmm160) REVERT: G 205 TYR cc_start: 0.8024 (m-10) cc_final: 0.7792 (m-10) REVERT: G 326 MET cc_start: 0.5487 (mmp) cc_final: 0.4562 (mtm) REVERT: H 100 ILE cc_start: 0.7570 (mm) cc_final: 0.7196 (mm) REVERT: H 118 GLU cc_start: 0.7566 (tt0) cc_final: 0.7167 (pt0) REVERT: H 148 ILE cc_start: 0.7648 (tp) cc_final: 0.7426 (tp) REVERT: H 170 ARG cc_start: 0.7982 (tpp-160) cc_final: 0.7682 (tpt90) REVERT: H 250 ARG cc_start: 0.7893 (ttp-110) cc_final: 0.7630 (ttp-110) REVERT: H 257 ASP cc_start: 0.7803 (t70) cc_final: 0.7555 (t0) REVERT: H 267 ASN cc_start: 0.7962 (t0) cc_final: 0.7603 (t0) outliers start: 30 outliers final: 15 residues processed: 353 average time/residue: 0.3223 time to fit residues: 166.5634 Evaluate side-chains 307 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 291 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 315 TYR Chi-restraints excluded: chain E residue 165 THR 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 97 SER 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 49 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS B 23 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 23 GLN C 135 GLN C 330 ASN D 196 ASN D 200 GLN E 188 ASN E 206 GLN F 135 GLN G 206 GLN H 196 ASN H 206 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.184421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.140698 restraints weight = 19147.242| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.57 r_work: 0.3414 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 18343 Z= 0.291 Angle : 0.817 8.863 24746 Z= 0.398 Chirality : 0.049 0.196 2840 Planarity : 0.005 0.057 3163 Dihedral : 9.853 140.084 2629 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.08 % Favored : 91.26 % Rotamer: Outliers : 3.07 % Allowed : 15.59 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.16), residues: 2277 helix: -0.56 (0.15), residues: 1100 sheet: -2.41 (0.29), residues: 278 loop : -2.27 (0.18), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 47 PHE 0.027 0.002 PHE A 327 TYR 0.030 0.002 TYR C 159 ARG 0.006 0.001 ARG G 170 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 727) hydrogen bonds : angle 5.24770 ( 2049) covalent geometry : bond 0.00696 (18343) covalent geometry : angle 0.81712 (24746) *********************** 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 414 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 357 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.5529 (mm-30) cc_final: 0.5328 (tm-30) REVERT: A 251 MET cc_start: 0.8061 (ttm) cc_final: 0.7784 (ttm) REVERT: B 27 ARG cc_start: 0.6990 (ttm110) cc_final: 0.6668 (mtt-85) REVERT: B 130 ARG cc_start: 0.7304 (mmp-170) cc_final: 0.6543 (mtp85) REVERT: B 154 GLU cc_start: 0.7500 (tt0) cc_final: 0.7117 (tm-30) REVERT: B 253 LEU cc_start: 0.7702 (mm) cc_final: 0.7424 (mp) REVERT: B 313 LYS cc_start: 0.6548 (mttp) cc_final: 0.5919 (pttp) REVERT: C 163 GLU cc_start: 0.7137 (tp30) cc_final: 0.6901 (tp30) REVERT: C 242 GLN cc_start: 0.8270 (mm110) cc_final: 0.7729 (mm-40) REVERT: C 243 MET cc_start: 0.7593 (mmt) cc_final: 0.7277 (mpp) REVERT: C 303 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.7121 (mtm110) REVERT: C 315 TYR cc_start: 0.7997 (t80) cc_final: 0.7421 (t80) REVERT: D 170 ARG cc_start: 0.8521 (tpp-160) cc_final: 0.7942 (tpp80) REVERT: D 315 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6524 (m-80) REVERT: D 326 MET cc_start: 0.7537 (mmp) cc_final: 0.6868 (tmm) REVERT: E 94 GLN cc_start: 0.7149 (mt0) cc_final: 0.6816 (mp10) REVERT: E 126 PHE cc_start: 0.7521 (m-80) cc_final: 0.7312 (m-10) REVERT: E 250 ARG cc_start: 0.7577 (ttp-110) cc_final: 0.7173 (tpp-160) REVERT: F 64 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7586 (mtpp) REVERT: F 198 ASP cc_start: 0.7918 (p0) cc_final: 0.7708 (p0) REVERT: G 59 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7511 (mm-30) REVERT: G 130 ARG cc_start: 0.7637 (mtt90) cc_final: 0.7067 (mmt180) REVERT: G 326 MET cc_start: 0.6326 (mmp) cc_final: 0.5306 (mtm) REVERT: G 330 ASN cc_start: 0.8388 (m110) cc_final: 0.8140 (m-40) REVERT: H 64 LYS cc_start: 0.4766 (tmmt) cc_final: 0.3934 (mmtt) REVERT: H 100 ILE cc_start: 0.7997 (mm) cc_final: 0.7541 (mm) REVERT: H 118 GLU cc_start: 0.7754 (tt0) cc_final: 0.7227 (pt0) REVERT: H 124 GLU cc_start: 0.8170 (tt0) cc_final: 0.7858 (tt0) REVERT: H 128 GLU cc_start: 0.6804 (tp30) cc_final: 0.6554 (tt0) REVERT: H 148 ILE cc_start: 0.7638 (tp) cc_final: 0.7374 (tp) REVERT: H 250 ARG cc_start: 0.7890 (ttp-110) cc_final: 0.7670 (ttp-110) outliers start: 57 outliers final: 34 residues processed: 388 average time/residue: 0.3291 time to fit residues: 186.3132 Evaluate side-chains 341 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 306 time to evaluate : 1.926 ------------------------------------------------------------------------------- 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 149 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 28 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 200 GLN 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 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 208 SER Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 CYS 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 142 VAL Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 169 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 208 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 179 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS C 135 GLN C 206 GLN C 330 ASN D 200 GLN E 206 GLN H 101 GLN H 135 GLN H 206 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.184921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.135872 restraints weight = 18965.458| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.71 r_work: 0.3421 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18343 Z= 0.143 Angle : 0.681 8.149 24746 Z= 0.324 Chirality : 0.043 0.233 2840 Planarity : 0.004 0.061 3163 Dihedral : 9.040 135.644 2629 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.63 % Favored : 92.71 % Rotamer: Outliers : 2.86 % Allowed : 18.12 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.17), residues: 2277 helix: -0.14 (0.16), residues: 1088 sheet: -2.11 (0.29), residues: 288 loop : -2.20 (0.18), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 294 PHE 0.025 0.001 PHE A 327 TYR 0.018 0.001 TYR H 315 ARG 0.006 0.000 ARG C 250 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 727) hydrogen bonds : angle 4.73895 ( 2049) covalent geometry : bond 0.00324 (18343) covalent geometry : angle 0.68066 (24746) *********************** 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 385 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 332 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 CYS cc_start: 0.6583 (m) cc_final: 0.6351 (m) REVERT: A 251 MET cc_start: 0.8015 (ttm) cc_final: 0.7668 (ttm) REVERT: B 27 ARG cc_start: 0.6880 (ttm110) cc_final: 0.6572 (mtt-85) REVERT: B 43 GLU cc_start: 0.7588 (mp0) cc_final: 0.7361 (mp0) REVERT: B 130 ARG cc_start: 0.6733 (mmp-170) cc_final: 0.6099 (mtp85) REVERT: B 154 GLU cc_start: 0.7585 (tt0) cc_final: 0.7027 (tm-30) REVERT: B 250 ARG cc_start: 0.7362 (ttp-110) cc_final: 0.6957 (ttm110) REVERT: B 313 LYS cc_start: 0.6322 (mttp) cc_final: 0.5641 (pttp) REVERT: B 326 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7329 (mmt) REVERT: C 94 GLN cc_start: 0.7173 (pp30) cc_final: 0.6569 (mt0) REVERT: C 101 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7458 (tp40) REVERT: C 163 GLU cc_start: 0.6865 (tp30) cc_final: 0.6235 (tp30) REVERT: C 202 GLN cc_start: 0.7729 (mp10) cc_final: 0.7221 (tt0) REVERT: C 242 GLN cc_start: 0.8151 (mm110) cc_final: 0.7535 (mm-40) REVERT: C 243 MET cc_start: 0.7475 (mmt) cc_final: 0.7203 (mpp) REVERT: C 303 ARG cc_start: 0.7676 (mtm-85) cc_final: 0.7469 (mtm110) REVERT: C 315 TYR cc_start: 0.7930 (t80) cc_final: 0.7213 (t80) REVERT: C 324 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7537 (mm-30) REVERT: D 170 ARG cc_start: 0.8283 (tpp-160) cc_final: 0.7527 (tpp80) REVERT: D 211 MET cc_start: 0.7769 (mmm) cc_final: 0.7389 (mtp) REVERT: D 315 TYR cc_start: 0.7358 (OUTLIER) cc_final: 0.6477 (m-80) REVERT: D 326 MET cc_start: 0.7536 (mmp) cc_final: 0.7320 (tpt) REVERT: D 332 ASP cc_start: 0.8050 (p0) cc_final: 0.7554 (p0) REVERT: E 94 GLN cc_start: 0.7047 (mt0) cc_final: 0.6590 (mp10) REVERT: E 250 ARG cc_start: 0.7373 (ttp-110) cc_final: 0.6790 (tpp-160) REVERT: E 251 MET cc_start: 0.7822 (mtm) cc_final: 0.7344 (tpp) REVERT: F 23 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8261 (mt0) REVERT: F 64 LYS cc_start: 0.7831 (mmmt) cc_final: 0.7481 (mtpp) REVERT: G 43 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: G 59 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7318 (mm-30) REVERT: G 130 ARG cc_start: 0.7419 (mtt90) cc_final: 0.6757 (mmt180) REVERT: G 258 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7584 (mp0) REVERT: G 326 MET cc_start: 0.6191 (mmp) cc_final: 0.5263 (mtm) REVERT: H 100 ILE cc_start: 0.7818 (mm) cc_final: 0.7361 (mm) REVERT: H 118 GLU cc_start: 0.7718 (tt0) cc_final: 0.7010 (pt0) REVERT: H 128 GLU cc_start: 0.7004 (tp30) cc_final: 0.6686 (tt0) REVERT: H 187 ASP cc_start: 0.8313 (t0) cc_final: 0.8094 (m-30) REVERT: H 250 ARG cc_start: 0.7854 (ttp-110) cc_final: 0.7587 (ttp-110) REVERT: H 304 LYS cc_start: 0.8090 (tppt) cc_final: 0.7875 (tppt) outliers start: 53 outliers final: 29 residues processed: 363 average time/residue: 0.3226 time to fit residues: 171.8335 Evaluate side-chains 334 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 300 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 326 MET 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 238 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 97 SER 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 200 GLN 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 E residue 172 LEU Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 238 LEU 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 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 84 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 0.0770 chunk 211 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 201 optimal weight: 0.3980 chunk 90 optimal weight: 0.9990 overall best weight: 0.8944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 330 ASN D 200 GLN E 188 ASN E 244 HIS H 101 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.185291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132619 restraints weight = 19061.877| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.86 r_work: 0.3399 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4058 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= 0.141 Angle : 0.665 7.688 24746 Z= 0.316 Chirality : 0.042 0.199 2840 Planarity : 0.004 0.058 3163 Dihedral : 8.543 126.690 2629 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.81 % Favored : 92.58 % Rotamer: Outliers : 3.83 % Allowed : 19.04 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.17), residues: 2277 helix: 0.02 (0.16), residues: 1094 sheet: -1.95 (0.30), residues: 278 loop : -2.23 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 47 PHE 0.025 0.001 PHE A 327 TYR 0.016 0.001 TYR H 315 ARG 0.006 0.000 ARG C 250 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 727) hydrogen bonds : angle 4.61786 ( 2049) covalent geometry : bond 0.00322 (18343) covalent geometry : angle 0.66534 (24746) *********************** 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 378 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 307 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7766 (mtt-85) REVERT: A 251 MET cc_start: 0.8017 (ttm) cc_final: 0.7666 (ttm) REVERT: A 292 ILE cc_start: 0.7003 (tp) cc_final: 0.6763 (mm) REVERT: B 27 ARG cc_start: 0.6818 (ttm110) cc_final: 0.6557 (mtt-85) REVERT: B 154 GLU cc_start: 0.7612 (tt0) cc_final: 0.6994 (tm-30) REVERT: B 253 LEU cc_start: 0.7552 (mt) cc_final: 0.7329 (mt) REVERT: B 326 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7308 (mmt) REVERT: C 94 GLN cc_start: 0.7111 (pp30) cc_final: 0.6494 (mt0) REVERT: C 101 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7354 (tp40) REVERT: C 242 GLN cc_start: 0.8108 (mm110) cc_final: 0.7447 (mm-40) REVERT: C 315 TYR cc_start: 0.7931 (t80) cc_final: 0.7168 (t80) REVERT: D 27 ARG cc_start: 0.6857 (ttp-110) cc_final: 0.6593 (ttm110) REVERT: D 170 ARG cc_start: 0.8281 (tpp-160) cc_final: 0.7473 (tpp80) REVERT: D 211 MET cc_start: 0.7771 (mmm) cc_final: 0.7436 (mtp) REVERT: D 249 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7546 (mm) REVERT: D 250 ARG cc_start: 0.7789 (tpt170) cc_final: 0.7331 (ttp-110) REVERT: D 315 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6472 (m-80) REVERT: D 326 MET cc_start: 0.7353 (mmp) cc_final: 0.6579 (tmm) REVERT: D 332 ASP cc_start: 0.7944 (p0) cc_final: 0.7551 (p0) REVERT: E 94 GLN cc_start: 0.6973 (mt0) cc_final: 0.6497 (mp10) REVERT: E 143 THR cc_start: 0.7620 (OUTLIER) cc_final: 0.7132 (p) REVERT: E 250 ARG cc_start: 0.7396 (ttp-110) cc_final: 0.6789 (tpp-160) REVERT: E 251 MET cc_start: 0.7795 (mtm) cc_final: 0.7346 (tpp) REVERT: F 23 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8236 (mt0) REVERT: F 198 ASP cc_start: 0.7822 (p0) cc_final: 0.7421 (t70) REVERT: G 43 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8102 (pm20) REVERT: G 59 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7244 (mm-30) REVERT: G 130 ARG cc_start: 0.7390 (mtt90) cc_final: 0.6678 (mmt180) REVERT: G 326 MET cc_start: 0.6182 (mmp) cc_final: 0.5388 (mtm) REVERT: H 100 ILE cc_start: 0.7781 (mm) cc_final: 0.7454 (mm) REVERT: H 118 GLU cc_start: 0.7746 (tt0) cc_final: 0.6948 (pt0) REVERT: H 187 ASP cc_start: 0.8444 (t0) cc_final: 0.8194 (m-30) REVERT: H 250 ARG cc_start: 0.7849 (ttp-110) cc_final: 0.7569 (ttp-110) REVERT: H 267 ASN cc_start: 0.8267 (t0) cc_final: 0.7968 (m-40) outliers start: 71 outliers final: 42 residues processed: 354 average time/residue: 0.3268 time to fit residues: 170.8034 Evaluate side-chains 347 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 297 time to evaluate : 1.800 ------------------------------------------------------------------------------- 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 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 183 SER Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 101 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 C residue 255 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 97 SER 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 200 GLN 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 80 LYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU 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 165 THR 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 251 MET 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 84 MET Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 245 LEU 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 97 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 330 ASN D 200 GLN H 101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.185552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134253 restraints weight = 19074.371| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.06 r_work: 0.3399 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4163 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= 0.141 Angle : 0.657 8.093 24746 Z= 0.311 Chirality : 0.042 0.181 2840 Planarity : 0.004 0.060 3163 Dihedral : 8.219 125.756 2629 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.94 % Favored : 92.53 % Rotamer: Outliers : 4.10 % Allowed : 19.04 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.17), residues: 2277 helix: 0.11 (0.16), residues: 1090 sheet: -1.95 (0.30), residues: 280 loop : -2.23 (0.18), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 294 PHE 0.025 0.001 PHE A 327 TYR 0.015 0.001 TYR H 315 ARG 0.007 0.000 ARG C 250 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 727) hydrogen bonds : angle 4.52730 ( 2049) covalent geometry : bond 0.00323 (18343) covalent geometry : angle 0.65709 (24746) *********************** 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 385 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 309 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7769 (mtt-85) REVERT: A 251 MET cc_start: 0.8023 (ttm) cc_final: 0.7679 (ttm) REVERT: A 292 ILE cc_start: 0.6973 (tp) cc_final: 0.6710 (mm) REVERT: B 27 ARG cc_start: 0.6856 (ttm110) cc_final: 0.6463 (mtt-85) REVERT: B 154 GLU cc_start: 0.7622 (tt0) cc_final: 0.7015 (tm-30) REVERT: B 229 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7267 (mtt180) REVERT: B 253 LEU cc_start: 0.7554 (mt) cc_final: 0.7352 (mt) REVERT: B 326 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7324 (mmt) REVERT: C 94 GLN cc_start: 0.7173 (pp30) cc_final: 0.6519 (mt0) REVERT: C 101 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7370 (tp40) REVERT: C 242 GLN cc_start: 0.8023 (mm110) cc_final: 0.7387 (mm-40) REVERT: C 315 TYR cc_start: 0.7897 (t80) cc_final: 0.7118 (t80) REVERT: C 332 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8303 (p0) REVERT: D 27 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6690 (ttp-170) REVERT: D 170 ARG cc_start: 0.8300 (tpp-160) cc_final: 0.7471 (tpp80) REVERT: D 211 MET cc_start: 0.7753 (mmm) cc_final: 0.7432 (mtp) REVERT: D 249 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7590 (mm) REVERT: D 250 ARG cc_start: 0.7804 (tpt170) cc_final: 0.7395 (ttm110) REVERT: D 315 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.6501 (m-80) REVERT: D 326 MET cc_start: 0.7359 (mmp) cc_final: 0.6660 (tmm) REVERT: D 332 ASP cc_start: 0.7990 (p0) cc_final: 0.7677 (p0) REVERT: E 94 GLN cc_start: 0.6974 (mt0) cc_final: 0.6503 (mp10) REVERT: E 143 THR cc_start: 0.7565 (OUTLIER) cc_final: 0.7077 (p) REVERT: E 211 MET cc_start: 0.7611 (mmt) cc_final: 0.7224 (mmt) REVERT: E 250 ARG cc_start: 0.7469 (ttp-110) cc_final: 0.6877 (tpp-160) REVERT: E 251 MET cc_start: 0.7893 (mtm) cc_final: 0.7392 (tpp) REVERT: F 23 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8252 (mt0) REVERT: F 64 LYS cc_start: 0.7697 (mmmt) cc_final: 0.7368 (mtpp) REVERT: F 198 ASP cc_start: 0.7922 (p0) cc_final: 0.7525 (t70) REVERT: F 202 GLN cc_start: 0.7775 (tp40) cc_final: 0.7456 (mm110) REVERT: G 59 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7251 (mm-30) REVERT: G 130 ARG cc_start: 0.7461 (mtt90) cc_final: 0.6758 (mmt180) REVERT: G 326 MET cc_start: 0.6182 (mmp) cc_final: 0.5491 (mtm) REVERT: H 100 ILE cc_start: 0.7808 (mm) cc_final: 0.7436 (mm) REVERT: H 118 GLU cc_start: 0.7769 (tt0) cc_final: 0.6930 (pt0) REVERT: H 187 ASP cc_start: 0.8475 (t0) cc_final: 0.8214 (m-30) REVERT: H 250 ARG cc_start: 0.7860 (ttp-110) cc_final: 0.7571 (ttp-110) REVERT: H 267 ASN cc_start: 0.8340 (t0) cc_final: 0.8070 (m-40) outliers start: 76 outliers final: 48 residues processed: 359 average time/residue: 0.3213 time to fit residues: 170.0028 Evaluate side-chains 350 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 293 time to evaluate : 2.023 ------------------------------------------------------------------------------- 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 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 183 SER Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 101 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 C residue 255 LEU Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 97 SER 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 200 GLN 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 80 LYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU 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 136 ILE 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 238 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 253 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 60 LEU Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 245 LEU 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 197 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 196 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 330 ASN D 200 GLN E 188 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.183698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.130234 restraints weight = 19003.260| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.87 r_work: 0.3365 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18343 Z= 0.184 Angle : 0.691 8.190 24746 Z= 0.330 Chirality : 0.044 0.169 2840 Planarity : 0.004 0.054 3163 Dihedral : 8.060 124.694 2629 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.51 % Favored : 91.96 % Rotamer: Outliers : 4.48 % Allowed : 19.15 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.17), residues: 2277 helix: 0.09 (0.16), residues: 1080 sheet: -2.13 (0.30), residues: 280 loop : -2.25 (0.18), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 294 PHE 0.016 0.001 PHE G 126 TYR 0.018 0.001 TYR G 315 ARG 0.008 0.000 ARG C 250 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 727) hydrogen bonds : angle 4.66194 ( 2049) covalent geometry : bond 0.00436 (18343) covalent geometry : angle 0.69149 (24746) *********************** 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 398 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 315 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.8049 (ttm) cc_final: 0.7703 (ttm) REVERT: A 292 ILE cc_start: 0.6984 (tp) cc_final: 0.6729 (mm) REVERT: B 27 ARG cc_start: 0.6818 (ttm110) cc_final: 0.6543 (mtt-85) REVERT: B 154 GLU cc_start: 0.7649 (tt0) cc_final: 0.7009 (tm-30) REVERT: B 178 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.7097 (m-10) REVERT: B 229 ARG cc_start: 0.7797 (ttm-80) cc_final: 0.7159 (mtt180) REVERT: B 313 LYS cc_start: 0.6292 (mttp) cc_final: 0.5628 (pttp) REVERT: B 326 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7303 (mmt) REVERT: C 94 GLN cc_start: 0.7201 (pp30) cc_final: 0.6526 (mt0) REVERT: C 101 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7441 (tp40) REVERT: C 202 GLN cc_start: 0.7715 (mp10) cc_final: 0.7121 (tt0) REVERT: C 242 GLN cc_start: 0.7968 (mm110) cc_final: 0.7327 (mm-40) REVERT: C 315 TYR cc_start: 0.7956 (t80) cc_final: 0.7118 (t80) REVERT: D 27 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6639 (ttm110) REVERT: D 170 ARG cc_start: 0.8360 (tpp-160) cc_final: 0.7529 (tpp80) REVERT: D 211 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7616 (mtt) REVERT: D 249 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7645 (mm) REVERT: D 250 ARG cc_start: 0.7783 (tpt170) cc_final: 0.7404 (ttm110) REVERT: D 326 MET cc_start: 0.7381 (mmp) cc_final: 0.6557 (tmm) REVERT: D 332 ASP cc_start: 0.7979 (p0) cc_final: 0.7584 (p0) REVERT: E 77 GLU cc_start: 0.7454 (tp30) cc_final: 0.7230 (tp30) REVERT: E 94 GLN cc_start: 0.6960 (mt0) cc_final: 0.6495 (mp10) REVERT: E 143 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.7091 (p) REVERT: E 211 MET cc_start: 0.7568 (mmt) cc_final: 0.7260 (mmt) REVERT: E 250 ARG cc_start: 0.7403 (ttp-110) cc_final: 0.6796 (tpp-160) REVERT: E 251 MET cc_start: 0.7902 (mtm) cc_final: 0.7370 (tpp) REVERT: F 23 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8226 (mt0) REVERT: F 64 LYS cc_start: 0.7726 (mmmt) cc_final: 0.7381 (mtpp) REVERT: F 198 ASP cc_start: 0.7980 (p0) cc_final: 0.7557 (t70) REVERT: F 202 GLN cc_start: 0.7856 (tp40) cc_final: 0.7532 (mm110) REVERT: G 59 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7264 (mm-30) REVERT: G 130 ARG cc_start: 0.7562 (mtt90) cc_final: 0.6782 (mmm160) REVERT: G 326 MET cc_start: 0.6269 (mmp) cc_final: 0.5519 (mtm) REVERT: H 64 LYS cc_start: 0.4717 (tmmt) cc_final: 0.3777 (mmtt) REVERT: H 100 ILE cc_start: 0.7865 (mm) cc_final: 0.7499 (mm) REVERT: H 118 GLU cc_start: 0.7780 (tt0) cc_final: 0.6783 (tt0) REVERT: H 250 ARG cc_start: 0.7834 (ttp-110) cc_final: 0.7540 (ttp-110) REVERT: H 267 ASN cc_start: 0.8464 (t0) cc_final: 0.8161 (m-40) outliers start: 83 outliers final: 58 residues processed: 367 average time/residue: 0.3278 time to fit residues: 176.4085 Evaluate side-chains 359 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 293 time to evaluate : 1.997 ------------------------------------------------------------------------------- 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 222 ASP 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 326 MET Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 101 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 C residue 255 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 97 SER 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 200 GLN Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 103 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 E residue 172 LEU 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 119 THR Chi-restraints excluded: chain F residue 136 ILE 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 50 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 255 LEU 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 84 MET Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 245 LEU 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 10 optimal weight: 0.0470 chunk 155 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN B 23 GLN B 101 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN C 135 GLN C 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.190028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.136579 restraints weight = 18563.795| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.88 r_work: 0.3400 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18343 Z= 0.157 Angle : 0.679 9.073 24746 Z= 0.323 Chirality : 0.043 0.167 2840 Planarity : 0.004 0.053 3163 Dihedral : 7.822 122.219 2629 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.25 % Favored : 92.23 % Rotamer: Outliers : 4.15 % Allowed : 20.01 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.17), residues: 2277 helix: 0.16 (0.16), residues: 1080 sheet: -2.11 (0.30), residues: 280 loop : -2.23 (0.18), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 294 PHE 0.020 0.001 PHE G 126 TYR 0.019 0.001 TYR B 301 ARG 0.008 0.000 ARG C 250 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 727) hydrogen bonds : angle 4.60181 ( 2049) covalent geometry : bond 0.00366 (18343) covalent geometry : angle 0.67916 (24746) *********************** 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 381 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 304 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ARG cc_start: 0.4902 (mmt180) cc_final: 0.4681 (mmt180) REVERT: A 251 MET cc_start: 0.8024 (ttm) cc_final: 0.7659 (ttm) REVERT: B 27 ARG cc_start: 0.6832 (ttm110) cc_final: 0.6568 (mtt-85) REVERT: B 154 GLU cc_start: 0.7670 (tt0) cc_final: 0.7002 (tm-30) REVERT: B 178 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.7139 (m-10) REVERT: B 229 ARG cc_start: 0.7715 (ttm-80) cc_final: 0.7211 (mtt180) REVERT: B 268 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7744 (tp40) REVERT: B 313 LYS cc_start: 0.6265 (mttp) cc_final: 0.5604 (pttp) REVERT: B 326 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7282 (mmt) REVERT: C 94 GLN cc_start: 0.7073 (pp30) cc_final: 0.6410 (mt0) REVERT: C 101 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7338 (tp40) REVERT: C 202 GLN cc_start: 0.7591 (mp10) cc_final: 0.7001 (tt0) REVERT: C 242 GLN cc_start: 0.7907 (mm110) cc_final: 0.7261 (mm-40) REVERT: C 315 TYR cc_start: 0.7905 (t80) cc_final: 0.7104 (t80) REVERT: D 27 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6549 (ttm110) REVERT: D 170 ARG cc_start: 0.8320 (tpp-160) cc_final: 0.7464 (tpp80) REVERT: D 211 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7532 (mtt) REVERT: D 249 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7618 (mm) REVERT: D 250 ARG cc_start: 0.7751 (tpt170) cc_final: 0.7361 (ttt-90) REVERT: D 326 MET cc_start: 0.7344 (mmp) cc_final: 0.6516 (tmm) REVERT: E 77 GLU cc_start: 0.7370 (tp30) cc_final: 0.7142 (tp30) REVERT: E 94 GLN cc_start: 0.6889 (mt0) cc_final: 0.6405 (mp10) REVERT: E 143 THR cc_start: 0.7595 (OUTLIER) cc_final: 0.7060 (p) REVERT: E 211 MET cc_start: 0.7556 (mmt) cc_final: 0.7318 (mmt) REVERT: E 250 ARG cc_start: 0.7342 (ttp-110) cc_final: 0.6730 (tpp-160) REVERT: E 251 MET cc_start: 0.7902 (mtm) cc_final: 0.7366 (tpp) REVERT: F 23 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8225 (mt0) REVERT: F 64 LYS cc_start: 0.7718 (mmmt) cc_final: 0.7346 (mtpp) REVERT: F 198 ASP cc_start: 0.7906 (p0) cc_final: 0.7503 (t70) REVERT: F 202 GLN cc_start: 0.7790 (tp40) cc_final: 0.7489 (mm110) REVERT: G 59 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7216 (mm-30) REVERT: G 130 ARG cc_start: 0.7555 (mtt90) cc_final: 0.6723 (mmm160) REVERT: G 326 MET cc_start: 0.6215 (mmp) cc_final: 0.5517 (mtm) REVERT: H 100 ILE cc_start: 0.7737 (mm) cc_final: 0.7402 (mm) REVERT: H 118 GLU cc_start: 0.7732 (tt0) cc_final: 0.6737 (tt0) REVERT: H 250 ARG cc_start: 0.7775 (ttp-110) cc_final: 0.7483 (ttp-110) REVERT: H 267 ASN cc_start: 0.8359 (t0) cc_final: 0.8076 (m-40) REVERT: H 304 LYS cc_start: 0.7965 (tttp) cc_final: 0.7466 (tppt) outliers start: 77 outliers final: 56 residues processed: 352 average time/residue: 0.3534 time to fit residues: 185.1705 Evaluate side-chains 357 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 292 time to evaluate : 1.931 ------------------------------------------------------------------------------- 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 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 268 GLN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 101 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 C residue 255 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 97 SER 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 211 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 103 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 E residue 172 LEU 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 136 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR 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 50 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 253 LEU 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 84 MET Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 245 LEU 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 31 optimal weight: 0.5980 chunk 218 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 211 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4157 r_free = 0.4157 target = 0.191696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138573 restraints weight = 18612.107| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.85 r_work: 0.3413 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4472 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= 0.145 Angle : 0.675 11.070 24746 Z= 0.319 Chirality : 0.042 0.167 2840 Planarity : 0.004 0.051 3163 Dihedral : 7.533 118.690 2629 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.11 % Favored : 92.36 % Rotamer: Outliers : 3.78 % Allowed : 20.87 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.17), residues: 2277 helix: 0.23 (0.16), residues: 1077 sheet: -2.07 (0.30), residues: 279 loop : -2.20 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 294 PHE 0.020 0.001 PHE G 126 TYR 0.018 0.001 TYR E 301 ARG 0.009 0.000 ARG C 250 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 727) hydrogen bonds : angle 4.53609 ( 2049) covalent geometry : bond 0.00334 (18343) covalent geometry : angle 0.67459 (24746) *********************** 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 369 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 299 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 CYS cc_start: 0.6533 (m) cc_final: 0.6207 (m) REVERT: A 229 ARG cc_start: 0.4927 (mmt180) cc_final: 0.4694 (mmt180) REVERT: A 251 MET cc_start: 0.8007 (ttm) cc_final: 0.7660 (ttm) REVERT: B 27 ARG cc_start: 0.6859 (ttm110) cc_final: 0.6589 (mtt-85) REVERT: B 154 GLU cc_start: 0.7700 (tt0) cc_final: 0.7029 (tm-30) REVERT: B 178 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.7111 (m-10) REVERT: B 229 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7227 (mtt180) REVERT: B 326 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7316 (mmt) REVERT: C 94 GLN cc_start: 0.7035 (pp30) cc_final: 0.6381 (mt0) REVERT: C 101 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7279 (tp40) REVERT: C 202 GLN cc_start: 0.7577 (mp10) cc_final: 0.7239 (tp40) REVERT: C 242 GLN cc_start: 0.7877 (mm110) cc_final: 0.7245 (mm-40) REVERT: C 303 ARG cc_start: 0.7697 (mtm110) cc_final: 0.7276 (mtm110) REVERT: C 315 TYR cc_start: 0.7903 (t80) cc_final: 0.7148 (t80) REVERT: D 27 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6611 (ttm110) REVERT: D 170 ARG cc_start: 0.8307 (tpp-160) cc_final: 0.7441 (tpp80) REVERT: D 211 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7390 (mtt) REVERT: D 249 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7568 (mm) REVERT: D 250 ARG cc_start: 0.7726 (tpt170) cc_final: 0.7335 (ttt-90) REVERT: E 77 GLU cc_start: 0.7358 (tp30) cc_final: 0.7139 (tp30) REVERT: E 94 GLN cc_start: 0.6875 (mt0) cc_final: 0.6399 (mp10) REVERT: E 143 THR cc_start: 0.7588 (OUTLIER) cc_final: 0.7058 (p) REVERT: E 250 ARG cc_start: 0.7344 (ttp-110) cc_final: 0.6718 (tpp-160) REVERT: E 251 MET cc_start: 0.7848 (mtm) cc_final: 0.7352 (tpp) REVERT: E 326 MET cc_start: 0.1609 (mmm) cc_final: 0.1286 (mmm) REVERT: F 23 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: F 43 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: F 64 LYS cc_start: 0.7782 (mmmt) cc_final: 0.7356 (mtpp) REVERT: F 187 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7586 (m-30) REVERT: F 198 ASP cc_start: 0.7879 (p0) cc_final: 0.7479 (t70) REVERT: F 202 GLN cc_start: 0.7761 (tp40) cc_final: 0.7474 (mm110) REVERT: G 59 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7230 (mm-30) REVERT: G 130 ARG cc_start: 0.7560 (mtt90) cc_final: 0.6732 (mmm160) REVERT: G 326 MET cc_start: 0.6223 (mmp) cc_final: 0.5579 (mtm) REVERT: H 100 ILE cc_start: 0.7737 (mm) cc_final: 0.7386 (mm) REVERT: H 118 GLU cc_start: 0.7721 (tt0) cc_final: 0.6722 (tt0) REVERT: H 250 ARG cc_start: 0.7772 (ttp-110) cc_final: 0.7485 (ttp-110) REVERT: H 267 ASN cc_start: 0.8341 (t0) cc_final: 0.8079 (m-40) REVERT: H 304 LYS cc_start: 0.8021 (tttp) cc_final: 0.7400 (tppt) outliers start: 70 outliers final: 53 residues processed: 342 average time/residue: 0.3181 time to fit residues: 160.3748 Evaluate side-chains 351 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 288 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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 149 ASP 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 297 THR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 101 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 C residue 255 LEU Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER 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 211 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 103 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 E residue 172 LEU 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 136 ILE 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 F residue 238 LEU Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 253 LEU 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 84 MET Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 245 LEU 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 142 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 128 optimal weight: 0.9980 chunk 208 optimal weight: 0.3980 chunk 33 optimal weight: 0.4980 chunk 5 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN B 268 GLN C 135 GLN C 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.189720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.137088 restraints weight = 18831.537| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.09 r_work: 0.3443 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.4498 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= 0.119 Angle : 0.654 10.616 24746 Z= 0.308 Chirality : 0.041 0.170 2840 Planarity : 0.003 0.051 3163 Dihedral : 6.999 109.555 2629 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.46 % Favored : 92.97 % Rotamer: Outliers : 3.24 % Allowed : 21.79 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2277 helix: 0.38 (0.16), residues: 1081 sheet: -1.87 (0.31), residues: 269 loop : -2.11 (0.18), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 294 PHE 0.017 0.001 PHE G 126 TYR 0.015 0.001 TYR G 315 ARG 0.009 0.000 ARG G 247 Details of bonding type rmsd hydrogen bonds : bond 0.02917 ( 727) hydrogen bonds : angle 4.37132 ( 2049) covalent geometry : bond 0.00265 (18343) covalent geometry : angle 0.65445 (24746) ********************** 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 358 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 298 time to evaluate : 1.952 Fit side-chains revert: symmetry clash REVERT: A 144 CYS cc_start: 0.6522 (m) cc_final: 0.6293 (m) REVERT: A 211 MET cc_start: 0.6107 (mmt) cc_final: 0.5298 (mmt) REVERT: A 229 ARG cc_start: 0.5010 (mmt180) cc_final: 0.4705 (mmt-90) REVERT: A 251 MET cc_start: 0.8012 (ttm) cc_final: 0.7659 (ttm) REVERT: B 27 ARG cc_start: 0.6829 (ttm110) cc_final: 0.6583 (mtt-85) REVERT: B 154 GLU cc_start: 0.7700 (tt0) cc_final: 0.7105 (tm-30) REVERT: B 178 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.6929 (m-80) REVERT: B 229 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7158 (mtt180) REVERT: B 326 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7297 (mmt) REVERT: C 94 GLN cc_start: 0.7012 (pp30) cc_final: 0.6378 (mt0) REVERT: C 101 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7186 (tp40) REVERT: C 242 GLN cc_start: 0.7869 (mm110) cc_final: 0.7247 (mm-40) REVERT: C 303 ARG cc_start: 0.7668 (mtm110) cc_final: 0.7461 (mtm110) REVERT: C 315 TYR cc_start: 0.7854 (t80) cc_final: 0.7175 (t80) REVERT: C 326 MET cc_start: 0.8208 (ttm) cc_final: 0.7793 (tpt) REVERT: D 170 ARG cc_start: 0.8257 (tpp-160) cc_final: 0.7387 (tpp80) REVERT: D 211 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7275 (mtp) REVERT: D 249 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7580 (mm) REVERT: D 250 ARG cc_start: 0.7719 (tpt170) cc_final: 0.7310 (ttt-90) REVERT: E 77 GLU cc_start: 0.7315 (tp30) cc_final: 0.7113 (tp30) REVERT: E 94 GLN cc_start: 0.6865 (mt0) cc_final: 0.6385 (mp10) REVERT: E 250 ARG cc_start: 0.7411 (ttp-110) cc_final: 0.6871 (tpp-160) REVERT: E 251 MET cc_start: 0.7854 (mtm) cc_final: 0.7298 (tpp) REVERT: E 326 MET cc_start: 0.1622 (mmm) cc_final: 0.1248 (mmt) REVERT: F 23 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: F 43 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: F 64 LYS cc_start: 0.7822 (mmmt) cc_final: 0.7345 (mtpp) REVERT: F 107 LYS cc_start: 0.5717 (tptt) cc_final: 0.4345 (ttpt) REVERT: F 198 ASP cc_start: 0.7827 (p0) cc_final: 0.7429 (t70) REVERT: F 202 GLN cc_start: 0.7797 (tp40) cc_final: 0.7468 (mm110) REVERT: F 230 THR cc_start: 0.7165 (t) cc_final: 0.6883 (p) REVERT: G 59 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7230 (mm-30) REVERT: G 130 ARG cc_start: 0.7540 (mtt90) cc_final: 0.6771 (mmt180) REVERT: G 205 TYR cc_start: 0.8100 (m-10) cc_final: 0.7638 (m-10) REVERT: G 326 MET cc_start: 0.6198 (mmp) cc_final: 0.5595 (mtm) REVERT: H 84 MET cc_start: 0.1725 (OUTLIER) cc_final: 0.1471 (tpt) REVERT: H 100 ILE cc_start: 0.7716 (mm) cc_final: 0.7351 (mm) REVERT: H 250 ARG cc_start: 0.7846 (ttp-110) cc_final: 0.7554 (ttp-110) outliers start: 60 outliers final: 37 residues processed: 334 average time/residue: 0.3168 time to fit residues: 156.2225 Evaluate side-chains 332 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 287 time to evaluate : 1.798 ------------------------------------------------------------------------------- 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 165 THR Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 101 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 97 SER 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 211 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU 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 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 253 LEU 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 84 MET Chi-restraints excluded: chain H residue 163 GLU 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 218 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 9 optimal weight: 0.0270 chunk 194 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 193 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 330 ASN E 93 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.188191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.134891 restraints weight = 19007.089| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.88 r_work: 0.3426 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18343 Z= 0.140 Angle : 0.672 10.107 24746 Z= 0.317 Chirality : 0.042 0.214 2840 Planarity : 0.004 0.049 3163 Dihedral : 6.782 99.725 2629 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.03 % Favored : 92.40 % Rotamer: Outliers : 3.07 % Allowed : 22.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.17), residues: 2277 helix: 0.38 (0.16), residues: 1082 sheet: -2.05 (0.30), residues: 271 loop : -2.11 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 294 PHE 0.018 0.001 PHE E 126 TYR 0.019 0.001 TYR E 301 ARG 0.009 0.000 ARG G 247 Details of bonding type rmsd hydrogen bonds : bond 0.03031 ( 727) hydrogen bonds : angle 4.41087 ( 2049) covalent geometry : bond 0.00323 (18343) covalent geometry : angle 0.67248 (24746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10353.34 seconds wall clock time: 177 minutes 45.29 seconds (10665.29 seconds total)