Starting phenix.real_space_refine on Fri Sep 27 03:31:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0l_32243/09_2024/7w0l_32243.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0l_32243/09_2024/7w0l_32243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0l_32243/09_2024/7w0l_32243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0l_32243/09_2024/7w0l_32243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0l_32243/09_2024/7w0l_32243.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0l_32243/09_2024/7w0l_32243.cif" } resolution = 3.57 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= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4236 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 7396 2.51 5 N 1932 2.21 5 O 2108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11526 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1819 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 457 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 56} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2376 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain: "R" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2393 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 11, 'TRANS': 286} Chain: "S" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1800 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Chain: "Q" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'8EH': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'8EH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.06, per 1000 atoms: 0.61 Number of scatterers: 11526 At special positions: 0 Unit cell: (125.8, 106.25, 136.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2108 8.00 N 1932 7.00 C 7396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS Q 102 " - pdb=" SG CYS Q 181 " distance=2.04 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.05 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.05 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: 2.88 Conformation dependent library (CDL) restraints added in 1.4 seconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2732 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 14 sheets defined 47.2% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.657A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.040A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.355A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.739A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.564A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.562A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.730A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.758A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 35 through 55 removed outlier: 3.966A pdb=" N ALA C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 75 removed outlier: 3.686A pdb=" N ALA C 64 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 56 Proline residue: Q 32 - end of helix removed outlier: 3.542A pdb=" N SER Q 56 " --> pdb=" O THR Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 61 Processing helix chain 'Q' and resid 62 through 81 removed outlier: 4.033A pdb=" N SER Q 70 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR Q 81 " --> pdb=" O THR Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 91 removed outlier: 3.711A pdb=" N TYR Q 88 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 137 removed outlier: 4.042A pdb=" N CYS Q 102 " --> pdb=" O GLY Q 98 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS Q 103 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE Q 131 " --> pdb=" O ARG Q 127 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL Q 132 " --> pdb=" O TYR Q 128 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG Q 133 " --> pdb=" O LEU Q 129 " (cutoff:3.500A) Proline residue: Q 134 - end of helix Processing helix chain 'Q' and resid 145 through 161 removed outlier: 3.518A pdb=" N ALA Q 161 " --> pdb=" O ALA Q 157 " (cutoff:3.500A) Processing helix chain 'Q' and resid 162 through 167 Processing helix chain 'Q' and resid 190 through 192 No H-bonds generated for 'chain 'Q' and resid 190 through 192' Processing helix chain 'Q' and resid 193 through 232 removed outlier: 3.957A pdb=" N TRP Q 197 " --> pdb=" O SER Q 193 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU Q 198 " --> pdb=" O GLU Q 194 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL Q 212 " --> pdb=" O VAL Q 208 " (cutoff:3.500A) Proline residue: Q 213 - end of helix removed outlier: 3.670A pdb=" N ILE Q 224 " --> pdb=" O CYS Q 220 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE Q 232 " --> pdb=" O ILE Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 238 through 278 removed outlier: 3.820A pdb=" N LYS Q 242 " --> pdb=" O GLU Q 238 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE Q 249 " --> pdb=" O ARG Q 245 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE Q 250 " --> pdb=" O LEU Q 246 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL Q 251 " --> pdb=" O LEU Q 247 " (cutoff:3.500A) Proline residue: Q 263 - end of helix removed outlier: 4.135A pdb=" N SER Q 275 " --> pdb=" O TYR Q 271 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU Q 276 " --> pdb=" O MET Q 272 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 299 Proline residue: Q 292 - end of helix removed outlier: 4.119A pdb=" N TYR Q 299 " --> pdb=" O THR Q 295 " (cutoff:3.500A) Processing helix chain 'Q' and resid 299 through 311 Proline residue: Q 306 - end of helix Processing helix chain 'Q' and resid 312 through 322 Processing helix chain 'R' and resid 30 through 61 removed outlier: 3.790A pdb=" N ILE R 34 " --> pdb=" O LEU R 30 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL R 49 " --> pdb=" O GLY R 45 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG R 58 " --> pdb=" O PHE R 54 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU R 59 " --> pdb=" O ARG R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 81 removed outlier: 4.005A pdb=" N ILE R 68 " --> pdb=" O ALA R 64 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 removed outlier: 4.560A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 132 removed outlier: 3.728A pdb=" N LYS R 103 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 139 No H-bonds generated for 'chain 'R' and resid 137 through 139' Processing helix chain 'R' and resid 140 through 145 removed outlier: 3.922A pdb=" N VAL R 144 " --> pdb=" O LEU R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 167 removed outlier: 3.841A pdb=" N THR R 150 " --> pdb=" O GLY R 146 " (cutoff:3.500A) Proline residue: R 163 - end of helix Processing helix chain 'R' and resid 184 through 188 removed outlier: 4.105A pdb=" N MET R 187 " --> pdb=" O ASP R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 232 removed outlier: 3.905A pdb=" N VAL R 208 " --> pdb=" O SER R 204 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL R 212 " --> pdb=" O VAL R 208 " (cutoff:3.500A) Proline residue: R 213 - end of helix removed outlier: 3.946A pdb=" N PHE R 232 " --> pdb=" O ILE R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 275 removed outlier: 3.558A pdb=" N LYS R 242 " --> pdb=" O GLU R 238 " (cutoff:3.500A) Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 281 through 298 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 311 Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 321 Processing helix chain 'S' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.096A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 225 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.941A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.743A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP B 83 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.701A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.599A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.834A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.623A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.069A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 171 through 172 Processing sheet with id=AB1, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.527A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 45 through 51 removed outlier: 3.614A pdb=" N GLU S 46 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 147 removed outlier: 3.909A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.758A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER S 208 " --> pdb=" O ALA S 211 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 186 through 189 removed outlier: 6.878A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 3.34 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: 3635 1.34 - 1.47: 3155 1.47 - 1.60: 4872 1.60 - 1.72: 2 1.72 - 1.85: 131 Bond restraints: 11795 Sorted by residual: bond pdb=" C30 8EH R 401 " pdb=" C31 8EH R 401 " ideal model delta sigma weight residual 1.472 1.567 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C30 8EH Q 401 " pdb=" C31 8EH Q 401 " ideal model delta sigma weight residual 1.472 1.564 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C30 8EH R 401 " pdb=" N29 8EH R 401 " ideal model delta sigma weight residual 1.313 1.404 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C30 8EH Q 401 " pdb=" N29 8EH Q 401 " ideal model delta sigma weight residual 1.313 1.403 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C12 8EH R 401 " pdb=" N28 8EH R 401 " ideal model delta sigma weight residual 1.307 1.393 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 11790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 15578 2.45 - 4.91: 369 4.91 - 7.36: 56 7.36 - 9.81: 7 9.81 - 12.27: 2 Bond angle restraints: 16012 Sorted by residual: angle pdb=" C ALA B 257 " pdb=" N ASP B 258 " pdb=" CA ASP B 258 " ideal model delta sigma weight residual 122.40 130.46 -8.06 1.45e+00 4.76e-01 3.09e+01 angle pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " pdb=" CG TYR S 235 " ideal model delta sigma weight residual 113.90 105.20 8.70 1.80e+00 3.09e-01 2.34e+01 angle pdb=" C GLY B 162 " pdb=" N ASP B 163 " pdb=" CA ASP B 163 " ideal model delta sigma weight residual 121.71 115.94 5.77 1.39e+00 5.18e-01 1.72e+01 angle pdb=" O15 8EH Q 401 " pdb=" S14 8EH Q 401 " pdb=" O16 8EH Q 401 " ideal model delta sigma weight residual 119.97 107.70 12.27 3.00e+00 1.11e-01 1.67e+01 angle pdb=" O15 8EH R 401 " pdb=" S14 8EH R 401 " pdb=" O16 8EH R 401 " ideal model delta sigma weight residual 119.97 107.73 12.24 3.00e+00 1.11e-01 1.66e+01 ... (remaining 16007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.86: 6721 30.86 - 61.71: 219 61.71 - 92.57: 12 92.57 - 123.43: 0 123.43 - 154.28: 2 Dihedral angle restraints: 6954 sinusoidal: 2716 harmonic: 4238 Sorted by residual: dihedral pdb=" CA GLU Q 174 " pdb=" C GLU Q 174 " pdb=" N ASN Q 175 " pdb=" CA ASN Q 175 " ideal model delta harmonic sigma weight residual -180.00 -150.69 -29.31 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA GLY A 352 " pdb=" C GLY A 352 " pdb=" N LEU A 353 " pdb=" CA LEU A 353 " ideal model delta harmonic sigma weight residual -180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual 180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 6951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1560 0.069 - 0.139: 232 0.139 - 0.208: 18 0.208 - 0.278: 2 0.278 - 0.347: 2 Chirality restraints: 1814 Sorted by residual: chirality pdb=" C19 8EH Q 401 " pdb=" C17 8EH Q 401 " pdb=" C21 8EH Q 401 " pdb=" O20 8EH Q 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.78 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C19 8EH R 401 " pdb=" C17 8EH R 401 " pdb=" C21 8EH R 401 " pdb=" O20 8EH R 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.77 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1811 not shown) Planarity restraints: 1995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 291 " 0.032 2.00e-02 2.50e+03 2.56e-02 1.15e+01 pdb=" CG PHE R 291 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE R 291 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 291 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE R 291 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE R 291 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE R 291 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 289 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ASN R 289 " -0.056 2.00e-02 2.50e+03 pdb=" O ASN R 289 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE R 290 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 190 " 0.028 2.00e-02 2.50e+03 1.87e-02 7.02e+00 pdb=" CG TYR S 190 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR S 190 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR S 190 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR S 190 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR S 190 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR S 190 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR S 190 " 0.004 2.00e-02 2.50e+03 ... (remaining 1992 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 72 2.49 - 3.09: 8734 3.09 - 3.70: 17063 3.70 - 4.30: 23276 4.30 - 4.90: 38672 Nonbonded interactions: 87817 Sorted by model distance: nonbonded pdb=" O ALA B 257 " pdb=" OD1 ASP B 258 " model vdw 1.891 3.040 nonbonded pdb=" O ILE B 37 " pdb=" NZ LYS B 301 " model vdw 2.207 3.120 nonbonded pdb=" O LYS B 280 " pdb=" OG SER B 281 " model vdw 2.207 3.040 nonbonded pdb=" OE1 GLN S 142 " pdb=" OG1 THR S 243 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR B 102 " pdb=" O SER B 147 " model vdw 2.214 3.040 ... (remaining 87812 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 'Q' and (resid 26 through 321 or resid 401)) selection = (chain 'R' and (resid 26 through 321 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.350 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 : 0.010 0.095 11795 Z= 0.644 Angle : 0.939 12.266 16012 Z= 0.526 Chirality : 0.051 0.347 1814 Planarity : 0.005 0.056 1995 Dihedral : 15.214 154.284 4213 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.62 % Favored : 91.31 % Rotamer: Outliers : 0.08 % Allowed : 9.37 % Favored : 90.55 % 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: -3.27 (0.19), residues: 1439 helix: -1.17 (0.18), residues: 622 sheet: -2.12 (0.29), residues: 278 loop : -3.30 (0.21), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 211 HIS 0.008 0.002 HIS B 183 PHE 0.057 0.003 PHE R 291 TYR 0.044 0.003 TYR S 190 ARG 0.006 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 374 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LYS cc_start: 0.8259 (mttp) cc_final: 0.8039 (mttp) REVERT: A 197 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7851 (mttp) REVERT: A 209 LYS cc_start: 0.8482 (mtpt) cc_final: 0.8217 (mtpt) REVERT: A 231 ASP cc_start: 0.7473 (t70) cc_final: 0.7240 (t70) REVERT: A 237 ASP cc_start: 0.8987 (t0) cc_final: 0.8771 (t0) REVERT: A 242 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7536 (mtt90) REVERT: A 247 MET cc_start: 0.7829 (mtm) cc_final: 0.7557 (mtm) REVERT: A 289 GLU cc_start: 0.7175 (pm20) cc_final: 0.6615 (pm20) REVERT: A 308 GLU cc_start: 0.7565 (tt0) cc_final: 0.7187 (tt0) REVERT: A 341 ASP cc_start: 0.8326 (t70) cc_final: 0.8056 (t70) REVERT: A 345 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7880 (mtpp) REVERT: B 14 LEU cc_start: 0.9095 (mp) cc_final: 0.8622 (mp) REVERT: B 34 THR cc_start: 0.7617 (p) cc_final: 0.7381 (t) REVERT: B 59 TYR cc_start: 0.8437 (m-10) cc_final: 0.8209 (m-80) REVERT: B 61 MET cc_start: 0.7405 (tmm) cc_final: 0.6946 (tmm) REVERT: B 79 LEU cc_start: 0.7931 (tp) cc_final: 0.7485 (tt) REVERT: B 98 SER cc_start: 0.8326 (m) cc_final: 0.7828 (t) REVERT: B 179 THR cc_start: 0.8609 (t) cc_final: 0.8348 (p) REVERT: B 195 ASP cc_start: 0.7773 (t70) cc_final: 0.7525 (t0) REVERT: B 291 ASP cc_start: 0.7635 (t70) cc_final: 0.7325 (t70) REVERT: B 300 LEU cc_start: 0.8370 (mt) cc_final: 0.8161 (mt) REVERT: B 308 LEU cc_start: 0.8160 (mt) cc_final: 0.7955 (mp) REVERT: B 338 ILE cc_start: 0.8370 (mt) cc_final: 0.8110 (mm) REVERT: C 42 GLN cc_start: 0.8148 (tp40) cc_final: 0.7903 (tp40) REVERT: Q 36 MET cc_start: 0.8180 (mmm) cc_final: 0.7468 (mpp) REVERT: Q 71 LEU cc_start: 0.8823 (tt) cc_final: 0.8606 (tt) REVERT: Q 88 TYR cc_start: 0.8528 (t80) cc_final: 0.8316 (t80) REVERT: Q 107 TYR cc_start: 0.8173 (t80) cc_final: 0.7897 (t80) REVERT: Q 201 LEU cc_start: 0.7888 (tp) cc_final: 0.7630 (tp) REVERT: Q 262 MET cc_start: 0.6484 (tmm) cc_final: 0.6230 (tmm) REVERT: Q 295 THR cc_start: 0.8152 (t) cc_final: 0.7828 (p) REVERT: Q 301 ASN cc_start: 0.8480 (t0) cc_final: 0.8218 (t0) REVERT: Q 308 LEU cc_start: 0.7691 (mm) cc_final: 0.7487 (mm) REVERT: R 46 ASN cc_start: 0.8696 (m-40) cc_final: 0.8361 (m-40) REVERT: R 165 MET cc_start: 0.8275 (tpt) cc_final: 0.7811 (tpp) REVERT: R 216 ILE cc_start: 0.8335 (mt) cc_final: 0.8135 (mt) REVERT: R 222 PHE cc_start: 0.7931 (t80) cc_final: 0.7700 (t80) REVERT: R 228 ILE cc_start: 0.8542 (tp) cc_final: 0.8165 (tt) REVERT: R 245 ARG cc_start: 0.7743 (ttt90) cc_final: 0.7479 (ttt90) REVERT: R 288 MET cc_start: 0.7108 (mmm) cc_final: 0.6832 (mmm) REVERT: S 3 GLN cc_start: 0.7457 (tm-30) cc_final: 0.6869 (tm-30) REVERT: S 140 MET cc_start: 0.7912 (mtp) cc_final: 0.7695 (mtp) outliers start: 1 outliers final: 0 residues processed: 375 average time/residue: 0.2582 time to fit residues: 133.1905 Evaluate side-chains 348 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.8980 chunk 107 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 50.0000 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 128 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 259 GLN Q 318 GLN ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11795 Z= 0.197 Angle : 0.681 8.989 16012 Z= 0.351 Chirality : 0.043 0.200 1814 Planarity : 0.004 0.059 1995 Dihedral : 7.810 100.396 1646 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.35 % Favored : 94.58 % Rotamer: Outliers : 1.68 % Allowed : 16.57 % Favored : 81.75 % 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: -1.80 (0.21), residues: 1439 helix: 0.35 (0.20), residues: 619 sheet: -1.58 (0.31), residues: 281 loop : -2.82 (0.22), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.018 0.002 PHE A 196 TYR 0.027 0.001 TYR S 235 ARG 0.009 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 339 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7821 (ptt-90) cc_final: 0.7592 (ptt-90) REVERT: A 46 LYS cc_start: 0.8621 (ptmt) cc_final: 0.8390 (ptpp) REVERT: A 209 LYS cc_start: 0.8412 (mtpt) cc_final: 0.8151 (mtpt) REVERT: A 231 ASP cc_start: 0.7320 (t70) cc_final: 0.7038 (t70) REVERT: A 242 ARG cc_start: 0.7672 (mtt90) cc_final: 0.7151 (mtt90) REVERT: A 247 MET cc_start: 0.7756 (mtm) cc_final: 0.7494 (mtm) REVERT: A 289 GLU cc_start: 0.6990 (pm20) cc_final: 0.6605 (pm20) REVERT: A 303 ILE cc_start: 0.8078 (mm) cc_final: 0.7788 (tp) REVERT: A 308 GLU cc_start: 0.7549 (tt0) cc_final: 0.7260 (tt0) REVERT: A 345 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7882 (mtpp) REVERT: B 19 ARG cc_start: 0.7710 (ttp-110) cc_final: 0.7401 (ttp-110) REVERT: B 61 MET cc_start: 0.7432 (tmm) cc_final: 0.6871 (tmm) REVERT: B 98 SER cc_start: 0.8301 (m) cc_final: 0.7790 (t) REVERT: B 111 TYR cc_start: 0.8539 (m-80) cc_final: 0.8089 (m-80) REVERT: B 120 ILE cc_start: 0.8383 (pt) cc_final: 0.7837 (mt) REVERT: B 188 MET cc_start: 0.8063 (mmm) cc_final: 0.7856 (mmm) REVERT: B 195 ASP cc_start: 0.7694 (t70) cc_final: 0.7395 (t0) REVERT: B 291 ASP cc_start: 0.7571 (t70) cc_final: 0.7217 (t70) REVERT: B 300 LEU cc_start: 0.8236 (mt) cc_final: 0.7856 (mt) REVERT: B 325 MET cc_start: 0.7811 (mtt) cc_final: 0.7604 (mtm) REVERT: B 338 ILE cc_start: 0.8204 (mt) cc_final: 0.7943 (mm) REVERT: C 55 ASN cc_start: 0.7718 (m-40) cc_final: 0.7355 (m-40) REVERT: Q 71 LEU cc_start: 0.8766 (tt) cc_final: 0.8516 (tp) REVERT: Q 107 TYR cc_start: 0.8002 (t80) cc_final: 0.7545 (t80) REVERT: Q 162 MET cc_start: 0.7624 (tpp) cc_final: 0.7157 (mpp) REVERT: Q 179 VAL cc_start: 0.7103 (OUTLIER) cc_final: 0.6655 (t) REVERT: Q 201 LEU cc_start: 0.7923 (tp) cc_final: 0.7665 (tp) REVERT: Q 262 MET cc_start: 0.6268 (tmm) cc_final: 0.6013 (tmm) REVERT: Q 283 PHE cc_start: 0.7124 (t80) cc_final: 0.6645 (t80) REVERT: Q 295 THR cc_start: 0.8320 (t) cc_final: 0.8023 (p) REVERT: Q 304 LEU cc_start: 0.8437 (pp) cc_final: 0.8184 (pp) REVERT: R 46 ASN cc_start: 0.8449 (m-40) cc_final: 0.8229 (m-40) REVERT: R 228 ILE cc_start: 0.8514 (tp) cc_final: 0.8157 (tt) REVERT: R 245 ARG cc_start: 0.7724 (ttt90) cc_final: 0.7462 (ttt90) REVERT: S 3 GLN cc_start: 0.7470 (tm-30) cc_final: 0.6897 (tm-30) REVERT: S 5 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8112 (t) REVERT: S 42 GLU cc_start: 0.7081 (mp0) cc_final: 0.6854 (mp0) REVERT: S 80 PHE cc_start: 0.8341 (m-80) cc_final: 0.7988 (m-80) REVERT: S 213 THR cc_start: 0.8390 (t) cc_final: 0.8039 (p) outliers start: 21 outliers final: 12 residues processed: 347 average time/residue: 0.2432 time to fit residues: 117.2839 Evaluate side-chains 338 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 324 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 169 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 87 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11795 Z= 0.216 Angle : 0.651 7.628 16012 Z= 0.336 Chirality : 0.042 0.198 1814 Planarity : 0.004 0.065 1995 Dihedral : 6.940 68.374 1646 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.12 % Favored : 93.82 % Rotamer: Outliers : 3.04 % Allowed : 19.06 % Favored : 77.90 % 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: -1.30 (0.22), residues: 1439 helix: 0.76 (0.21), residues: 622 sheet: -1.33 (0.31), residues: 288 loop : -2.57 (0.23), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.018 0.001 PHE R 78 TYR 0.026 0.001 TYR S 235 ARG 0.009 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 342 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7773 (ptt-90) cc_final: 0.7554 (ptt-90) REVERT: A 209 LYS cc_start: 0.8422 (mtpt) cc_final: 0.8178 (mtpt) REVERT: A 231 ASP cc_start: 0.7345 (t70) cc_final: 0.7033 (t0) REVERT: A 242 ARG cc_start: 0.7851 (mtt90) cc_final: 0.7274 (mtt90) REVERT: A 247 MET cc_start: 0.7700 (mtm) cc_final: 0.7464 (mtm) REVERT: A 289 GLU cc_start: 0.7011 (pm20) cc_final: 0.6658 (pm20) REVERT: A 308 GLU cc_start: 0.7562 (tt0) cc_final: 0.7260 (tt0) REVERT: A 345 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7874 (mtpp) REVERT: B 61 MET cc_start: 0.7211 (tmm) cc_final: 0.6757 (tmm) REVERT: B 98 SER cc_start: 0.8313 (m) cc_final: 0.7744 (t) REVERT: B 111 TYR cc_start: 0.8557 (m-80) cc_final: 0.8072 (m-80) REVERT: B 114 CYS cc_start: 0.8343 (t) cc_final: 0.8136 (t) REVERT: B 120 ILE cc_start: 0.8380 (pt) cc_final: 0.7777 (mt) REVERT: B 195 ASP cc_start: 0.7623 (t70) cc_final: 0.7354 (t0) REVERT: B 237 ASN cc_start: 0.7682 (t0) cc_final: 0.7307 (t0) REVERT: B 239 ASN cc_start: 0.8388 (m-40) cc_final: 0.7859 (m-40) REVERT: B 291 ASP cc_start: 0.7723 (t70) cc_final: 0.7320 (t70) REVERT: B 300 LEU cc_start: 0.8222 (mt) cc_final: 0.7792 (mt) REVERT: B 338 ILE cc_start: 0.8166 (mt) cc_final: 0.7914 (mm) REVERT: C 55 ASN cc_start: 0.7703 (m-40) cc_final: 0.7351 (m-40) REVERT: Q 107 TYR cc_start: 0.7994 (t80) cc_final: 0.7559 (t80) REVERT: Q 179 VAL cc_start: 0.7102 (OUTLIER) cc_final: 0.6792 (m) REVERT: Q 201 LEU cc_start: 0.7948 (tp) cc_final: 0.7706 (tp) REVERT: Q 253 LEU cc_start: 0.8548 (mm) cc_final: 0.8341 (mm) REVERT: Q 262 MET cc_start: 0.6283 (tmm) cc_final: 0.5993 (tmm) REVERT: Q 283 PHE cc_start: 0.7177 (t80) cc_final: 0.6671 (t80) REVERT: R 46 ASN cc_start: 0.8445 (m-40) cc_final: 0.8241 (m-40) REVERT: R 55 ARG cc_start: 0.7800 (ttm110) cc_final: 0.7004 (ttm110) REVERT: R 220 CYS cc_start: 0.8092 (m) cc_final: 0.7655 (m) REVERT: R 228 ILE cc_start: 0.8553 (tp) cc_final: 0.8233 (tt) REVERT: R 245 ARG cc_start: 0.7719 (ttt90) cc_final: 0.7500 (ttt90) REVERT: R 317 ARG cc_start: 0.7194 (mtm-85) cc_final: 0.6892 (mtm-85) REVERT: S 3 GLN cc_start: 0.7468 (tm-30) cc_final: 0.6840 (tm-30) REVERT: S 42 GLU cc_start: 0.7103 (mp0) cc_final: 0.6873 (mp0) REVERT: S 77 ASN cc_start: 0.8919 (m-40) cc_final: 0.8702 (m-40) outliers start: 38 outliers final: 19 residues processed: 359 average time/residue: 0.2344 time to fit residues: 117.1715 Evaluate side-chains 354 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 334 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 169 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 129 optimal weight: 0.4980 chunk 137 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 36 optimal weight: 0.0770 chunk 114 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11795 Z= 0.183 Angle : 0.630 10.324 16012 Z= 0.320 Chirality : 0.041 0.171 1814 Planarity : 0.004 0.063 1995 Dihedral : 6.042 53.821 1646 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.79 % Rotamer: Outliers : 3.76 % Allowed : 21.54 % Favored : 74.70 % 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: -1.00 (0.22), residues: 1439 helix: 0.99 (0.21), residues: 623 sheet: -1.17 (0.31), residues: 291 loop : -2.39 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.001 PHE R 78 TYR 0.025 0.001 TYR S 235 ARG 0.011 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 331 time to evaluate : 1.285 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7805 (t0) cc_final: 0.7593 (t0) REVERT: A 209 LYS cc_start: 0.8404 (mtpt) cc_final: 0.8158 (mtpt) REVERT: A 231 ASP cc_start: 0.7282 (t70) cc_final: 0.6951 (t0) REVERT: A 247 MET cc_start: 0.7655 (mtm) cc_final: 0.7389 (mtm) REVERT: A 289 GLU cc_start: 0.7019 (pm20) cc_final: 0.6765 (pm20) REVERT: A 308 GLU cc_start: 0.7566 (tt0) cc_final: 0.7288 (tt0) REVERT: A 345 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7864 (mtpp) REVERT: B 61 MET cc_start: 0.7190 (tmm) cc_final: 0.6760 (tmm) REVERT: B 98 SER cc_start: 0.8269 (m) cc_final: 0.7685 (t) REVERT: B 111 TYR cc_start: 0.8561 (m-80) cc_final: 0.8100 (m-80) REVERT: B 188 MET cc_start: 0.7823 (mmm) cc_final: 0.7320 (mmm) REVERT: B 195 ASP cc_start: 0.7641 (t70) cc_final: 0.7335 (t0) REVERT: B 237 ASN cc_start: 0.7679 (t0) cc_final: 0.7176 (t0) REVERT: B 239 ASN cc_start: 0.8398 (m-40) cc_final: 0.7785 (m110) REVERT: B 291 ASP cc_start: 0.7753 (t70) cc_final: 0.7362 (t70) REVERT: B 300 LEU cc_start: 0.8209 (mt) cc_final: 0.7789 (mt) REVERT: C 55 ASN cc_start: 0.7665 (m-40) cc_final: 0.7328 (m-40) REVERT: Q 71 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8547 (tp) REVERT: Q 107 TYR cc_start: 0.7961 (t80) cc_final: 0.7485 (t80) REVERT: Q 162 MET cc_start: 0.7637 (mmm) cc_final: 0.7406 (mmm) REVERT: Q 179 VAL cc_start: 0.7131 (OUTLIER) cc_final: 0.6701 (t) REVERT: Q 201 LEU cc_start: 0.7954 (tp) cc_final: 0.7723 (tp) REVERT: Q 262 MET cc_start: 0.6246 (tmm) cc_final: 0.5847 (tmm) REVERT: Q 268 LYS cc_start: 0.8679 (tttm) cc_final: 0.8406 (ttmt) REVERT: Q 283 PHE cc_start: 0.7193 (t80) cc_final: 0.6680 (t80) REVERT: R 35 TYR cc_start: 0.8259 (m-80) cc_final: 0.7975 (m-80) REVERT: R 79 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8240 (p) REVERT: R 160 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8284 (mp) REVERT: R 166 VAL cc_start: 0.8538 (m) cc_final: 0.8242 (p) REVERT: R 220 CYS cc_start: 0.8072 (m) cc_final: 0.7648 (m) REVERT: R 228 ILE cc_start: 0.8525 (tp) cc_final: 0.8212 (tt) REVERT: R 317 ARG cc_start: 0.7187 (mtm-85) cc_final: 0.6871 (mtm-85) REVERT: S 3 GLN cc_start: 0.7557 (tm-30) cc_final: 0.6873 (tm-30) REVERT: S 42 GLU cc_start: 0.7044 (mp0) cc_final: 0.6826 (mp0) REVERT: S 65 LYS cc_start: 0.8596 (tmtt) cc_final: 0.8262 (tmtt) REVERT: S 77 ASN cc_start: 0.8908 (m-40) cc_final: 0.8680 (m-40) outliers start: 47 outliers final: 24 residues processed: 356 average time/residue: 0.2404 time to fit residues: 119.9084 Evaluate side-chains 356 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 328 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain Q residue 40 LEU Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 0.2980 chunk 94 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 123 optimal weight: 0.0170 chunk 34 optimal weight: 0.0870 chunk 46 optimal weight: 2.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 259 GLN ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11795 Z= 0.166 Angle : 0.616 9.328 16012 Z= 0.314 Chirality : 0.041 0.156 1814 Planarity : 0.004 0.064 1995 Dihedral : 5.665 49.355 1646 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.63 % Favored : 94.30 % Rotamer: Outliers : 3.44 % Allowed : 22.82 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1439 helix: 1.09 (0.21), residues: 624 sheet: -0.92 (0.32), residues: 295 loop : -2.32 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.001 PHE R 222 TYR 0.022 0.001 TYR S 235 ARG 0.011 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 335 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8389 (mtpt) cc_final: 0.8128 (mtpt) REVERT: A 218 VAL cc_start: 0.7368 (m) cc_final: 0.7145 (t) REVERT: A 231 ASP cc_start: 0.7233 (t70) cc_final: 0.6916 (t0) REVERT: A 247 MET cc_start: 0.7591 (mtm) cc_final: 0.7371 (mtm) REVERT: A 256 ASN cc_start: 0.8221 (t0) cc_final: 0.8007 (t0) REVERT: A 308 GLU cc_start: 0.7529 (tt0) cc_final: 0.7240 (tt0) REVERT: A 345 LYS cc_start: 0.8237 (mtpt) cc_final: 0.7875 (mtpp) REVERT: B 17 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7593 (tm-30) REVERT: B 61 MET cc_start: 0.7212 (tmm) cc_final: 0.6698 (tmm) REVERT: B 98 SER cc_start: 0.8255 (m) cc_final: 0.7698 (t) REVERT: B 111 TYR cc_start: 0.8559 (m-80) cc_final: 0.8134 (m-80) REVERT: B 114 CYS cc_start: 0.7941 (t) cc_final: 0.7657 (t) REVERT: B 188 MET cc_start: 0.7799 (mmm) cc_final: 0.7313 (mmm) REVERT: B 195 ASP cc_start: 0.7631 (t70) cc_final: 0.7305 (t0) REVERT: B 237 ASN cc_start: 0.7690 (t0) cc_final: 0.7158 (t0) REVERT: B 239 ASN cc_start: 0.8378 (m-40) cc_final: 0.7784 (m110) REVERT: B 291 ASP cc_start: 0.7767 (t70) cc_final: 0.7342 (t70) REVERT: B 300 LEU cc_start: 0.8101 (mt) cc_final: 0.7741 (mt) REVERT: C 55 ASN cc_start: 0.7646 (m-40) cc_final: 0.7245 (m-40) REVERT: Q 107 TYR cc_start: 0.7946 (t80) cc_final: 0.7556 (t80) REVERT: Q 179 VAL cc_start: 0.7141 (OUTLIER) cc_final: 0.6762 (m) REVERT: Q 253 LEU cc_start: 0.8523 (mm) cc_final: 0.8318 (mm) REVERT: Q 262 MET cc_start: 0.6196 (tmm) cc_final: 0.5816 (tmm) REVERT: Q 268 LYS cc_start: 0.8668 (tttm) cc_final: 0.8399 (ttmt) REVERT: Q 283 PHE cc_start: 0.7078 (t80) cc_final: 0.6537 (t80) REVERT: Q 288 MET cc_start: 0.7980 (mmt) cc_final: 0.7743 (mmt) REVERT: R 79 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8323 (p) REVERT: R 160 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8290 (mp) REVERT: R 165 MET cc_start: 0.7951 (tpt) cc_final: 0.7587 (tpp) REVERT: R 166 VAL cc_start: 0.8522 (m) cc_final: 0.8274 (p) REVERT: R 220 CYS cc_start: 0.8053 (m) cc_final: 0.7605 (m) REVERT: R 244 ARG cc_start: 0.7354 (tpp80) cc_final: 0.7148 (tpp80) REVERT: S 3 GLN cc_start: 0.7532 (tm-30) cc_final: 0.6878 (tm-30) REVERT: S 42 GLU cc_start: 0.7104 (mp0) cc_final: 0.6863 (mp0) REVERT: S 65 LYS cc_start: 0.8539 (tmtt) cc_final: 0.8214 (tmtt) REVERT: S 77 ASN cc_start: 0.8900 (m-40) cc_final: 0.8689 (m-40) outliers start: 43 outliers final: 29 residues processed: 360 average time/residue: 0.2211 time to fit residues: 111.7414 Evaluate side-chains 363 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 331 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 40 LEU Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.0070 chunk 27 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 0.0570 chunk 137 optimal weight: 0.0060 chunk 114 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 72 optimal weight: 50.0000 chunk 132 optimal weight: 0.0870 overall best weight: 0.2110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 259 GLN R 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11795 Z= 0.153 Angle : 0.610 9.975 16012 Z= 0.307 Chirality : 0.040 0.200 1814 Planarity : 0.004 0.058 1995 Dihedral : 5.537 68.642 1646 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 3.04 % Allowed : 24.34 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1439 helix: 1.17 (0.21), residues: 623 sheet: -0.88 (0.32), residues: 281 loop : -2.23 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 47 HIS 0.003 0.000 HIS S 35 PHE 0.032 0.001 PHE R 222 TYR 0.021 0.001 TYR S 235 ARG 0.012 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 331 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8427 (mtmm) cc_final: 0.8178 (mttm) REVERT: A 209 LYS cc_start: 0.8357 (mtpt) cc_final: 0.8099 (mtpt) REVERT: A 218 VAL cc_start: 0.7384 (m) cc_final: 0.7162 (t) REVERT: A 231 ASP cc_start: 0.7154 (t70) cc_final: 0.6830 (t0) REVERT: A 280 LYS cc_start: 0.7924 (tppt) cc_final: 0.7519 (tppt) REVERT: A 308 GLU cc_start: 0.7486 (tt0) cc_final: 0.7199 (tt0) REVERT: A 345 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7839 (mtpp) REVERT: B 17 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7630 (tm-30) REVERT: B 19 ARG cc_start: 0.7692 (ttp-110) cc_final: 0.7271 (ttp-110) REVERT: B 61 MET cc_start: 0.7211 (tmm) cc_final: 0.6694 (tmm) REVERT: B 98 SER cc_start: 0.8251 (m) cc_final: 0.7669 (t) REVERT: B 111 TYR cc_start: 0.8564 (m-80) cc_final: 0.8173 (m-80) REVERT: B 188 MET cc_start: 0.7768 (mmm) cc_final: 0.7263 (mmm) REVERT: B 195 ASP cc_start: 0.7627 (t70) cc_final: 0.7305 (t0) REVERT: B 217 MET cc_start: 0.6863 (ptm) cc_final: 0.6655 (ptm) REVERT: B 237 ASN cc_start: 0.7705 (t0) cc_final: 0.7359 (t0) REVERT: B 239 ASN cc_start: 0.8358 (m-40) cc_final: 0.7960 (m-40) REVERT: B 273 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7415 (pt) REVERT: B 291 ASP cc_start: 0.7789 (t70) cc_final: 0.7343 (t70) REVERT: B 300 LEU cc_start: 0.8142 (mt) cc_final: 0.7818 (mt) REVERT: C 55 ASN cc_start: 0.7653 (m-40) cc_final: 0.7260 (m-40) REVERT: Q 179 VAL cc_start: 0.7048 (OUTLIER) cc_final: 0.6654 (t) REVERT: Q 262 MET cc_start: 0.6233 (tmm) cc_final: 0.5818 (tmm) REVERT: Q 268 LYS cc_start: 0.8667 (tttm) cc_final: 0.8398 (ttmt) REVERT: Q 283 PHE cc_start: 0.7026 (t80) cc_final: 0.6542 (t80) REVERT: Q 288 MET cc_start: 0.7965 (mmt) cc_final: 0.7759 (mmm) REVERT: R 44 THR cc_start: 0.8461 (t) cc_final: 0.8214 (t) REVERT: R 79 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8308 (p) REVERT: R 160 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8276 (mp) REVERT: R 165 MET cc_start: 0.7872 (tpt) cc_final: 0.7492 (tpp) REVERT: R 166 VAL cc_start: 0.8475 (m) cc_final: 0.8242 (p) REVERT: R 204 SER cc_start: 0.8466 (t) cc_final: 0.8207 (p) REVERT: R 220 CYS cc_start: 0.8099 (m) cc_final: 0.7680 (m) REVERT: R 299 TYR cc_start: 0.8396 (m-80) cc_final: 0.8188 (m-80) REVERT: R 300 VAL cc_start: 0.8584 (t) cc_final: 0.8336 (p) REVERT: R 317 ARG cc_start: 0.7167 (mtm-85) cc_final: 0.6874 (mtm-85) REVERT: S 3 GLN cc_start: 0.7499 (tm-30) cc_final: 0.6814 (tm-30) REVERT: S 42 GLU cc_start: 0.7011 (mp0) cc_final: 0.6797 (mp0) REVERT: S 65 LYS cc_start: 0.8481 (tmtt) cc_final: 0.8172 (tmtt) outliers start: 38 outliers final: 25 residues processed: 351 average time/residue: 0.2503 time to fit residues: 122.8585 Evaluate side-chains 350 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 321 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain Q residue 290 ILE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.1980 chunk 78 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN S 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11795 Z= 0.218 Angle : 0.633 9.339 16012 Z= 0.322 Chirality : 0.042 0.178 1814 Planarity : 0.004 0.063 1995 Dihedral : 5.807 74.998 1646 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.77 % Favored : 94.16 % Rotamer: Outliers : 3.12 % Allowed : 25.06 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1439 helix: 1.14 (0.21), residues: 622 sheet: -0.86 (0.32), residues: 297 loop : -2.27 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 261 HIS 0.005 0.001 HIS B 142 PHE 0.018 0.001 PHE S 80 TYR 0.024 0.001 TYR S 235 ARG 0.013 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 335 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8426 (mtmm) cc_final: 0.8151 (mttm) REVERT: A 209 LYS cc_start: 0.8413 (mtpt) cc_final: 0.8208 (mtpt) REVERT: A 231 ASP cc_start: 0.7265 (t70) cc_final: 0.6949 (t0) REVERT: A 308 GLU cc_start: 0.7502 (tt0) cc_final: 0.7202 (tt0) REVERT: A 345 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7836 (mtpp) REVERT: B 17 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7663 (tm-30) REVERT: B 61 MET cc_start: 0.7224 (tmm) cc_final: 0.6654 (tmm) REVERT: B 98 SER cc_start: 0.8243 (m) cc_final: 0.7696 (t) REVERT: B 111 TYR cc_start: 0.8568 (m-80) cc_final: 0.8135 (m-80) REVERT: B 114 CYS cc_start: 0.8051 (t) cc_final: 0.7790 (t) REVERT: B 188 MET cc_start: 0.7860 (mmm) cc_final: 0.7359 (mmm) REVERT: B 195 ASP cc_start: 0.7638 (t70) cc_final: 0.7305 (t0) REVERT: B 237 ASN cc_start: 0.7724 (t0) cc_final: 0.7316 (t0) REVERT: B 291 ASP cc_start: 0.7824 (t70) cc_final: 0.7376 (t70) REVERT: B 300 LEU cc_start: 0.8159 (mt) cc_final: 0.7805 (mt) REVERT: C 55 ASN cc_start: 0.7615 (m-40) cc_final: 0.7212 (m-40) REVERT: Q 107 TYR cc_start: 0.8010 (t80) cc_final: 0.7683 (t80) REVERT: Q 162 MET cc_start: 0.7609 (tpp) cc_final: 0.7213 (mpp) REVERT: Q 179 VAL cc_start: 0.6993 (OUTLIER) cc_final: 0.6631 (m) REVERT: Q 262 MET cc_start: 0.6278 (tmm) cc_final: 0.5865 (tmm) REVERT: Q 268 LYS cc_start: 0.8656 (tttm) cc_final: 0.8392 (ttmt) REVERT: Q 283 PHE cc_start: 0.7037 (t80) cc_final: 0.6585 (t80) REVERT: Q 288 MET cc_start: 0.8001 (mmt) cc_final: 0.7794 (mmt) REVERT: R 79 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8311 (p) REVERT: R 91 ARG cc_start: 0.8332 (ttp80) cc_final: 0.8125 (tmm-80) REVERT: R 160 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8319 (mp) REVERT: R 165 MET cc_start: 0.7932 (tpt) cc_final: 0.7571 (tpp) REVERT: R 166 VAL cc_start: 0.8519 (m) cc_final: 0.8257 (p) REVERT: R 220 CYS cc_start: 0.8099 (m) cc_final: 0.7682 (m) REVERT: R 317 ARG cc_start: 0.7166 (mtm-85) cc_final: 0.6918 (mtm-85) REVERT: S 3 GLN cc_start: 0.7467 (tm-30) cc_final: 0.6782 (tm-30) REVERT: S 42 GLU cc_start: 0.7136 (mp0) cc_final: 0.6890 (mp0) REVERT: S 65 LYS cc_start: 0.8544 (tmtt) cc_final: 0.8215 (tmtt) REVERT: S 245 LEU cc_start: 0.8393 (mt) cc_final: 0.8137 (mt) outliers start: 39 outliers final: 29 residues processed: 357 average time/residue: 0.2142 time to fit residues: 107.5644 Evaluate side-chains 367 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 335 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 173 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain Q residue 290 ILE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 93 optimal weight: 0.0270 chunk 67 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 0.0470 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 259 GLN C 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11795 Z= 0.178 Angle : 0.629 9.297 16012 Z= 0.318 Chirality : 0.041 0.163 1814 Planarity : 0.004 0.062 1995 Dihedral : 5.721 71.476 1646 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.42 % Favored : 94.51 % Rotamer: Outliers : 2.96 % Allowed : 25.14 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.22), residues: 1439 helix: 1.19 (0.21), residues: 621 sheet: -0.72 (0.33), residues: 277 loop : -2.17 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 261 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE R 222 TYR 0.023 0.001 TYR S 235 ARG 0.010 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 337 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8312 (mtmm) cc_final: 0.8066 (mttm) REVERT: A 209 LYS cc_start: 0.8431 (mtpt) cc_final: 0.8192 (mtpt) REVERT: A 218 VAL cc_start: 0.7356 (m) cc_final: 0.7118 (t) REVERT: A 231 ASP cc_start: 0.7238 (t70) cc_final: 0.6913 (t0) REVERT: A 280 LYS cc_start: 0.7962 (tppt) cc_final: 0.7570 (tppt) REVERT: A 308 GLU cc_start: 0.7504 (tt0) cc_final: 0.7207 (tt0) REVERT: A 345 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7825 (mtpp) REVERT: B 17 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7672 (tm-30) REVERT: B 61 MET cc_start: 0.7239 (tmm) cc_final: 0.6651 (tmm) REVERT: B 98 SER cc_start: 0.8241 (m) cc_final: 0.7699 (t) REVERT: B 111 TYR cc_start: 0.8574 (m-80) cc_final: 0.8133 (m-80) REVERT: B 114 CYS cc_start: 0.7939 (t) cc_final: 0.7700 (t) REVERT: B 188 MET cc_start: 0.7826 (mmm) cc_final: 0.7366 (mmm) REVERT: B 195 ASP cc_start: 0.7647 (t70) cc_final: 0.7307 (t0) REVERT: B 237 ASN cc_start: 0.7733 (t0) cc_final: 0.7327 (t0) REVERT: B 291 ASP cc_start: 0.7835 (t70) cc_final: 0.7377 (t70) REVERT: B 300 LEU cc_start: 0.8148 (mt) cc_final: 0.7791 (mt) REVERT: C 55 ASN cc_start: 0.7621 (m-40) cc_final: 0.7232 (m-40) REVERT: Q 107 TYR cc_start: 0.7972 (t80) cc_final: 0.7670 (t80) REVERT: Q 162 MET cc_start: 0.7573 (tpp) cc_final: 0.7233 (mpp) REVERT: Q 179 VAL cc_start: 0.7053 (OUTLIER) cc_final: 0.6690 (m) REVERT: Q 253 LEU cc_start: 0.8557 (mm) cc_final: 0.8300 (mm) REVERT: Q 262 MET cc_start: 0.6262 (tmm) cc_final: 0.5856 (tmm) REVERT: Q 268 LYS cc_start: 0.8644 (tttm) cc_final: 0.8385 (ttmt) REVERT: Q 283 PHE cc_start: 0.7033 (t80) cc_final: 0.6583 (t80) REVERT: Q 288 MET cc_start: 0.7993 (mmt) cc_final: 0.7773 (mmt) REVERT: R 79 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8306 (p) REVERT: R 91 ARG cc_start: 0.8307 (ttp80) cc_final: 0.7782 (ttp80) REVERT: R 160 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8404 (mp) REVERT: R 165 MET cc_start: 0.7918 (tpt) cc_final: 0.7552 (tpp) REVERT: R 166 VAL cc_start: 0.8517 (m) cc_final: 0.8262 (p) REVERT: R 220 CYS cc_start: 0.8107 (m) cc_final: 0.7686 (m) REVERT: R 300 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8311 (p) REVERT: R 317 ARG cc_start: 0.7163 (mtm-85) cc_final: 0.6909 (mtm-85) REVERT: S 3 GLN cc_start: 0.7453 (tm-30) cc_final: 0.6734 (tm-30) REVERT: S 42 GLU cc_start: 0.7071 (mp0) cc_final: 0.6838 (mp0) REVERT: S 65 LYS cc_start: 0.8512 (tmtt) cc_final: 0.8204 (tmtt) REVERT: S 245 LEU cc_start: 0.8408 (mt) cc_final: 0.8192 (mt) outliers start: 37 outliers final: 30 residues processed: 354 average time/residue: 0.2325 time to fit residues: 116.0773 Evaluate side-chains 367 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 333 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 173 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 120 optimal weight: 0.0670 chunk 83 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11795 Z= 0.214 Angle : 0.654 10.831 16012 Z= 0.331 Chirality : 0.042 0.177 1814 Planarity : 0.004 0.062 1995 Dihedral : 5.871 73.614 1646 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.12 % Favored : 93.82 % Rotamer: Outliers : 3.20 % Allowed : 25.38 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1439 helix: 1.16 (0.21), residues: 622 sheet: -0.81 (0.32), residues: 297 loop : -2.20 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 261 HIS 0.004 0.001 HIS B 142 PHE 0.016 0.001 PHE R 78 TYR 0.025 0.001 TYR S 235 ARG 0.010 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 334 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8207 (mtpt) REVERT: A 231 ASP cc_start: 0.7276 (t70) cc_final: 0.6966 (t0) REVERT: A 280 LYS cc_start: 0.7984 (tppt) cc_final: 0.7563 (tppt) REVERT: A 308 GLU cc_start: 0.7529 (tt0) cc_final: 0.7245 (tt0) REVERT: A 345 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7829 (mtpp) REVERT: B 17 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7654 (tm-30) REVERT: B 61 MET cc_start: 0.7232 (tmm) cc_final: 0.6646 (tmm) REVERT: B 98 SER cc_start: 0.8240 (m) cc_final: 0.7705 (t) REVERT: B 114 CYS cc_start: 0.8038 (t) cc_final: 0.7817 (t) REVERT: B 188 MET cc_start: 0.7885 (mmm) cc_final: 0.7409 (mmm) REVERT: B 195 ASP cc_start: 0.7683 (t70) cc_final: 0.7331 (t0) REVERT: B 237 ASN cc_start: 0.7760 (t0) cc_final: 0.7318 (t0) REVERT: B 291 ASP cc_start: 0.7846 (t70) cc_final: 0.7401 (t70) REVERT: B 300 LEU cc_start: 0.8180 (mt) cc_final: 0.7820 (mt) REVERT: C 55 ASN cc_start: 0.7538 (m-40) cc_final: 0.7183 (m-40) REVERT: Q 107 TYR cc_start: 0.8018 (t80) cc_final: 0.7593 (t80) REVERT: Q 140 LEU cc_start: -0.1216 (OUTLIER) cc_final: -0.1452 (pp) REVERT: Q 162 MET cc_start: 0.7594 (tpp) cc_final: 0.7263 (mpp) REVERT: Q 179 VAL cc_start: 0.7053 (OUTLIER) cc_final: 0.6682 (m) REVERT: Q 253 LEU cc_start: 0.8566 (mm) cc_final: 0.8338 (mm) REVERT: Q 262 MET cc_start: 0.6306 (tmm) cc_final: 0.5895 (tmm) REVERT: Q 268 LYS cc_start: 0.8630 (tttm) cc_final: 0.8376 (ttmt) REVERT: Q 283 PHE cc_start: 0.7059 (t80) cc_final: 0.6602 (t80) REVERT: Q 288 MET cc_start: 0.8022 (mmt) cc_final: 0.7801 (mmt) REVERT: R 44 THR cc_start: 0.8468 (t) cc_final: 0.8266 (t) REVERT: R 79 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8307 (p) REVERT: R 160 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8336 (mp) REVERT: R 165 MET cc_start: 0.7948 (tpt) cc_final: 0.7576 (tpp) REVERT: R 166 VAL cc_start: 0.8515 (m) cc_final: 0.8244 (p) REVERT: R 220 CYS cc_start: 0.8094 (m) cc_final: 0.7672 (m) REVERT: R 295 THR cc_start: 0.8309 (m) cc_final: 0.7902 (t) REVERT: R 317 ARG cc_start: 0.7161 (mtm-85) cc_final: 0.6909 (mtm-85) REVERT: S 3 GLN cc_start: 0.7467 (tm-30) cc_final: 0.6756 (tm-30) REVERT: S 42 GLU cc_start: 0.7140 (mp0) cc_final: 0.6910 (mp0) REVERT: S 65 LYS cc_start: 0.8532 (tmtt) cc_final: 0.8223 (tmtt) REVERT: S 245 LEU cc_start: 0.8374 (mt) cc_final: 0.8130 (mt) outliers start: 40 outliers final: 32 residues processed: 356 average time/residue: 0.2410 time to fit residues: 119.9006 Evaluate side-chains 368 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 332 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 173 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.0970 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 141 optimal weight: 0.0570 chunk 130 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11795 Z= 0.170 Angle : 0.646 11.053 16012 Z= 0.324 Chirality : 0.041 0.161 1814 Planarity : 0.004 0.058 1995 Dihedral : 5.682 72.383 1646 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.42 % Favored : 94.51 % Rotamer: Outliers : 2.64 % Allowed : 26.18 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.22), residues: 1439 helix: 1.23 (0.21), residues: 623 sheet: -0.71 (0.33), residues: 285 loop : -2.21 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 261 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.001 PHE A 250 TYR 0.023 0.001 TYR S 235 ARG 0.010 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 327 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8316 (mtmm) cc_final: 0.8076 (mttm) REVERT: A 209 LYS cc_start: 0.8435 (mtpt) cc_final: 0.8196 (mtpt) REVERT: A 218 VAL cc_start: 0.7329 (m) cc_final: 0.7085 (t) REVERT: A 231 ASP cc_start: 0.7185 (t70) cc_final: 0.6865 (t0) REVERT: A 280 LYS cc_start: 0.8024 (tppt) cc_final: 0.7590 (tppt) REVERT: A 308 GLU cc_start: 0.7495 (tt0) cc_final: 0.7184 (tt0) REVERT: A 345 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7820 (mtpp) REVERT: B 14 LEU cc_start: 0.8913 (mp) cc_final: 0.8608 (mp) REVERT: B 17 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7671 (tm-30) REVERT: B 61 MET cc_start: 0.7237 (tmm) cc_final: 0.6666 (tmm) REVERT: B 98 SER cc_start: 0.8227 (m) cc_final: 0.7893 (p) REVERT: B 111 TYR cc_start: 0.8580 (m-80) cc_final: 0.8152 (m-80) REVERT: B 114 CYS cc_start: 0.7918 (t) cc_final: 0.7658 (t) REVERT: B 188 MET cc_start: 0.7861 (mmm) cc_final: 0.7320 (mmm) REVERT: B 195 ASP cc_start: 0.7640 (t70) cc_final: 0.7331 (t0) REVERT: B 237 ASN cc_start: 0.7730 (t0) cc_final: 0.7269 (t0) REVERT: B 291 ASP cc_start: 0.7838 (t70) cc_final: 0.7405 (t70) REVERT: B 300 LEU cc_start: 0.8161 (mt) cc_final: 0.7836 (mt) REVERT: C 55 ASN cc_start: 0.7579 (m-40) cc_final: 0.7238 (m-40) REVERT: Q 107 TYR cc_start: 0.7910 (t80) cc_final: 0.7581 (t80) REVERT: Q 140 LEU cc_start: -0.1218 (OUTLIER) cc_final: -0.1462 (pp) REVERT: Q 162 MET cc_start: 0.7525 (tpp) cc_final: 0.7217 (mpp) REVERT: Q 179 VAL cc_start: 0.7111 (OUTLIER) cc_final: 0.6716 (t) REVERT: Q 262 MET cc_start: 0.6349 (tmm) cc_final: 0.5907 (tmm) REVERT: Q 268 LYS cc_start: 0.8633 (tttm) cc_final: 0.8369 (ttmt) REVERT: Q 283 PHE cc_start: 0.7016 (t80) cc_final: 0.6563 (t80) REVERT: R 44 THR cc_start: 0.8474 (t) cc_final: 0.8250 (t) REVERT: R 79 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8326 (p) REVERT: R 160 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8280 (mp) REVERT: R 165 MET cc_start: 0.7904 (tpt) cc_final: 0.7532 (tpp) REVERT: R 166 VAL cc_start: 0.8515 (m) cc_final: 0.8273 (p) REVERT: R 220 CYS cc_start: 0.8089 (m) cc_final: 0.7665 (m) REVERT: R 300 VAL cc_start: 0.8584 (t) cc_final: 0.8301 (p) REVERT: R 317 ARG cc_start: 0.7162 (mtm-85) cc_final: 0.6893 (mtm-85) REVERT: S 3 GLN cc_start: 0.7447 (tm-30) cc_final: 0.6714 (tm-30) REVERT: S 42 GLU cc_start: 0.7073 (mp0) cc_final: 0.6837 (mp0) REVERT: S 65 LYS cc_start: 0.8489 (tmtt) cc_final: 0.8202 (tmtt) REVERT: S 245 LEU cc_start: 0.8402 (mt) cc_final: 0.8181 (mt) outliers start: 33 outliers final: 26 residues processed: 344 average time/residue: 0.2353 time to fit residues: 113.6018 Evaluate side-chains 356 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 326 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 173 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 119 ASN B 259 GLN S 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.127322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.102586 restraints weight = 19191.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106260 restraints weight = 8898.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108649 restraints weight = 5505.688| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11795 Z= 0.225 Angle : 0.662 10.405 16012 Z= 0.336 Chirality : 0.043 0.174 1814 Planarity : 0.004 0.058 1995 Dihedral : 5.906 78.491 1646 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.25 % Favored : 93.68 % Rotamer: Outliers : 2.72 % Allowed : 26.34 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.22), residues: 1439 helix: 1.19 (0.21), residues: 622 sheet: -0.78 (0.32), residues: 298 loop : -2.20 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP R 261 HIS 0.004 0.001 HIS B 142 PHE 0.029 0.002 PHE A 191 TYR 0.027 0.001 TYR S 235 ARG 0.011 0.001 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2891.59 seconds wall clock time: 53 minutes 8.37 seconds (3188.37 seconds total)