Starting phenix.real_space_refine on Wed Sep 17 15:46:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k3l_62018/09_2025/9k3l_62018.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k3l_62018/09_2025/9k3l_62018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k3l_62018/09_2025/9k3l_62018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k3l_62018/09_2025/9k3l_62018.map" model { file = "/net/cci-nas-00/data/ceres_data/9k3l_62018/09_2025/9k3l_62018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k3l_62018/09_2025/9k3l_62018.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5869 2.51 5 N 1578 2.21 5 O 1738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9251 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1860 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2535 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 63 Chain: "G" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 360 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "N" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 937 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 118} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1788 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 5, 'ASP:plan': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Time building chain proxies: 2.38, per 1000 atoms: 0.26 Number of scatterers: 9251 At special positions: 0 Unit cell: (86.751, 132.804, 128.52, 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 66 16.00 O 1738 8.00 N 1578 7.00 C 5869 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 245 " - pdb=" SG CYS R 251 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 396.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 15 sheets defined 33.9% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.583A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 279 removed outlier: 4.260A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.711A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.450A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.292A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.562A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.563A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.971A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.958A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 49 removed outlier: 3.557A pdb=" N ASN R 42 " --> pdb=" O GLY R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 79 removed outlier: 3.728A pdb=" N TYR R 76 " --> pdb=" O LEU R 72 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 109 removed outlier: 4.432A pdb=" N LEU R 109 " --> pdb=" O ILE R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 115 removed outlier: 3.669A pdb=" N SER R 113 " --> pdb=" O LEU R 109 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU R 114 " --> pdb=" O PHE R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 134 removed outlier: 4.652A pdb=" N LEU R 121 " --> pdb=" O SER R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 166 removed outlier: 3.635A pdb=" N VAL R 149 " --> pdb=" O ARG R 145 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TRP R 155 " --> pdb=" O LEU R 151 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL R 166 " --> pdb=" O GLY R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 177 Processing helix chain 'R' and resid 177 through 207 removed outlier: 3.710A pdb=" N LEU R 181 " --> pdb=" O THR R 177 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE R 182 " --> pdb=" O PHE R 178 " (cutoff:3.500A) Proline residue: R 183 - end of helix removed outlier: 4.250A pdb=" N ILE R 189 " --> pdb=" O MET R 185 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU R 192 " --> pdb=" O PHE R 188 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR R 193 " --> pdb=" O ILE R 189 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS R 195 " --> pdb=" O CYS R 191 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER R 202 " --> pdb=" O LEU R 198 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS R 206 " --> pdb=" O SER R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 245 removed outlier: 3.647A pdb=" N ALA R 218 " --> pdb=" O ASN R 214 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE R 219 " --> pdb=" O MET R 215 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR R 220 " --> pdb=" O LYS R 216 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE R 223 " --> pdb=" O ILE R 219 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU R 224 " --> pdb=" O THR R 220 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE R 228 " --> pdb=" O LEU R 224 " (cutoff:3.500A) Proline residue: R 234 - end of helix removed outlier: 3.802A pdb=" N THR R 243 " --> pdb=" O VAL R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 256 Processing helix chain 'R' and resid 257 through 268 removed outlier: 3.583A pdb=" N LEU R 264 " --> pdb=" O VAL R 260 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE R 265 " --> pdb=" O ASN R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 276 Processing helix chain 'R' and resid 280 through 286 removed outlier: 4.148A pdb=" N ASP R 285 " --> pdb=" O PRO R 281 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA R 286 " --> pdb=" O GLU R 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.714A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.601A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 3.654A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.527A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP B 83 " --> pdb=" O ASN B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.758A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.606A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.627A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.705A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.726A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.539A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.111A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.858A pdb=" N LEU S 81 " --> pdb=" O LEU S 20 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE S 80 " --> pdb=" O SER S 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.314A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.314A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.686A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 155 through 160 410 hydrogen bonds defined for protein. 1137 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: 1.42 Time building geometry restraints manager: 1.29 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: 3006 1.34 - 1.46: 2036 1.46 - 1.58: 4304 1.58 - 1.69: 0 1.69 - 1.81: 97 Bond restraints: 9443 Sorted by residual: bond pdb=" CB VAL B 90 " pdb=" CG2 VAL B 90 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.96e+00 bond pdb=" CG GLU A 344 " pdb=" CD GLU A 344 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.86e+00 bond pdb=" CB PRO S 236 " pdb=" CG PRO S 236 " ideal model delta sigma weight residual 1.506 1.461 0.045 3.90e-02 6.57e+02 1.34e+00 bond pdb=" CB THR S 172 " pdb=" CG2 THR S 172 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" CD GLU A 344 " pdb=" OE1 GLU A 344 " ideal model delta sigma weight residual 1.249 1.230 0.019 1.90e-02 2.77e+03 1.04e+00 ... (remaining 9438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 12654 2.37 - 4.75: 142 4.75 - 7.12: 18 7.12 - 9.50: 3 9.50 - 11.87: 3 Bond angle restraints: 12820 Sorted by residual: angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 129.74 -8.20 1.91e+00 2.74e-01 1.84e+01 angle pdb=" C ASP A 343 " pdb=" N GLU A 344 " pdb=" CA GLU A 344 " ideal model delta sigma weight residual 120.29 115.20 5.09 1.42e+00 4.96e-01 1.29e+01 angle pdb=" CB MET R 242 " pdb=" CG MET R 242 " pdb=" SD MET R 242 " ideal model delta sigma weight residual 112.70 122.51 -9.81 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CA LEU A 270 " pdb=" CB LEU A 270 " pdb=" CG LEU A 270 " ideal model delta sigma weight residual 116.30 126.29 -9.99 3.50e+00 8.16e-02 8.14e+00 angle pdb=" N GLU A 344 " pdb=" CA GLU A 344 " pdb=" CB GLU A 344 " ideal model delta sigma weight residual 110.16 114.23 -4.07 1.48e+00 4.57e-01 7.55e+00 ... (remaining 12815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 5033 16.81 - 33.61: 460 33.61 - 50.42: 80 50.42 - 67.23: 11 67.23 - 84.03: 8 Dihedral angle restraints: 5592 sinusoidal: 2081 harmonic: 3511 Sorted by residual: dihedral pdb=" CA MET R 185 " pdb=" C MET R 185 " pdb=" N LEU R 186 " pdb=" CA LEU R 186 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LEU B 139 " pdb=" C LEU B 139 " pdb=" N ALA B 140 " pdb=" CA ALA B 140 " ideal model delta harmonic sigma weight residual -180.00 -158.07 -21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA PHE A 238 " pdb=" C PHE A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 5589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 945 0.040 - 0.080: 401 0.080 - 0.119: 106 0.119 - 0.159: 20 0.159 - 0.199: 2 Chirality restraints: 1474 Sorted by residual: chirality pdb=" CB VAL R 270 " pdb=" CA VAL R 270 " pdb=" CG1 VAL R 270 " pdb=" CG2 VAL R 270 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA PRO S 181 " pdb=" N PRO S 181 " pdb=" C PRO S 181 " pdb=" CB PRO S 181 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CG LEU S 174 " pdb=" CB LEU S 174 " pdb=" CD1 LEU S 174 " pdb=" CD2 LEU S 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 1471 not shown) Planarity restraints: 1629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 182 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.85e+00 pdb=" N PRO R 183 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 183 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 183 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 188 " 0.012 2.00e-02 2.50e+03 1.55e-02 4.22e+00 pdb=" CG PHE R 188 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE R 188 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE R 188 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE R 188 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 188 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 188 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO G 49 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.025 5.00e-02 4.00e+02 ... (remaining 1626 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 283 2.70 - 3.25: 9212 3.25 - 3.80: 14708 3.80 - 4.35: 19007 4.35 - 4.90: 32271 Nonbonded interactions: 75481 Sorted by model distance: nonbonded pdb=" NH2 ARG A 228 " pdb=" OE1 GLU A 230 " model vdw 2.146 3.120 nonbonded pdb=" NE2 GLN A 213 " pdb=" OD1 ASN A 218 " model vdw 2.152 3.120 nonbonded pdb=" O GLY S 10 " pdb=" OG1 THR S 118 " model vdw 2.167 3.040 nonbonded pdb=" OE1 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.189 3.040 nonbonded pdb=" OG SER A 13 " pdb=" OD1 ASP A 16 " model vdw 2.197 3.040 ... (remaining 75476 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.410 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 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 : 0.005 0.046 9448 Z= 0.209 Angle : 0.694 11.871 12830 Z= 0.378 Chirality : 0.046 0.199 1474 Planarity : 0.004 0.055 1629 Dihedral : 13.288 84.032 3313 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.24), residues: 1193 helix: 0.31 (0.28), residues: 359 sheet: -0.94 (0.29), residues: 316 loop : -1.42 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 38 TYR 0.012 0.002 TYR S 190 PHE 0.036 0.002 PHE R 188 TRP 0.017 0.002 TRP A 234 HIS 0.005 0.001 HIS R 195 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9443) covalent geometry : angle 0.69338 (12820) SS BOND : bond 0.00237 ( 5) SS BOND : angle 0.93388 ( 10) hydrogen bonds : bond 0.20033 ( 398) hydrogen bonds : angle 8.40652 ( 1137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: B 143 THR cc_start: 0.7516 (p) cc_final: 0.7268 (p) REVERT: B 175 GLN cc_start: 0.7083 (mm110) cc_final: 0.6783 (mm110) REVERT: B 237 ASN cc_start: 0.7642 (t0) cc_final: 0.7359 (t0) REVERT: B 239 ASN cc_start: 0.7022 (m-40) cc_final: 0.6806 (m-40) REVERT: B 249 THR cc_start: 0.7682 (p) cc_final: 0.7365 (t) REVERT: B 273 ILE cc_start: 0.7250 (mt) cc_final: 0.6947 (mt) REVERT: G 47 GLU cc_start: 0.7006 (mp0) cc_final: 0.6798 (mp0) REVERT: R 204 THR cc_start: 0.7822 (m) cc_final: 0.7579 (m) REVERT: R 266 MET cc_start: 0.5874 (mpp) cc_final: 0.5537 (mpp) REVERT: S 173 TYR cc_start: 0.7861 (m-80) cc_final: 0.7588 (m-80) REVERT: S 204 SER cc_start: 0.7584 (t) cc_final: 0.7372 (t) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.1185 time to fit residues: 37.3852 Evaluate side-chains 224 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN B 110 ASN G 44 HIS ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 195 HIS R 261 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.155227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.130505 restraints weight = 13627.734| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.26 r_work: 0.3542 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9448 Z= 0.197 Angle : 0.660 11.645 12830 Z= 0.343 Chirality : 0.045 0.195 1474 Planarity : 0.005 0.041 1629 Dihedral : 5.305 24.296 1307 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.94 % Allowed : 8.05 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.24), residues: 1193 helix: 0.63 (0.28), residues: 352 sheet: -0.47 (0.30), residues: 308 loop : -1.47 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 52 TYR 0.011 0.001 TYR S 102 PHE 0.016 0.002 PHE R 274 TRP 0.016 0.002 TRP A 234 HIS 0.008 0.002 HIS R 195 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 9443) covalent geometry : angle 0.65939 (12820) SS BOND : bond 0.00285 ( 5) SS BOND : angle 1.15514 ( 10) hydrogen bonds : bond 0.04657 ( 398) hydrogen bonds : angle 5.77294 ( 1137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 229 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 213 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7652 (mm-40) REVERT: B 143 THR cc_start: 0.8069 (p) cc_final: 0.7826 (p) REVERT: B 175 GLN cc_start: 0.7734 (mm110) cc_final: 0.7416 (mm110) REVERT: B 237 ASN cc_start: 0.8111 (t0) cc_final: 0.7718 (t0) REVERT: B 239 ASN cc_start: 0.7445 (m-40) cc_final: 0.7088 (m-40) REVERT: B 263 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.8013 (p) REVERT: B 273 ILE cc_start: 0.7834 (mt) cc_final: 0.7572 (mt) REVERT: B 289 TYR cc_start: 0.8226 (m-80) cc_final: 0.7690 (m-80) REVERT: R 42 ASN cc_start: 0.7760 (m-40) cc_final: 0.7196 (m-40) REVERT: R 71 MET cc_start: 0.5097 (OUTLIER) cc_final: 0.4757 (mmp) REVERT: R 186 LEU cc_start: 0.8418 (pp) cc_final: 0.8089 (pp) REVERT: R 266 MET cc_start: 0.6502 (mpp) cc_final: 0.6038 (mpp) REVERT: S 140 MET cc_start: 0.8002 (mtp) cc_final: 0.7792 (mtp) REVERT: S 173 TYR cc_start: 0.8287 (m-80) cc_final: 0.7786 (m-80) REVERT: S 204 SER cc_start: 0.8185 (t) cc_final: 0.7961 (t) outliers start: 19 outliers final: 11 residues processed: 232 average time/residue: 0.1155 time to fit residues: 35.2991 Evaluate side-chains 236 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 223 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 225 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 236 GLN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN G 44 HIS R 261 ASN S 142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.155746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.130379 restraints weight = 13699.650| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.31 r_work: 0.3548 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9448 Z= 0.168 Angle : 0.630 11.321 12830 Z= 0.326 Chirality : 0.044 0.205 1474 Planarity : 0.004 0.041 1629 Dihedral : 5.141 22.240 1307 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.04 % Allowed : 11.72 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.25), residues: 1193 helix: 0.75 (0.29), residues: 356 sheet: -0.32 (0.30), residues: 306 loop : -1.39 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 52 TYR 0.011 0.001 TYR S 102 PHE 0.026 0.002 PHE R 274 TRP 0.016 0.002 TRP A 234 HIS 0.008 0.002 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9443) covalent geometry : angle 0.62930 (12820) SS BOND : bond 0.00244 ( 5) SS BOND : angle 0.98476 ( 10) hydrogen bonds : bond 0.04200 ( 398) hydrogen bonds : angle 5.45668 ( 1137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 236 GLN cc_start: 0.8078 (mt0) cc_final: 0.7863 (mt0) REVERT: A 285 ILE cc_start: 0.8630 (mm) cc_final: 0.8284 (mm) REVERT: B 175 GLN cc_start: 0.7731 (mm110) cc_final: 0.7432 (mm110) REVERT: B 237 ASN cc_start: 0.8118 (t0) cc_final: 0.7758 (t0) REVERT: B 239 ASN cc_start: 0.7382 (m-40) cc_final: 0.7033 (m-40) REVERT: B 249 THR cc_start: 0.7980 (p) cc_final: 0.7683 (t) REVERT: G 38 MET cc_start: 0.7365 (ptm) cc_final: 0.7047 (ptm) REVERT: R 71 MET cc_start: 0.5147 (OUTLIER) cc_final: 0.4841 (mmp) REVERT: R 133 PHE cc_start: 0.8701 (m-80) cc_final: 0.8444 (m-80) REVERT: R 186 LEU cc_start: 0.8358 (pp) cc_final: 0.7913 (pp) REVERT: R 225 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7315 (mt) REVERT: R 266 MET cc_start: 0.6498 (mpp) cc_final: 0.6045 (mpp) REVERT: S 173 TYR cc_start: 0.8202 (m-80) cc_final: 0.7736 (m-80) REVERT: S 204 SER cc_start: 0.8169 (t) cc_final: 0.7933 (t) outliers start: 20 outliers final: 13 residues processed: 238 average time/residue: 0.1178 time to fit residues: 36.7637 Evaluate side-chains 245 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 230 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 111 optimal weight: 0.9990 chunk 35 optimal weight: 0.0170 chunk 55 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN B 110 ASN R 261 ASN S 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.156581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.131124 restraints weight = 13673.945| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.34 r_work: 0.3564 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9448 Z= 0.134 Angle : 0.600 12.545 12830 Z= 0.310 Chirality : 0.043 0.193 1474 Planarity : 0.004 0.040 1629 Dihedral : 4.881 20.854 1307 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.55 % Allowed : 13.05 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.25), residues: 1193 helix: 0.97 (0.29), residues: 356 sheet: -0.26 (0.31), residues: 307 loop : -1.34 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 52 TYR 0.011 0.001 TYR S 95 PHE 0.026 0.001 PHE R 274 TRP 0.014 0.002 TRP B 82 HIS 0.008 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9443) covalent geometry : angle 0.59955 (12820) SS BOND : bond 0.00225 ( 5) SS BOND : angle 0.93965 ( 10) hydrogen bonds : bond 0.03773 ( 398) hydrogen bonds : angle 5.16634 ( 1137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7634 (mm-40) REVERT: A 227 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8094 (mm-40) REVERT: A 236 GLN cc_start: 0.8053 (mt0) cc_final: 0.7812 (mt0) REVERT: A 295 ASP cc_start: 0.8016 (p0) cc_final: 0.7691 (p0) REVERT: A 314 GLU cc_start: 0.7392 (mp0) cc_final: 0.7175 (mp0) REVERT: B 175 GLN cc_start: 0.7745 (mm110) cc_final: 0.7444 (mm110) REVERT: B 237 ASN cc_start: 0.8127 (t0) cc_final: 0.7812 (t0) REVERT: B 239 ASN cc_start: 0.7340 (m-40) cc_final: 0.7140 (m-40) REVERT: B 249 THR cc_start: 0.7893 (p) cc_final: 0.7631 (t) REVERT: B 252 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8219 (tp) REVERT: G 38 MET cc_start: 0.7380 (ptm) cc_final: 0.7054 (ptm) REVERT: R 71 MET cc_start: 0.5100 (OUTLIER) cc_final: 0.4838 (mmp) REVERT: R 174 THR cc_start: 0.6282 (OUTLIER) cc_final: 0.6052 (m) REVERT: R 186 LEU cc_start: 0.8367 (pp) cc_final: 0.7944 (pp) REVERT: R 266 MET cc_start: 0.6476 (mpp) cc_final: 0.6117 (mpp) REVERT: S 173 TYR cc_start: 0.8326 (m-80) cc_final: 0.7946 (m-80) REVERT: S 204 SER cc_start: 0.8141 (t) cc_final: 0.7885 (t) outliers start: 25 outliers final: 17 residues processed: 250 average time/residue: 0.1198 time to fit residues: 39.6674 Evaluate side-chains 253 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain S residue 48 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 100 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 117 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 0.0970 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN B 110 ASN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 261 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.155458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130154 restraints weight = 13721.273| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.33 r_work: 0.3548 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9448 Z= 0.168 Angle : 0.620 12.914 12830 Z= 0.319 Chirality : 0.043 0.150 1474 Planarity : 0.004 0.047 1629 Dihedral : 4.949 20.420 1307 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.75 % Allowed : 14.98 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.25), residues: 1193 helix: 1.00 (0.29), residues: 360 sheet: -0.19 (0.31), residues: 308 loop : -1.29 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 52 TYR 0.013 0.001 TYR S 190 PHE 0.022 0.002 PHE R 274 TRP 0.013 0.002 TRP A 234 HIS 0.008 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9443) covalent geometry : angle 0.61995 (12820) SS BOND : bond 0.00223 ( 5) SS BOND : angle 0.91955 ( 10) hydrogen bonds : bond 0.03934 ( 398) hydrogen bonds : angle 5.17066 ( 1137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 GLN cc_start: 0.8061 (mt0) cc_final: 0.7800 (mt0) REVERT: A 285 ILE cc_start: 0.8566 (mm) cc_final: 0.8245 (mm) REVERT: A 314 GLU cc_start: 0.7419 (mp0) cc_final: 0.7204 (mp0) REVERT: B 175 GLN cc_start: 0.7723 (mm110) cc_final: 0.7423 (mm110) REVERT: B 237 ASN cc_start: 0.8138 (t0) cc_final: 0.7767 (t0) REVERT: B 239 ASN cc_start: 0.7430 (m-40) cc_final: 0.7080 (m-40) REVERT: B 249 THR cc_start: 0.7916 (p) cc_final: 0.7661 (t) REVERT: B 252 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8175 (tp) REVERT: G 38 MET cc_start: 0.7363 (ptm) cc_final: 0.7048 (ptm) REVERT: R 71 MET cc_start: 0.5179 (OUTLIER) cc_final: 0.4893 (mmp) REVERT: R 144 MET cc_start: 0.6848 (tpt) cc_final: 0.6628 (tpt) REVERT: R 186 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7879 (pp) REVERT: R 225 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7327 (mt) REVERT: R 266 MET cc_start: 0.6491 (mpp) cc_final: 0.6138 (mpp) REVERT: S 204 SER cc_start: 0.8177 (t) cc_final: 0.7928 (t) outliers start: 27 outliers final: 18 residues processed: 241 average time/residue: 0.1174 time to fit residues: 37.5615 Evaluate side-chains 253 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 231 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 4 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 95 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 227 GLN B 110 ASN ** R 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 261 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.155402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.130009 restraints weight = 13761.344| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.33 r_work: 0.3548 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9448 Z= 0.164 Angle : 0.608 11.748 12830 Z= 0.314 Chirality : 0.043 0.164 1474 Planarity : 0.004 0.041 1629 Dihedral : 4.902 19.980 1307 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.85 % Allowed : 16.72 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.25), residues: 1193 helix: 1.09 (0.29), residues: 360 sheet: -0.18 (0.31), residues: 310 loop : -1.25 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 52 TYR 0.013 0.001 TYR S 190 PHE 0.012 0.002 PHE B 199 TRP 0.015 0.002 TRP A 234 HIS 0.008 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9443) covalent geometry : angle 0.60758 (12820) SS BOND : bond 0.00226 ( 5) SS BOND : angle 0.93316 ( 10) hydrogen bonds : bond 0.03826 ( 398) hydrogen bonds : angle 5.07491 ( 1137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ARG cc_start: 0.7726 (mtm110) cc_final: 0.7142 (ptm-80) REVERT: A 236 GLN cc_start: 0.8056 (mt0) cc_final: 0.7808 (mt0) REVERT: A 285 ILE cc_start: 0.8539 (mm) cc_final: 0.8150 (mm) REVERT: A 314 GLU cc_start: 0.7373 (mp0) cc_final: 0.7168 (mp0) REVERT: B 175 GLN cc_start: 0.7722 (mm110) cc_final: 0.7421 (mm110) REVERT: B 220 GLN cc_start: 0.8169 (mp10) cc_final: 0.7589 (mt0) REVERT: B 237 ASN cc_start: 0.8131 (t0) cc_final: 0.7750 (t0) REVERT: B 239 ASN cc_start: 0.7455 (m-40) cc_final: 0.7071 (m-40) REVERT: B 249 THR cc_start: 0.7925 (p) cc_final: 0.7669 (t) REVERT: B 289 TYR cc_start: 0.8231 (m-80) cc_final: 0.7770 (m-80) REVERT: G 38 MET cc_start: 0.7355 (ptm) cc_final: 0.7044 (ptm) REVERT: R 71 MET cc_start: 0.5137 (OUTLIER) cc_final: 0.4857 (mmp) REVERT: R 144 MET cc_start: 0.6855 (tpt) cc_final: 0.6589 (tpt) REVERT: R 186 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7860 (pp) REVERT: R 225 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7321 (mt) REVERT: R 266 MET cc_start: 0.6469 (mpp) cc_final: 0.6100 (mpp) REVERT: S 173 TYR cc_start: 0.8345 (m-80) cc_final: 0.8007 (m-80) REVERT: S 204 SER cc_start: 0.8201 (t) cc_final: 0.7948 (t) outliers start: 28 outliers final: 19 residues processed: 241 average time/residue: 0.1143 time to fit residues: 36.5786 Evaluate side-chains 255 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 107 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 80 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 50 ASN B 110 ASN B 340 ASN ** R 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 203 HIS R 261 ASN S 142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.156195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.130798 restraints weight = 13770.690| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.35 r_work: 0.3556 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9448 Z= 0.130 Angle : 0.588 11.137 12830 Z= 0.302 Chirality : 0.042 0.177 1474 Planarity : 0.004 0.040 1629 Dihedral : 4.740 19.842 1307 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.55 % Allowed : 17.53 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.25), residues: 1193 helix: 1.31 (0.29), residues: 356 sheet: -0.11 (0.30), residues: 310 loop : -1.17 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 52 TYR 0.011 0.001 TYR A 358 PHE 0.014 0.001 PHE A 212 TRP 0.014 0.001 TRP A 234 HIS 0.009 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9443) covalent geometry : angle 0.58792 (12820) SS BOND : bond 0.00224 ( 5) SS BOND : angle 0.74883 ( 10) hydrogen bonds : bond 0.03589 ( 398) hydrogen bonds : angle 4.96929 ( 1137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ARG cc_start: 0.7694 (mtm110) cc_final: 0.7306 (ptm-80) REVERT: A 236 GLN cc_start: 0.8044 (mt0) cc_final: 0.7786 (mt0) REVERT: B 175 GLN cc_start: 0.7722 (mm110) cc_final: 0.7415 (mm110) REVERT: B 210 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7785 (tp) REVERT: B 220 GLN cc_start: 0.8181 (mp10) cc_final: 0.7583 (mt0) REVERT: B 237 ASN cc_start: 0.8099 (t0) cc_final: 0.7802 (t0) REVERT: B 239 ASN cc_start: 0.7357 (m-40) cc_final: 0.7018 (m-40) REVERT: B 249 THR cc_start: 0.7934 (p) cc_final: 0.7672 (t) REVERT: B 252 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8076 (tp) REVERT: G 38 MET cc_start: 0.7337 (ptm) cc_final: 0.7019 (ptm) REVERT: R 71 MET cc_start: 0.5251 (OUTLIER) cc_final: 0.4953 (mmp) REVERT: R 144 MET cc_start: 0.6822 (tpt) cc_final: 0.6516 (tpt) REVERT: R 266 MET cc_start: 0.6406 (mpp) cc_final: 0.6022 (mpp) REVERT: S 27 PHE cc_start: 0.8254 (p90) cc_final: 0.7900 (p90) REVERT: S 173 TYR cc_start: 0.8342 (m-80) cc_final: 0.8051 (m-80) REVERT: S 204 SER cc_start: 0.8178 (t) cc_final: 0.7922 (t) outliers start: 25 outliers final: 19 residues processed: 244 average time/residue: 0.1142 time to fit residues: 37.3832 Evaluate side-chains 257 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 235 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 38 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 46 optimal weight: 0.2980 chunk 73 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 227 GLN B 110 ASN ** R 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 261 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.156074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131144 restraints weight = 13757.580| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.23 r_work: 0.3565 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9448 Z= 0.144 Angle : 0.597 11.317 12830 Z= 0.306 Chirality : 0.043 0.183 1474 Planarity : 0.004 0.038 1629 Dihedral : 4.734 20.306 1307 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.75 % Allowed : 17.74 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.25), residues: 1193 helix: 1.34 (0.29), residues: 356 sheet: -0.12 (0.30), residues: 310 loop : -1.16 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 52 TYR 0.025 0.001 TYR S 190 PHE 0.014 0.001 PHE A 212 TRP 0.014 0.001 TRP A 234 HIS 0.009 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9443) covalent geometry : angle 0.59685 (12820) SS BOND : bond 0.00221 ( 5) SS BOND : angle 0.73198 ( 10) hydrogen bonds : bond 0.03637 ( 398) hydrogen bonds : angle 4.93994 ( 1137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8646 (t) cc_final: 0.8260 (p) REVERT: A 228 ARG cc_start: 0.7712 (mtm110) cc_final: 0.7277 (ptm-80) REVERT: A 236 GLN cc_start: 0.8032 (mt0) cc_final: 0.7782 (mt0) REVERT: B 175 GLN cc_start: 0.7704 (mm110) cc_final: 0.7403 (mm110) REVERT: B 210 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7831 (tp) REVERT: B 237 ASN cc_start: 0.8084 (t0) cc_final: 0.7812 (t0) REVERT: B 239 ASN cc_start: 0.7389 (m-40) cc_final: 0.7050 (m-40) REVERT: B 249 THR cc_start: 0.7936 (p) cc_final: 0.7683 (t) REVERT: B 252 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8096 (tp) REVERT: G 38 MET cc_start: 0.7331 (ptm) cc_final: 0.7016 (ptm) REVERT: R 71 MET cc_start: 0.5197 (OUTLIER) cc_final: 0.4924 (mmp) REVERT: R 144 MET cc_start: 0.6799 (tpt) cc_final: 0.6507 (tpt) REVERT: R 225 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7179 (mt) REVERT: R 266 MET cc_start: 0.6311 (mpp) cc_final: 0.5952 (mpp) REVERT: S 93 MET cc_start: 0.8392 (ttp) cc_final: 0.8171 (ttp) REVERT: S 173 TYR cc_start: 0.8331 (m-80) cc_final: 0.8075 (m-80) REVERT: S 204 SER cc_start: 0.8144 (t) cc_final: 0.7897 (t) outliers start: 27 outliers final: 19 residues processed: 242 average time/residue: 0.1183 time to fit residues: 38.1546 Evaluate side-chains 253 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 61 optimal weight: 0.0070 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 0.0060 chunk 72 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 overall best weight: 0.4214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN B 110 ASN ** R 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 203 HIS R 261 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.156876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.131657 restraints weight = 13725.310| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.34 r_work: 0.3570 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9448 Z= 0.122 Angle : 0.584 11.271 12830 Z= 0.299 Chirality : 0.042 0.190 1474 Planarity : 0.004 0.055 1629 Dihedral : 4.610 18.631 1307 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.65 % Allowed : 18.14 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.25), residues: 1193 helix: 1.52 (0.29), residues: 346 sheet: -0.03 (0.31), residues: 301 loop : -1.16 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 52 TYR 0.016 0.001 TYR A 358 PHE 0.015 0.001 PHE A 212 TRP 0.013 0.001 TRP A 234 HIS 0.008 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9443) covalent geometry : angle 0.58357 (12820) SS BOND : bond 0.00201 ( 5) SS BOND : angle 0.66570 ( 10) hydrogen bonds : bond 0.03446 ( 398) hydrogen bonds : angle 4.82239 ( 1137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7638 (mm-40) REVERT: A 36 VAL cc_start: 0.8611 (t) cc_final: 0.8194 (p) REVERT: A 228 ARG cc_start: 0.7677 (mtm110) cc_final: 0.7286 (ptm-80) REVERT: A 236 GLN cc_start: 0.8047 (mt0) cc_final: 0.7796 (mt0) REVERT: B 175 GLN cc_start: 0.7721 (mm110) cc_final: 0.7415 (mm110) REVERT: B 210 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7824 (tp) REVERT: B 237 ASN cc_start: 0.8074 (t0) cc_final: 0.7795 (t0) REVERT: B 239 ASN cc_start: 0.7222 (m-40) cc_final: 0.6919 (m-40) REVERT: B 249 THR cc_start: 0.7907 (p) cc_final: 0.7643 (t) REVERT: B 252 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8226 (tp) REVERT: G 38 MET cc_start: 0.7339 (ptm) cc_final: 0.7018 (ptm) REVERT: R 71 MET cc_start: 0.5170 (OUTLIER) cc_final: 0.4922 (mmp) REVERT: R 144 MET cc_start: 0.6811 (tpt) cc_final: 0.6467 (tpt) REVERT: R 266 MET cc_start: 0.6342 (mpp) cc_final: 0.5973 (mpp) REVERT: S 93 MET cc_start: 0.8427 (ttp) cc_final: 0.8207 (ttp) REVERT: S 173 TYR cc_start: 0.8290 (m-80) cc_final: 0.8060 (m-80) REVERT: S 183 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7923 (mm-40) outliers start: 26 outliers final: 19 residues processed: 232 average time/residue: 0.1175 time to fit residues: 35.9902 Evaluate side-chains 245 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 0.0030 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.4968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 227 GLN B 110 ASN ** R 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 261 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.156832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.131466 restraints weight = 13767.407| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.35 r_work: 0.3565 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9448 Z= 0.130 Angle : 0.593 11.055 12830 Z= 0.302 Chirality : 0.042 0.184 1474 Planarity : 0.004 0.056 1629 Dihedral : 4.613 18.919 1307 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.55 % Allowed : 18.25 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.25), residues: 1193 helix: 1.53 (0.29), residues: 346 sheet: 0.02 (0.31), residues: 301 loop : -1.16 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 52 TYR 0.013 0.001 TYR A 358 PHE 0.014 0.001 PHE A 212 TRP 0.014 0.001 TRP A 234 HIS 0.008 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9443) covalent geometry : angle 0.59265 (12820) SS BOND : bond 0.00178 ( 5) SS BOND : angle 0.68180 ( 10) hydrogen bonds : bond 0.03511 ( 398) hydrogen bonds : angle 4.81676 ( 1137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7628 (mm-40) REVERT: A 36 VAL cc_start: 0.8619 (t) cc_final: 0.8215 (p) REVERT: A 228 ARG cc_start: 0.7678 (mtm110) cc_final: 0.7254 (ptm-80) REVERT: A 236 GLN cc_start: 0.8037 (mt0) cc_final: 0.7785 (mt0) REVERT: B 49 ARG cc_start: 0.7926 (mtt90) cc_final: 0.7652 (mtt90) REVERT: B 175 GLN cc_start: 0.7690 (mm110) cc_final: 0.7387 (mm110) REVERT: B 210 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7820 (tp) REVERT: B 237 ASN cc_start: 0.8053 (t0) cc_final: 0.7786 (t0) REVERT: B 239 ASN cc_start: 0.7362 (m-40) cc_final: 0.7035 (m-40) REVERT: B 249 THR cc_start: 0.7926 (p) cc_final: 0.7664 (t) REVERT: B 252 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8073 (tp) REVERT: G 38 MET cc_start: 0.7354 (ptm) cc_final: 0.7025 (ptm) REVERT: R 71 MET cc_start: 0.5171 (OUTLIER) cc_final: 0.4927 (mmp) REVERT: R 144 MET cc_start: 0.6794 (tpt) cc_final: 0.6487 (tpt) REVERT: R 185 MET cc_start: 0.7818 (mmp) cc_final: 0.7499 (tmm) REVERT: R 225 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7145 (mt) REVERT: R 266 MET cc_start: 0.6330 (mpp) cc_final: 0.5969 (mpp) REVERT: S 93 MET cc_start: 0.8437 (ttp) cc_final: 0.8220 (ttp) REVERT: S 173 TYR cc_start: 0.8292 (m-80) cc_final: 0.8048 (m-80) REVERT: S 183 GLN cc_start: 0.8402 (mm-40) cc_final: 0.7941 (mm-40) outliers start: 25 outliers final: 17 residues processed: 232 average time/residue: 0.1149 time to fit residues: 35.1189 Evaluate side-chains 246 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 225 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 113 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.0270 chunk 16 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 44 optimal weight: 0.0170 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** R 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.157860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.132990 restraints weight = 13663.360| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.22 r_work: 0.3592 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9448 Z= 0.113 Angle : 0.592 10.434 12830 Z= 0.298 Chirality : 0.042 0.187 1474 Planarity : 0.004 0.047 1629 Dihedral : 4.507 18.315 1307 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.24 % Allowed : 18.76 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.25), residues: 1193 helix: 1.64 (0.29), residues: 346 sheet: 0.04 (0.31), residues: 301 loop : -1.12 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 52 TYR 0.012 0.001 TYR A 339 PHE 0.014 0.001 PHE A 212 TRP 0.013 0.001 TRP A 234 HIS 0.008 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9443) covalent geometry : angle 0.59167 (12820) SS BOND : bond 0.00182 ( 5) SS BOND : angle 0.59389 ( 10) hydrogen bonds : bond 0.03337 ( 398) hydrogen bonds : angle 4.73230 ( 1137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3055.93 seconds wall clock time: 52 minutes 58.10 seconds (3178.10 seconds total)