Starting phenix.real_space_refine on Wed Mar 4 03:02:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k2t_22644/03_2026/7k2t_22644.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k2t_22644/03_2026/7k2t_22644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k2t_22644/03_2026/7k2t_22644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k2t_22644/03_2026/7k2t_22644.map" model { file = "/net/cci-nas-00/data/ceres_data/7k2t_22644/03_2026/7k2t_22644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k2t_22644/03_2026/7k2t_22644.cif" } resolution = 3.6 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= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 6842 2.51 5 N 1607 2.21 5 O 1790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10275 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3005 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 12, 'TRANS': 361} Chain breaks: 2 Chain: "B" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2082 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 1 Chain: "C" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2993 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 12, 'TRANS': 359} Chain breaks: 2 Chain: "D" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.63, per 1000 atoms: 0.26 Number of scatterers: 10275 At special positions: 0 Unit cell: (101.363, 79.0034, 138.629, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 6 15.00 Mg 2 11.99 O 1790 8.00 N 1607 7.00 C 6842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 476.8 milliseconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 9 sheets defined 50.3% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 16 through 27 Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 101 through 112 removed outlier: 3.828A pdb=" N TYR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 removed outlier: 3.706A pdb=" N GLU A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.590A pdb=" N HIS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 190 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 21 through 47 removed outlier: 4.065A pdb=" N TRP B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Proline residue: B 32 - end of helix removed outlier: 4.514A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 83 removed outlier: 3.792A pdb=" N PHE B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Proline residue: B 70 - end of helix removed outlier: 3.827A pdb=" N THR B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 100 through 128 removed outlier: 3.735A pdb=" N LEU B 120 " --> pdb=" O ILE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 138 removed outlier: 3.929A pdb=" N LYS B 135 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TYR B 138 " --> pdb=" O LYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 163 removed outlier: 3.663A pdb=" N LEU B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 180 removed outlier: 3.767A pdb=" N GLY B 173 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.885A pdb=" N LEU B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 218 Processing helix chain 'B' and resid 223 through 256 removed outlier: 3.503A pdb=" N LEU B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.681A pdb=" N LEU B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASP B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 25 removed outlier: 4.256A pdb=" N LEU C 21 " --> pdb=" O PRO C 17 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 68 Processing helix chain 'C' and resid 99 through 111 removed outlier: 3.605A pdb=" N ASN C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 126 removed outlier: 3.673A pdb=" N ASP C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N SER C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 143 through 158 Processing helix chain 'C' and resid 173 through 190 Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'D' and resid 3 through 17 Processing helix chain 'D' and resid 26 through 44 Proline residue: D 32 - end of helix removed outlier: 3.553A pdb=" N PHE D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 82 Proline residue: D 70 - end of helix Processing helix chain 'D' and resid 100 through 129 removed outlier: 3.842A pdb=" N VAL D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 138 removed outlier: 4.277A pdb=" N GLY D 133 " --> pdb=" O GLY D 130 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE D 134 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS D 135 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TYR D 138 " --> pdb=" O LYS D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 165 removed outlier: 3.826A pdb=" N SER D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 160 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.513A pdb=" N LYS D 198 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU D 199 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 217 removed outlier: 4.445A pdb=" N VAL D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 214 " --> pdb=" O SER D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.505A pdb=" N LEU D 227 " --> pdb=" O HIS D 223 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 233 " --> pdb=" O GLY D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 240 Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 248 through 253 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 43 removed outlier: 6.411A pdb=" N LYS A 9 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS A 38 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL A 7 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A 40 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE A 5 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU A 42 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG A 3 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL A 7 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS A 75 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 87 removed outlier: 3.673A pdb=" N VAL A 197 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N HIS A 215 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILE A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 265 removed outlier: 6.560A pdb=" N ASP A 285 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL A 262 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU A 283 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU A 264 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE A 281 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 282 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 286 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 288 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN C 390 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 276 removed outlier: 5.975A pdb=" N SER A 276 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE A 374 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYS A 367 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS A 350 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 296 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASP A 303 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP A 308 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 388 through 392 removed outlier: 3.742A pdb=" N ASN A 390 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C 331 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 392 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 329 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 261 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU C 287 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE C 259 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 32 through 44 removed outlier: 6.343A pdb=" N LYS C 9 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS C 38 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL C 7 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE C 40 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE C 5 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU C 42 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG C 3 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 50 through 53 removed outlier: 6.469A pdb=" N GLY C 51 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU C 214 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL C 53 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N HIS C 215 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE C 219 " --> pdb=" O HIS C 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 84 through 87 removed outlier: 3.702A pdb=" N ILE C 164 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 87 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 276 removed outlier: 4.513A pdb=" N SER C 276 " --> pdb=" O ASN C 372 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N PHE C 374 " --> pdb=" O SER C 276 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA C 297 " --> pdb=" O ASN C 313 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN C 313 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE C 299 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY C 311 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE C 301 " --> pdb=" O ILE C 309 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1437 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: 1.66 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3058 1.34 - 1.46: 2468 1.46 - 1.58: 4957 1.58 - 1.69: 10 1.69 - 1.81: 46 Bond restraints: 10539 Sorted by residual: bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.30e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.85e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.09e+01 bond pdb=" C5 ATP A 501 " pdb=" C6 ATP A 501 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.87e+01 bond pdb=" C5 ATP A 501 " pdb=" N7 ATP A 501 " ideal model delta sigma weight residual 1.387 1.341 0.046 1.00e-02 1.00e+04 2.09e+01 ... (remaining 10534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 14219 4.34 - 8.68: 40 8.68 - 13.02: 2 13.02 - 17.36: 0 17.36 - 21.69: 4 Bond angle restraints: 14265 Sorted by residual: angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 118.18 21.69 1.00e+00 1.00e+00 4.71e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 119.92 19.95 1.00e+00 1.00e+00 3.98e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 118.26 18.57 1.00e+00 1.00e+00 3.45e+02 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 118.49 18.34 1.00e+00 1.00e+00 3.36e+02 angle pdb=" C5 ATP A 501 " pdb=" C4 ATP A 501 " pdb=" N3 ATP A 501 " ideal model delta sigma weight residual 126.80 118.57 8.23 1.00e+00 1.00e+00 6.77e+01 ... (remaining 14260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 5543 17.55 - 35.09: 547 35.09 - 52.64: 84 52.64 - 70.19: 22 70.19 - 87.73: 11 Dihedral angle restraints: 6207 sinusoidal: 2571 harmonic: 3636 Sorted by residual: dihedral pdb=" CA LEU C 98 " pdb=" C LEU C 98 " pdb=" N SER C 99 " pdb=" CA SER C 99 " ideal model delta harmonic sigma weight residual 180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA TYR B 18 " pdb=" C TYR B 18 " pdb=" N ALA B 19 " pdb=" CA ALA B 19 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA LYS D 50 " pdb=" C LYS D 50 " pdb=" N LEU D 51 " pdb=" CA LEU D 51 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 6204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1124 0.042 - 0.084: 363 0.084 - 0.126: 106 0.126 - 0.168: 11 0.168 - 0.210: 1 Chirality restraints: 1605 Sorted by residual: chirality pdb=" CB ILE C 219 " pdb=" CA ILE C 219 " pdb=" CG1 ILE C 219 " pdb=" CG2 ILE C 219 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE C 212 " pdb=" N ILE C 212 " pdb=" C ILE C 212 " pdb=" CB ILE C 212 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ILE A 363 " pdb=" N ILE A 363 " pdb=" C ILE A 363 " pdb=" CB ILE A 363 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 1602 not shown) Planarity restraints: 1735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 132 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.71e+00 pdb=" C ASP C 132 " -0.028 2.00e-02 2.50e+03 pdb=" O ASP C 132 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP C 133 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 339 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO A 340 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 340 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 340 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 146 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.64e+00 pdb=" C LEU D 146 " 0.022 2.00e-02 2.50e+03 pdb=" O LEU D 146 " -0.008 2.00e-02 2.50e+03 pdb=" N MET D 147 " -0.007 2.00e-02 2.50e+03 ... (remaining 1732 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 71 2.54 - 3.13: 8222 3.13 - 3.72: 15256 3.72 - 4.31: 21819 4.31 - 4.90: 37083 Nonbonded interactions: 82451 Sorted by model distance: nonbonded pdb=" O1G ATP A 501 " pdb="MG MG A 502 " model vdw 1.955 2.170 nonbonded pdb=" O1G ATP C 501 " pdb="MG MG C 502 " model vdw 2.042 2.170 nonbonded pdb=" O1B ATP A 501 " pdb="MG MG A 502 " model vdw 2.079 2.170 nonbonded pdb=" O1B ATP C 501 " pdb="MG MG C 502 " model vdw 2.134 2.170 nonbonded pdb=" OG SER A 61 " pdb="MG MG A 502 " model vdw 2.180 2.170 ... (remaining 82446 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 241 or resid 255 through 502)) selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 2 through 47 or resid 55 through 256)) } 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=0.15 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.830 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 0.079 10539 Z= 0.287 Angle : 0.775 21.694 14265 Z= 0.529 Chirality : 0.044 0.210 1605 Planarity : 0.003 0.032 1735 Dihedral : 14.489 87.734 3875 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.21), residues: 1231 helix: -1.83 (0.19), residues: 604 sheet: -1.78 (0.33), residues: 185 loop : -2.65 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 210 TYR 0.013 0.001 TYR D 63 PHE 0.017 0.002 PHE D 179 TRP 0.013 0.002 TRP D 71 HIS 0.012 0.001 HIS D 213 Details of bonding type rmsd covalent geometry : bond 0.00513 (10539) covalent geometry : angle 0.77504 (14265) hydrogen bonds : bond 0.18686 ( 500) hydrogen bonds : angle 7.78720 ( 1437) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7241 (tt0) cc_final: 0.6878 (tp30) REVERT: A 365 ASN cc_start: 0.6626 (p0) cc_final: 0.6416 (p0) REVERT: C 121 LYS cc_start: 0.8880 (mttt) cc_final: 0.8567 (mtpp) REVERT: C 123 GLU cc_start: 0.6424 (mp0) cc_final: 0.6021 (mp0) REVERT: C 146 MET cc_start: 0.8748 (mtp) cc_final: 0.8133 (mtm) REVERT: C 212 ILE cc_start: 0.8912 (mt) cc_final: 0.8656 (tt) REVERT: C 263 ARG cc_start: 0.6648 (mtm-85) cc_final: 0.6314 (mtp85) REVERT: C 368 ASN cc_start: 0.7508 (t0) cc_final: 0.6707 (m-40) REVERT: C 388 GLU cc_start: 0.8141 (tt0) cc_final: 0.7649 (tt0) REVERT: D 8 GLU cc_start: 0.8220 (tp30) cc_final: 0.7521 (tp30) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1320 time to fit residues: 40.6154 Evaluate side-chains 154 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS B 223 HIS ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN C 272 ASN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN D 113 ASN D 177 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.138703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113387 restraints weight = 14729.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.113875 restraints weight = 9404.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115165 restraints weight = 8004.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115717 restraints weight = 6563.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116150 restraints weight = 5660.805| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10539 Z= 0.146 Angle : 0.605 8.212 14265 Z= 0.311 Chirality : 0.043 0.151 1605 Planarity : 0.004 0.042 1735 Dihedral : 9.062 78.525 1408 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.78 % Allowed : 11.33 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.23), residues: 1231 helix: -0.33 (0.21), residues: 617 sheet: -1.03 (0.33), residues: 198 loop : -2.23 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 263 TYR 0.020 0.001 TYR C 142 PHE 0.030 0.001 PHE B 131 TRP 0.012 0.001 TRP D 71 HIS 0.010 0.001 HIS D 213 Details of bonding type rmsd covalent geometry : bond 0.00321 (10539) covalent geometry : angle 0.60546 (14265) hydrogen bonds : bond 0.04659 ( 500) hydrogen bonds : angle 5.41406 ( 1437) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.6399 (mtm) cc_final: 0.6170 (mtt) REVERT: B 35 LEU cc_start: 0.8488 (tp) cc_final: 0.8271 (tp) REVERT: B 72 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8687 (m-80) REVERT: B 199 LEU cc_start: 0.8433 (mm) cc_final: 0.8181 (pp) REVERT: C 146 MET cc_start: 0.8878 (mtp) cc_final: 0.8260 (mtm) REVERT: C 212 ILE cc_start: 0.8907 (mt) cc_final: 0.8595 (tt) REVERT: C 263 ARG cc_start: 0.6974 (mtm-85) cc_final: 0.6109 (mtm110) REVERT: C 368 ASN cc_start: 0.7399 (t0) cc_final: 0.6884 (m-40) REVERT: D 8 GLU cc_start: 0.8272 (tp30) cc_final: 0.7744 (tp30) REVERT: D 98 ARG cc_start: 0.8326 (tpp80) cc_final: 0.7880 (tpp80) REVERT: D 218 ASN cc_start: 0.8485 (t0) cc_final: 0.8054 (t0) outliers start: 20 outliers final: 12 residues processed: 201 average time/residue: 0.1102 time to fit residues: 30.9981 Evaluate side-chains 163 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 34 optimal weight: 8.9990 chunk 1 optimal weight: 0.2980 chunk 114 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN B 177 GLN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.133104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107021 restraints weight = 15240.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107328 restraints weight = 10303.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108817 restraints weight = 9687.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110274 restraints weight = 6939.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110545 restraints weight = 6020.860| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10539 Z= 0.192 Angle : 0.615 8.741 14265 Z= 0.312 Chirality : 0.044 0.149 1605 Planarity : 0.004 0.047 1735 Dihedral : 8.358 72.423 1408 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.85 % Allowed : 14.45 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.23), residues: 1231 helix: 0.13 (0.21), residues: 610 sheet: -0.85 (0.33), residues: 204 loop : -1.91 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 80 TYR 0.023 0.001 TYR C 142 PHE 0.020 0.002 PHE C 389 TRP 0.011 0.002 TRP D 71 HIS 0.008 0.001 HIS D 213 Details of bonding type rmsd covalent geometry : bond 0.00459 (10539) covalent geometry : angle 0.61512 (14265) hydrogen bonds : bond 0.04453 ( 500) hydrogen bonds : angle 5.07190 ( 1437) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 72 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8728 (m-80) REVERT: B 156 MET cc_start: 0.8761 (tpp) cc_final: 0.8505 (mmm) REVERT: C 146 MET cc_start: 0.8839 (mtp) cc_final: 0.8166 (mtm) REVERT: C 158 THR cc_start: 0.8956 (m) cc_final: 0.8635 (m) REVERT: C 263 ARG cc_start: 0.6471 (mtm-85) cc_final: 0.5561 (mtp85) REVERT: C 342 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7752 (mptt) REVERT: D 8 GLU cc_start: 0.8381 (tp30) cc_final: 0.7771 (tp30) REVERT: D 37 LEU cc_start: 0.9120 (mt) cc_final: 0.8869 (mp) REVERT: D 72 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7051 (t80) REVERT: D 218 ASN cc_start: 0.8507 (t0) cc_final: 0.8266 (t0) outliers start: 32 outliers final: 20 residues processed: 175 average time/residue: 0.1000 time to fit residues: 24.8791 Evaluate side-chains 168 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 112 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 54 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107429 restraints weight = 15112.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107776 restraints weight = 9241.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109241 restraints weight = 8035.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109748 restraints weight = 6176.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110119 restraints weight = 5763.358| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10539 Z= 0.146 Angle : 0.581 8.131 14265 Z= 0.296 Chirality : 0.043 0.149 1605 Planarity : 0.003 0.047 1735 Dihedral : 7.924 69.240 1408 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.03 % Allowed : 14.90 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.24), residues: 1231 helix: 0.44 (0.21), residues: 613 sheet: -0.64 (0.34), residues: 204 loop : -1.72 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 263 TYR 0.020 0.001 TYR C 142 PHE 0.018 0.001 PHE D 72 TRP 0.012 0.001 TRP D 71 HIS 0.008 0.001 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00336 (10539) covalent geometry : angle 0.58135 (14265) hydrogen bonds : bond 0.03994 ( 500) hydrogen bonds : angle 4.86844 ( 1437) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 213 LEU cc_start: 0.9241 (tp) cc_final: 0.8952 (tt) REVERT: B 72 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8804 (m-10) REVERT: B 156 MET cc_start: 0.8781 (tpp) cc_final: 0.8528 (tpp) REVERT: B 225 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6630 (t80) REVERT: C 123 GLU cc_start: 0.5960 (mp0) cc_final: 0.5573 (mp0) REVERT: C 146 MET cc_start: 0.8756 (mtp) cc_final: 0.8166 (mtm) REVERT: C 158 THR cc_start: 0.8883 (m) cc_final: 0.8594 (m) REVERT: C 263 ARG cc_start: 0.6289 (mtm-85) cc_final: 0.5441 (mtp85) REVERT: C 342 LYS cc_start: 0.8099 (mtmt) cc_final: 0.7719 (mptt) REVERT: C 365 ASN cc_start: 0.7864 (p0) cc_final: 0.7617 (m-40) REVERT: D 8 GLU cc_start: 0.8348 (tp30) cc_final: 0.7736 (tp30) REVERT: D 37 LEU cc_start: 0.9100 (mt) cc_final: 0.8827 (mp) REVERT: D 72 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7140 (t80) REVERT: D 134 ILE cc_start: 0.8660 (tt) cc_final: 0.8422 (mm) REVERT: D 175 PHE cc_start: 0.8747 (t80) cc_final: 0.8341 (t80) REVERT: D 218 ASN cc_start: 0.8410 (t0) cc_final: 0.8204 (t0) outliers start: 34 outliers final: 22 residues processed: 179 average time/residue: 0.0901 time to fit residues: 23.8115 Evaluate side-chains 169 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 42 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 199 HIS ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106286 restraints weight = 15200.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106747 restraints weight = 10155.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.108178 restraints weight = 9443.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.109187 restraints weight = 6779.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109583 restraints weight = 5984.168| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10539 Z= 0.196 Angle : 0.604 9.378 14265 Z= 0.307 Chirality : 0.044 0.161 1605 Planarity : 0.004 0.046 1735 Dihedral : 7.754 68.268 1408 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.57 % Allowed : 16.06 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.24), residues: 1231 helix: 0.49 (0.21), residues: 621 sheet: -0.40 (0.36), residues: 185 loop : -1.77 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 20 TYR 0.021 0.001 TYR C 328 PHE 0.019 0.002 PHE D 72 TRP 0.011 0.002 TRP D 71 HIS 0.008 0.001 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00470 (10539) covalent geometry : angle 0.60393 (14265) hydrogen bonds : bond 0.04186 ( 500) hydrogen bonds : angle 4.87964 ( 1437) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8819 (pm20) REVERT: A 148 MET cc_start: 0.8016 (tmt) cc_final: 0.7468 (tmm) REVERT: A 222 GLU cc_start: 0.7225 (tt0) cc_final: 0.6962 (tp30) REVERT: A 241 ASN cc_start: 0.6174 (t0) cc_final: 0.5847 (m-40) REVERT: B 72 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8771 (m-10) REVERT: B 116 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8241 (mm) REVERT: B 156 MET cc_start: 0.8766 (tpp) cc_final: 0.8500 (tpp) REVERT: B 225 TYR cc_start: 0.6922 (OUTLIER) cc_final: 0.6576 (t80) REVERT: C 23 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8319 (pp20) REVERT: C 146 MET cc_start: 0.8823 (mtp) cc_final: 0.8528 (mtm) REVERT: C 263 ARG cc_start: 0.6442 (mtm-85) cc_final: 0.5655 (mtp85) REVERT: C 342 LYS cc_start: 0.8055 (mtmt) cc_final: 0.7681 (mptt) REVERT: D 8 GLU cc_start: 0.8373 (tp30) cc_final: 0.7741 (tp30) REVERT: D 37 LEU cc_start: 0.9124 (mt) cc_final: 0.8838 (mp) REVERT: D 134 ILE cc_start: 0.8677 (tt) cc_final: 0.8413 (mm) REVERT: D 175 PHE cc_start: 0.8832 (t80) cc_final: 0.8514 (t80) outliers start: 40 outliers final: 30 residues processed: 177 average time/residue: 0.0957 time to fit residues: 23.9908 Evaluate side-chains 176 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN A 368 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.134117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108199 restraints weight = 15260.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108821 restraints weight = 9720.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110166 restraints weight = 8799.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111967 restraints weight = 6507.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112187 restraints weight = 5418.029| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10539 Z= 0.128 Angle : 0.557 9.329 14265 Z= 0.285 Chirality : 0.042 0.152 1605 Planarity : 0.003 0.047 1735 Dihedral : 7.562 65.523 1408 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.30 % Allowed : 17.75 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.24), residues: 1231 helix: 0.65 (0.21), residues: 625 sheet: -0.16 (0.37), residues: 180 loop : -1.68 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 166 TYR 0.018 0.001 TYR C 142 PHE 0.018 0.001 PHE D 72 TRP 0.012 0.001 TRP D 71 HIS 0.008 0.001 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00295 (10539) covalent geometry : angle 0.55735 (14265) hydrogen bonds : bond 0.03763 ( 500) hydrogen bonds : angle 4.73344 ( 1437) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 148 MET cc_start: 0.8303 (tmt) cc_final: 0.7947 (tmm) REVERT: A 213 LEU cc_start: 0.9232 (tp) cc_final: 0.8943 (tt) REVERT: A 222 GLU cc_start: 0.7247 (tt0) cc_final: 0.6989 (tp30) REVERT: A 241 ASN cc_start: 0.6249 (t0) cc_final: 0.5923 (m-40) REVERT: B 72 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8694 (m-10) REVERT: B 116 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8133 (mm) REVERT: B 156 MET cc_start: 0.8810 (tpp) cc_final: 0.8560 (tpp) REVERT: B 170 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8315 (mm-30) REVERT: B 225 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.6533 (t80) REVERT: C 23 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8297 (pp20) REVERT: C 123 GLU cc_start: 0.5844 (mp0) cc_final: 0.5488 (mp0) REVERT: C 146 MET cc_start: 0.8786 (mtp) cc_final: 0.8327 (mtm) REVERT: C 263 ARG cc_start: 0.6324 (mtm-85) cc_final: 0.5385 (mtp85) REVERT: C 264 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7042 (mt) REVERT: C 342 LYS cc_start: 0.8232 (mtmt) cc_final: 0.7755 (mptt) REVERT: C 379 PHE cc_start: 0.8580 (p90) cc_final: 0.8274 (p90) REVERT: D 8 GLU cc_start: 0.8313 (tp30) cc_final: 0.7714 (tp30) REVERT: D 134 ILE cc_start: 0.8637 (tt) cc_final: 0.8392 (mm) outliers start: 37 outliers final: 23 residues processed: 182 average time/residue: 0.0913 time to fit residues: 23.9488 Evaluate side-chains 173 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 2 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 111 optimal weight: 0.0170 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN B 177 GLN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.133116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107669 restraints weight = 15063.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.107885 restraints weight = 10163.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109296 restraints weight = 9475.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111434 restraints weight = 6868.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111715 restraints weight = 5586.115| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10539 Z= 0.156 Angle : 0.576 9.671 14265 Z= 0.292 Chirality : 0.043 0.186 1605 Planarity : 0.003 0.047 1735 Dihedral : 7.490 62.660 1408 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.57 % Allowed : 18.38 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.24), residues: 1231 helix: 0.73 (0.21), residues: 625 sheet: -0.10 (0.37), residues: 180 loop : -1.64 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 17 TYR 0.018 0.001 TYR C 142 PHE 0.025 0.001 PHE D 72 TRP 0.011 0.001 TRP D 71 HIS 0.009 0.001 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00371 (10539) covalent geometry : angle 0.57570 (14265) hydrogen bonds : bond 0.03862 ( 500) hydrogen bonds : angle 4.74129 ( 1437) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 148 MET cc_start: 0.8333 (tmt) cc_final: 0.8036 (tmm) REVERT: A 213 LEU cc_start: 0.9241 (tp) cc_final: 0.8963 (tt) REVERT: A 222 GLU cc_start: 0.7231 (tt0) cc_final: 0.6971 (tp30) REVERT: A 365 ASN cc_start: 0.7861 (p0) cc_final: 0.7132 (p0) REVERT: B 72 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8722 (m-10) REVERT: B 116 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8158 (mm) REVERT: B 156 MET cc_start: 0.8824 (tpp) cc_final: 0.8567 (tpp) REVERT: B 170 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8169 (mm-30) REVERT: B 225 TYR cc_start: 0.6898 (OUTLIER) cc_final: 0.6544 (t80) REVERT: C 23 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8268 (pp20) REVERT: C 146 MET cc_start: 0.8763 (mtp) cc_final: 0.8539 (mtm) REVERT: C 263 ARG cc_start: 0.6456 (mtm-85) cc_final: 0.5479 (mtp85) REVERT: C 342 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7842 (mptt) REVERT: C 379 PHE cc_start: 0.8580 (p90) cc_final: 0.8285 (p90) REVERT: D 8 GLU cc_start: 0.8322 (tp30) cc_final: 0.7712 (tp30) REVERT: D 72 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7240 (t80) REVERT: D 134 ILE cc_start: 0.8608 (tt) cc_final: 0.8373 (mm) REVERT: D 175 PHE cc_start: 0.8800 (t80) cc_final: 0.8486 (t80) REVERT: D 232 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8025 (mp) outliers start: 40 outliers final: 31 residues processed: 175 average time/residue: 0.0908 time to fit residues: 22.9710 Evaluate side-chains 182 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.132058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107201 restraints weight = 14998.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107992 restraints weight = 9945.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.109463 restraints weight = 8737.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110554 restraints weight = 6058.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110957 restraints weight = 5310.080| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10539 Z= 0.152 Angle : 0.575 9.079 14265 Z= 0.293 Chirality : 0.043 0.178 1605 Planarity : 0.003 0.046 1735 Dihedral : 7.389 59.627 1408 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.75 % Allowed : 18.55 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.24), residues: 1231 helix: 0.78 (0.21), residues: 625 sheet: 0.01 (0.38), residues: 180 loop : -1.58 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 80 TYR 0.019 0.001 TYR C 142 PHE 0.024 0.001 PHE D 72 TRP 0.011 0.001 TRP D 71 HIS 0.009 0.001 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00359 (10539) covalent geometry : angle 0.57535 (14265) hydrogen bonds : bond 0.03824 ( 500) hydrogen bonds : angle 4.71504 ( 1437) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8773 (pm20) REVERT: A 148 MET cc_start: 0.8301 (tmt) cc_final: 0.8022 (tmm) REVERT: A 213 LEU cc_start: 0.9245 (tp) cc_final: 0.8973 (tt) REVERT: A 222 GLU cc_start: 0.7214 (tt0) cc_final: 0.6946 (tp30) REVERT: A 241 ASN cc_start: 0.6311 (t0) cc_final: 0.5736 (m-40) REVERT: A 365 ASN cc_start: 0.7818 (p0) cc_final: 0.7112 (p0) REVERT: B 72 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8654 (m-10) REVERT: B 116 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8136 (mm) REVERT: B 156 MET cc_start: 0.8757 (tpp) cc_final: 0.8493 (tpp) REVERT: B 170 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8132 (mm-30) REVERT: B 225 TYR cc_start: 0.6996 (OUTLIER) cc_final: 0.6615 (t80) REVERT: C 123 GLU cc_start: 0.5747 (mp0) cc_final: 0.5398 (mp0) REVERT: C 146 MET cc_start: 0.8760 (mtp) cc_final: 0.8247 (mtm) REVERT: C 263 ARG cc_start: 0.6373 (mtm-85) cc_final: 0.5705 (mtp85) REVERT: C 342 LYS cc_start: 0.8270 (mtmt) cc_final: 0.7890 (mptt) REVERT: C 379 PHE cc_start: 0.8566 (p90) cc_final: 0.8323 (p90) REVERT: D 8 GLU cc_start: 0.8328 (tp30) cc_final: 0.7721 (tp30) REVERT: D 72 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7224 (t80) REVERT: D 134 ILE cc_start: 0.8615 (tt) cc_final: 0.8372 (mm) REVERT: D 175 PHE cc_start: 0.8794 (t80) cc_final: 0.8482 (t80) REVERT: D 232 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8062 (mp) outliers start: 42 outliers final: 31 residues processed: 178 average time/residue: 0.0849 time to fit residues: 21.9461 Evaluate side-chains 183 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 57 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 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 177 GLN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.133955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108670 restraints weight = 14946.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.109606 restraints weight = 10216.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111085 restraints weight = 8903.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.111903 restraints weight = 6172.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112267 restraints weight = 5592.245| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10539 Z= 0.136 Angle : 0.565 9.115 14265 Z= 0.288 Chirality : 0.042 0.167 1605 Planarity : 0.003 0.047 1735 Dihedral : 7.278 57.627 1408 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.57 % Allowed : 19.27 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.24), residues: 1231 helix: 0.87 (0.22), residues: 619 sheet: -0.11 (0.38), residues: 185 loop : -1.44 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 166 TYR 0.017 0.001 TYR C 142 PHE 0.023 0.001 PHE D 72 TRP 0.011 0.001 TRP D 71 HIS 0.008 0.001 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00320 (10539) covalent geometry : angle 0.56471 (14265) hydrogen bonds : bond 0.03711 ( 500) hydrogen bonds : angle 4.67194 ( 1437) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 148 MET cc_start: 0.8402 (tmt) cc_final: 0.8013 (tmm) REVERT: A 213 LEU cc_start: 0.9238 (tp) cc_final: 0.8941 (tt) REVERT: A 222 GLU cc_start: 0.7212 (tt0) cc_final: 0.6957 (tp30) REVERT: A 241 ASN cc_start: 0.6313 (t0) cc_final: 0.5769 (m-40) REVERT: B 72 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8632 (m-10) REVERT: B 116 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8139 (mm) REVERT: B 156 MET cc_start: 0.8758 (tpp) cc_final: 0.8500 (mmm) REVERT: B 170 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8124 (mm-30) REVERT: B 205 MET cc_start: 0.8282 (tpp) cc_final: 0.8051 (tpp) REVERT: B 225 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.6604 (t80) REVERT: C 123 GLU cc_start: 0.5762 (mp0) cc_final: 0.5441 (mp0) REVERT: C 146 MET cc_start: 0.8735 (mtp) cc_final: 0.8230 (mtm) REVERT: C 263 ARG cc_start: 0.6087 (mtm-85) cc_final: 0.5518 (mtp85) REVERT: C 342 LYS cc_start: 0.8416 (mtmt) cc_final: 0.7964 (mptt) REVERT: C 379 PHE cc_start: 0.8553 (p90) cc_final: 0.8289 (p90) REVERT: D 8 GLU cc_start: 0.8318 (tp30) cc_final: 0.7717 (tp30) REVERT: D 72 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7221 (t80) REVERT: D 134 ILE cc_start: 0.8594 (tt) cc_final: 0.8366 (mm) REVERT: D 232 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7904 (mt) outliers start: 40 outliers final: 29 residues processed: 176 average time/residue: 0.0833 time to fit residues: 21.1111 Evaluate side-chains 182 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 77 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109216 restraints weight = 14946.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110311 restraints weight = 10382.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.111771 restraints weight = 9004.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112632 restraints weight = 6131.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.113006 restraints weight = 5546.277| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10539 Z= 0.134 Angle : 0.574 9.056 14265 Z= 0.293 Chirality : 0.042 0.164 1605 Planarity : 0.003 0.046 1735 Dihedral : 7.176 56.637 1408 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.12 % Allowed : 19.80 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.24), residues: 1231 helix: 0.91 (0.22), residues: 616 sheet: -0.10 (0.37), residues: 185 loop : -1.33 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 166 TYR 0.016 0.001 TYR C 142 PHE 0.022 0.001 PHE D 72 TRP 0.012 0.001 TRP B 71 HIS 0.008 0.001 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00315 (10539) covalent geometry : angle 0.57368 (14265) hydrogen bonds : bond 0.03704 ( 500) hydrogen bonds : angle 4.67105 ( 1437) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 148 MET cc_start: 0.8393 (tmt) cc_final: 0.8007 (tmm) REVERT: A 222 GLU cc_start: 0.7205 (tt0) cc_final: 0.6944 (tp30) REVERT: A 241 ASN cc_start: 0.6279 (t0) cc_final: 0.5754 (m-40) REVERT: B 72 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8605 (m-10) REVERT: B 116 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8127 (mm) REVERT: B 156 MET cc_start: 0.8778 (tpp) cc_final: 0.8522 (tpp) REVERT: B 170 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8163 (mm-30) REVERT: B 225 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.6597 (t80) REVERT: C 123 GLU cc_start: 0.5750 (mp0) cc_final: 0.5417 (mp0) REVERT: C 146 MET cc_start: 0.8719 (mtp) cc_final: 0.8241 (mtm) REVERT: C 263 ARG cc_start: 0.6051 (mtm-85) cc_final: 0.5502 (mtp85) REVERT: C 274 PHE cc_start: 0.8070 (m-80) cc_final: 0.7718 (m-10) REVERT: C 342 LYS cc_start: 0.8434 (mtmt) cc_final: 0.7935 (mptt) REVERT: C 379 PHE cc_start: 0.8531 (p90) cc_final: 0.8299 (p90) REVERT: D 8 GLU cc_start: 0.8317 (tp30) cc_final: 0.7724 (tp30) REVERT: D 72 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7197 (t80) REVERT: D 134 ILE cc_start: 0.8590 (tt) cc_final: 0.8367 (mm) REVERT: D 175 PHE cc_start: 0.8771 (t80) cc_final: 0.8455 (t80) REVERT: D 232 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7946 (mt) outliers start: 35 outliers final: 28 residues processed: 171 average time/residue: 0.0911 time to fit residues: 22.4601 Evaluate side-chains 178 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105982 restraints weight = 15259.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.106164 restraints weight = 10341.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107548 restraints weight = 9528.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.109226 restraints weight = 7101.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109480 restraints weight = 5986.455| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10539 Z= 0.201 Angle : 0.616 9.557 14265 Z= 0.315 Chirality : 0.044 0.159 1605 Planarity : 0.004 0.047 1735 Dihedral : 7.366 56.967 1408 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.03 % Allowed : 19.71 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.24), residues: 1231 helix: 0.83 (0.22), residues: 616 sheet: -0.24 (0.37), residues: 185 loop : -1.39 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 166 TYR 0.020 0.001 TYR C 142 PHE 0.022 0.002 PHE D 72 TRP 0.011 0.002 TRP D 27 HIS 0.008 0.001 HIS D 45 Details of bonding type rmsd covalent geometry : bond 0.00485 (10539) covalent geometry : angle 0.61620 (14265) hydrogen bonds : bond 0.04178 ( 500) hydrogen bonds : angle 4.79906 ( 1437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1525.04 seconds wall clock time: 27 minutes 16.20 seconds (1636.20 seconds total)