Starting phenix.real_space_refine on Thu Jul 2 21:17:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k2t_22644/07_2026/7k2t_22644.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k2t_22644/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7k2t_22644/07_2026/7k2t_22644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k2t_22644/07_2026/7k2t_22644.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7k2t_22644/07_2026/7k2t_22644.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k2t_22644/07_2026/7k2t_22644.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k2t_22644/07_2026/7k2t_22644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k2t_22644/07_2026/7k2t_22644.map" } 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-6108/lib/python3.11/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: 2.14, per 1000 atoms: 0.21 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: 1.05 Conformation dependent library (CDL) restraints added in 389.5 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: 0.16 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: 1.80 Time building geometry restraints manager: 1.36 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: 5523 17.55 - 35.09: 521 35.09 - 52.64: 74 52.64 - 70.19: 18 70.19 - 87.73: 9 Dihedral angle restraints: 6145 sinusoidal: 2509 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 6142 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: 1.830 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.980 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 13.976 87.734 3813 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/Z covalent geometry : bond 0.00513 / 0.29 (10539) covalent geometry : angle 0.77504 / 0.53 (14265) hydrogen bonds : bond 0.18686 / 11.70 ( 500) hydrogen bonds : angle 7.78720 / 5.27 ( 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 : 0.353 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: 0.1213 time to fit residues: 37.3196 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 : 0.300 ------------------------------------------------------------------------------- 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... 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 = 0.3646 r_free = 0.3646 target = 0.139672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114188 restraints weight = 14818.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115947 restraints weight = 10450.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117327 restraints weight = 8887.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117357 restraints weight = 5789.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117672 restraints weight = 6320.024| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (11 function evaluations) r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10539 Z= 0.143 Angle : 0.604 8.119 14265 Z= 0.309 Chirality : 0.043 0.151 1605 Planarity : 0.004 0.040 1735 Dihedral : 6.399 81.980 1346 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.78 % Allowed : 11.42 % Favored : 86.80 % 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: -0.34 (0.21), residues: 617 sheet: -1.03 (0.33), residues: 198 loop : -2.21 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 263 TYR 0.019 0.001 TYR C 142 PHE 0.032 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/Z covalent geometry : bond 0.00319 / 0.14 (10539) covalent geometry : angle 0.60399 / 0.31 (14265) hydrogen bonds : bond 0.04605 / 3.12 ( 500) hydrogen bonds : angle 5.36120 / 3.64 ( 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 208 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8676 (m-80) REVERT: C 146 MET cc_start: 0.8867 (mtp) cc_final: 0.8314 (mtm) REVERT: C 212 ILE cc_start: 0.8912 (mt) cc_final: 0.8598 (tt) REVERT: C 263 ARG cc_start: 0.6982 (mtm-85) cc_final: 0.6100 (mtm110) REVERT: C 368 ASN cc_start: 0.7378 (t0) cc_final: 0.6861 (m-40) REVERT: D 8 GLU cc_start: 0.8277 (tp30) cc_final: 0.7755 (tp30) REVERT: D 98 ARG cc_start: 0.8319 (tpp80) cc_final: 0.7876 (tpp80) REVERT: D 218 ASN cc_start: 0.8479 (t0) cc_final: 0.8048 (t0) outliers start: 20 outliers final: 13 residues processed: 200 average time/residue: 0.1009 time to fit residues: 28.3703 Evaluate side-chains 166 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 280 LEU 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: 5.9990 chunk 1 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN D 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.100538 restraints weight = 15627.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.100209 restraints weight = 10318.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.101348 restraints weight = 9548.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102662 restraints weight = 7725.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102896 restraints weight = 6427.215| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 10539 Z= 0.291 Angle : 0.693 9.124 14265 Z= 0.352 Chirality : 0.046 0.158 1605 Planarity : 0.004 0.046 1735 Dihedral : 6.620 83.794 1346 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.85 % Allowed : 14.36 % Favored : 82.78 % 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: -1.36 (0.23), residues: 1231 helix: -0.05 (0.21), residues: 611 sheet: -1.03 (0.33), residues: 204 loop : -1.99 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 20 TYR 0.023 0.002 TYR C 142 PHE 0.022 0.002 PHE C 163 TRP 0.013 0.002 TRP D 27 HIS 0.010 0.001 HIS D 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.29 (10539) covalent geometry : angle 0.69287 / 0.35 (14265) hydrogen bonds : bond 0.04991 / 3.38 ( 500) hydrogen bonds : angle 5.24407 / 3.56 ( 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 185 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: B 156 MET cc_start: 0.8602 (tpp) cc_final: 0.8347 (mmm) REVERT: C 123 GLU cc_start: 0.6267 (mp0) cc_final: 0.5883 (mp0) REVERT: C 146 MET cc_start: 0.8916 (mtp) cc_final: 0.8316 (mtm) REVERT: C 263 ARG cc_start: 0.6653 (mtm-85) cc_final: 0.5643 (mtp85) REVERT: C 342 LYS cc_start: 0.8079 (mtmt) cc_final: 0.7701 (mptt) REVERT: D 8 GLU cc_start: 0.8423 (tp30) cc_final: 0.7743 (tp30) REVERT: D 218 ASN cc_start: 0.8547 (t0) cc_final: 0.8330 (t0) outliers start: 32 outliers final: 25 residues processed: 172 average time/residue: 0.0948 time to fit residues: 23.3353 Evaluate side-chains 168 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 280 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 122 THR 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 217 VAL Chi-restraints excluded: chain B residue 220 LEU 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 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 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 240 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 112 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107557 restraints weight = 15089.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108258 restraints weight = 9754.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109773 restraints weight = 8972.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110706 restraints weight = 6374.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111070 restraints weight = 5711.379| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 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 = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10539 Z= 0.129 Angle : 0.578 8.376 14265 Z= 0.291 Chirality : 0.042 0.148 1605 Planarity : 0.004 0.049 1735 Dihedral : 6.321 88.832 1346 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.12 % Allowed : 15.52 % Favored : 81.36 % 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: -0.84 (0.24), residues: 1231 helix: 0.35 (0.21), residues: 615 sheet: -0.76 (0.34), residues: 204 loop : -1.73 (0.30), residues: 412 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 0.017 0.001 PHE C 389 TRP 0.013 0.001 TRP D 71 HIS 0.008 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10539) covalent geometry : angle 0.57812 / 0.29 (14265) hydrogen bonds : bond 0.03987 / 2.71 ( 500) hydrogen bonds : angle 4.89733 / 3.34 ( 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 202 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 213 LEU cc_start: 0.9243 (tp) cc_final: 0.8950 (tt) REVERT: A 241 ASN cc_start: 0.6222 (t0) cc_final: 0.5900 (m-40) REVERT: B 72 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8753 (m-80) REVERT: B 116 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8179 (mm) REVERT: B 156 MET cc_start: 0.8845 (tpp) cc_final: 0.8642 (tpp) REVERT: B 225 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.6632 (t80) REVERT: C 146 MET cc_start: 0.8782 (mtp) cc_final: 0.8310 (mtm) REVERT: C 158 THR cc_start: 0.8842 (m) cc_final: 0.8553 (m) REVERT: C 263 ARG cc_start: 0.6385 (mtm-85) cc_final: 0.5584 (mtp85) REVERT: C 342 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7698 (mptt) REVERT: D 8 GLU cc_start: 0.8275 (tp30) cc_final: 0.7694 (tp30) REVERT: D 134 ILE cc_start: 0.8644 (tt) cc_final: 0.8400 (mm) REVERT: D 175 PHE cc_start: 0.8716 (t80) cc_final: 0.8259 (t80) REVERT: D 218 ASN cc_start: 0.8415 (t0) cc_final: 0.8193 (t0) outliers start: 35 outliers final: 18 residues processed: 188 average time/residue: 0.0907 time to fit residues: 24.7947 Evaluate side-chains 167 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 308 ASP 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 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 C residue 308 ASP Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 199 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 42 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN ** 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** C 350 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106327 restraints weight = 15045.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106633 restraints weight = 9616.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107979 restraints weight = 8920.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109938 restraints weight = 6647.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110167 restraints weight = 5440.242| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10539 Z= 0.170 Angle : 0.598 9.379 14265 Z= 0.301 Chirality : 0.044 0.154 1605 Planarity : 0.004 0.047 1735 Dihedral : 6.264 89.451 1346 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.21 % Allowed : 16.95 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.68 (0.24), residues: 1231 helix: 0.48 (0.21), residues: 619 sheet: -0.44 (0.36), residues: 185 loop : -1.76 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 20 TYR 0.020 0.001 TYR C 142 PHE 0.021 0.002 PHE D 72 TRP 0.011 0.001 TRP D 71 HIS 0.008 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (10539) covalent geometry : angle 0.59837 / 0.30 (14265) hydrogen bonds : bond 0.04074 / 2.77 ( 500) hydrogen bonds : angle 4.84819 / 3.29 ( 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 188 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 213 LEU cc_start: 0.9243 (tp) cc_final: 0.8960 (tt) REVERT: A 222 GLU cc_start: 0.7231 (tt0) cc_final: 0.6985 (tp30) REVERT: A 241 ASN cc_start: 0.6226 (t0) cc_final: 0.5905 (m-40) REVERT: B 72 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8752 (m-80) REVERT: B 116 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8212 (mm) REVERT: B 156 MET cc_start: 0.8827 (tpp) cc_final: 0.8577 (tpp) REVERT: B 225 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.6559 (t80) REVERT: C 23 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8360 (pp20) REVERT: C 123 GLU cc_start: 0.5821 (mp0) cc_final: 0.5418 (mp0) REVERT: C 146 MET cc_start: 0.8804 (mtp) cc_final: 0.8539 (mtm) REVERT: C 158 THR cc_start: 0.8799 (m) cc_final: 0.8514 (m) REVERT: C 263 ARG cc_start: 0.6452 (mtm-85) cc_final: 0.5642 (mtp85) REVERT: C 264 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7282 (mt) REVERT: C 342 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7711 (mptt) REVERT: D 8 GLU cc_start: 0.8371 (tp30) cc_final: 0.7704 (tp30) REVERT: D 134 ILE cc_start: 0.8591 (tt) cc_final: 0.8355 (mm) REVERT: D 175 PHE cc_start: 0.8784 (t80) cc_final: 0.8444 (t80) outliers start: 36 outliers final: 25 residues processed: 175 average time/residue: 0.0888 time to fit residues: 22.8201 Evaluate side-chains 173 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 308 ASP 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 156 ILE Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain D residue 47 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 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: 0.9980 chunk 57 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3560 r_free = 0.3560 target = 0.133769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107836 restraints weight = 15281.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108566 restraints weight = 9686.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.109978 restraints weight = 8865.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110962 restraints weight = 6469.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111290 restraints weight = 5689.074| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- 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: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10539 Z= 0.133 Angle : 0.567 9.109 14265 Z= 0.285 Chirality : 0.042 0.162 1605 Planarity : 0.003 0.046 1735 Dihedral : 6.098 89.798 1346 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.75 % Allowed : 17.31 % 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: -0.41 (0.24), residues: 1231 helix: 0.68 (0.22), residues: 617 sheet: -0.34 (0.37), residues: 185 loop : -1.58 (0.29), residues: 429 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 0.018 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/Z covalent geometry : bond 0.00309 / 0.13 (10539) covalent geometry : angle 0.56693 / 0.28 (14265) hydrogen bonds : bond 0.03789 / 2.58 ( 500) hydrogen bonds : angle 4.74340 / 3.24 ( 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 197 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 213 LEU cc_start: 0.9239 (tp) cc_final: 0.8958 (tt) REVERT: A 222 GLU cc_start: 0.7237 (tt0) cc_final: 0.6981 (tp30) REVERT: A 241 ASN cc_start: 0.6284 (t0) cc_final: 0.5972 (m-40) REVERT: B 72 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8820 (m-10) REVERT: B 116 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8162 (mm) REVERT: B 156 MET cc_start: 0.8844 (tpp) cc_final: 0.8590 (tpp) REVERT: B 225 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.6527 (t80) REVERT: C 23 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8293 (pp20) REVERT: C 146 MET cc_start: 0.8813 (mtp) cc_final: 0.8320 (mtm) REVERT: C 263 ARG cc_start: 0.6375 (mtm-85) cc_final: 0.5413 (mtp85) REVERT: C 264 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7210 (mt) REVERT: C 342 LYS cc_start: 0.8194 (mtmt) cc_final: 0.7834 (mptt) REVERT: C 379 PHE cc_start: 0.8572 (p90) cc_final: 0.8267 (p90) REVERT: D 8 GLU cc_start: 0.8322 (tp30) cc_final: 0.7695 (tp30) REVERT: D 134 ILE cc_start: 0.8553 (tt) cc_final: 0.8343 (mm) REVERT: D 232 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7886 (mt) outliers start: 42 outliers final: 28 residues processed: 180 average time/residue: 0.0834 time to fit residues: 22.0923 Evaluate side-chains 178 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 334 MET 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 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 264 LEU Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain D residue 13 GLU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 2 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN 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 = 0.3564 r_free = 0.3564 target = 0.134015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108570 restraints weight = 15017.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109058 restraints weight = 9923.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110434 restraints weight = 9100.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112292 restraints weight = 6635.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112558 restraints weight = 5474.745| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10539 Z= 0.132 Angle : 0.562 8.958 14265 Z= 0.283 Chirality : 0.042 0.191 1605 Planarity : 0.003 0.046 1735 Dihedral : 5.987 88.957 1346 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.39 % Allowed : 18.29 % Favored : 78.32 % 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: -0.27 (0.24), residues: 1231 helix: 0.77 (0.22), residues: 619 sheet: -0.27 (0.36), residues: 185 loop : -1.48 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 166 TYR 0.020 0.001 TYR C 328 PHE 0.022 0.001 PHE D 126 TRP 0.011 0.001 TRP D 71 HIS 0.008 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10539) covalent geometry : angle 0.56232 / 0.28 (14265) hydrogen bonds : bond 0.03724 / 2.53 ( 500) hydrogen bonds : angle 4.71052 / 3.21 ( 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: 38 poor density : 151 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 213 LEU cc_start: 0.9236 (tp) cc_final: 0.8938 (tt) REVERT: A 222 GLU cc_start: 0.7216 (tt0) cc_final: 0.6963 (tp30) REVERT: A 365 ASN cc_start: 0.7833 (p0) cc_final: 0.7104 (p0) REVERT: B 72 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8781 (m-10) REVERT: B 156 MET cc_start: 0.8839 (tpp) cc_final: 0.8585 (tpp) REVERT: B 170 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8174 (mm-30) REVERT: B 225 TYR cc_start: 0.6892 (OUTLIER) cc_final: 0.6528 (t80) REVERT: C 23 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8280 (pp20) REVERT: C 123 GLU cc_start: 0.5673 (mp0) cc_final: 0.5314 (mp0) REVERT: C 146 MET cc_start: 0.8744 (mtp) cc_final: 0.8256 (mtm) REVERT: C 263 ARG cc_start: 0.6155 (mtm-85) cc_final: 0.5387 (mtp85) REVERT: C 342 LYS cc_start: 0.8245 (mtmt) cc_final: 0.7882 (mptt) REVERT: C 379 PHE cc_start: 0.8561 (p90) cc_final: 0.8299 (p90) REVERT: D 8 GLU cc_start: 0.8312 (tp30) cc_final: 0.7699 (tp30) REVERT: D 134 ILE cc_start: 0.8501 (tt) cc_final: 0.8283 (mm) REVERT: D 232 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7919 (mt) outliers start: 38 outliers final: 26 residues processed: 175 average time/residue: 0.0907 time to fit residues: 23.0975 Evaluate side-chains 173 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 122 THR 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 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 388 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.132650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107558 restraints weight = 15151.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108069 restraints weight = 10213.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109431 restraints weight = 9389.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111180 restraints weight = 6823.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111424 restraints weight = 5709.538| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10539 Z= 0.164 Angle : 0.584 8.933 14265 Z= 0.296 Chirality : 0.043 0.179 1605 Planarity : 0.003 0.049 1735 Dihedral : 5.989 88.856 1346 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: -0.24 (0.24), residues: 1231 helix: 0.83 (0.22), residues: 616 sheet: -0.36 (0.37), residues: 190 loop : -1.46 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 166 TYR 0.019 0.001 TYR C 142 PHE 0.018 0.002 PHE A 330 TRP 0.011 0.001 TRP D 71 HIS 0.009 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (10539) covalent geometry : angle 0.58427 / 0.30 (14265) hydrogen bonds : bond 0.03895 / 2.61 ( 500) hydrogen bonds : angle 4.73652 / 3.22 ( 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 189 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7219 (tt0) cc_final: 0.6953 (tp30) REVERT: A 241 ASN cc_start: 0.6306 (t0) cc_final: 0.5750 (m-40) REVERT: A 365 ASN cc_start: 0.7938 (p0) cc_final: 0.7217 (p0) REVERT: B 72 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8789 (m-10) REVERT: B 116 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8210 (mm) REVERT: B 156 MET cc_start: 0.8753 (tpp) cc_final: 0.8478 (tpp) REVERT: B 170 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8281 (mm-30) REVERT: B 225 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.6621 (t80) REVERT: C 23 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8263 (pp20) REVERT: C 123 GLU cc_start: 0.5695 (mp0) cc_final: 0.5296 (mp0) REVERT: C 146 MET cc_start: 0.8788 (mtp) cc_final: 0.8548 (mtm) REVERT: C 263 ARG cc_start: 0.5898 (mtm-85) cc_final: 0.5600 (mtp85) REVERT: C 342 LYS cc_start: 0.8404 (mtmt) cc_final: 0.7950 (mptt) REVERT: C 379 PHE cc_start: 0.8570 (p90) cc_final: 0.8301 (p90) REVERT: C 394 ILE cc_start: 0.3273 (OUTLIER) cc_final: 0.2889 (mm) REVERT: D 8 GLU cc_start: 0.8323 (tp30) cc_final: 0.7708 (tp30) REVERT: D 134 ILE cc_start: 0.8513 (tt) cc_final: 0.8299 (mm) REVERT: D 175 PHE cc_start: 0.8799 (t80) cc_final: 0.8477 (t80) REVERT: D 232 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8084 (mp) outliers start: 42 outliers final: 30 residues processed: 176 average time/residue: 0.0960 time to fit residues: 24.7685 Evaluate side-chains 179 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 334 MET 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 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 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 262 VAL Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 394 ILE 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 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: 0.4980 chunk 77 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109713 restraints weight = 14957.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110414 restraints weight = 10060.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111829 restraints weight = 9115.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112811 restraints weight = 6380.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113090 restraints weight = 5654.909| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | 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: 25 | |-----------------------------------------------------------------------------| |-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: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10539 Z= 0.119 Angle : 0.562 8.105 14265 Z= 0.285 Chirality : 0.042 0.170 1605 Planarity : 0.003 0.048 1735 Dihedral : 5.841 87.188 1346 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.03 % Allowed : 19.09 % Favored : 77.88 % 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: -0.04 (0.24), residues: 1231 helix: 0.98 (0.22), residues: 608 sheet: -0.27 (0.37), residues: 191 loop : -1.31 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 263 TYR 0.016 0.001 TYR C 142 PHE 0.017 0.001 PHE A 330 TRP 0.012 0.001 TRP D 71 HIS 0.009 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (10539) covalent geometry : angle 0.56176 / 0.28 (14265) hydrogen bonds : bond 0.03577 / 2.40 ( 500) hydrogen bonds : angle 4.62870 / 3.15 ( 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 189 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.9194 (pm20) cc_final: 0.8658 (mp0) REVERT: A 222 GLU cc_start: 0.7187 (tt0) cc_final: 0.6936 (tp30) REVERT: A 241 ASN cc_start: 0.6265 (t0) cc_final: 0.5715 (m-40) REVERT: B 72 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8722 (m-10) REVERT: B 116 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8139 (mm) REVERT: B 156 MET cc_start: 0.8872 (tpp) cc_final: 0.8603 (mmm) REVERT: B 170 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8238 (mm-30) REVERT: B 205 MET cc_start: 0.8750 (mmm) cc_final: 0.8478 (tpp) REVERT: B 225 TYR cc_start: 0.6975 (OUTLIER) cc_final: 0.6581 (t80) REVERT: C 263 ARG cc_start: 0.6343 (mtm-85) cc_final: 0.5574 (mtp85) REVERT: C 274 PHE cc_start: 0.7886 (m-80) cc_final: 0.7551 (m-10) REVERT: C 342 LYS cc_start: 0.8452 (mtmt) cc_final: 0.7911 (mmtm) REVERT: C 379 PHE cc_start: 0.8525 (p90) cc_final: 0.8278 (p90) REVERT: C 394 ILE cc_start: 0.3305 (OUTLIER) cc_final: 0.2968 (mm) REVERT: D 8 GLU cc_start: 0.8307 (tp30) cc_final: 0.7678 (tp30) REVERT: D 134 ILE cc_start: 0.8487 (tt) cc_final: 0.8281 (mm) REVERT: D 232 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7960 (mt) outliers start: 34 outliers final: 24 residues processed: 175 average time/residue: 0.0939 time to fit residues: 23.8761 Evaluate side-chains 178 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 280 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 122 THR 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 296 VAL Chi-restraints excluded: chain C residue 394 ILE 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 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 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 77 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109768 restraints weight = 14941.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110117 restraints weight = 10189.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.111585 restraints weight = 9275.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113425 restraints weight = 6736.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113729 restraints weight = 5591.409| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10539 Z= 0.127 Angle : 0.576 8.520 14265 Z= 0.292 Chirality : 0.042 0.170 1605 Planarity : 0.003 0.047 1735 Dihedral : 5.761 87.254 1346 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.77 % Allowed : 19.27 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.02 (0.24), residues: 1231 helix: 1.03 (0.22), residues: 610 sheet: -0.24 (0.37), residues: 191 loop : -1.29 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 263 TYR 0.016 0.001 TYR B 18 PHE 0.020 0.001 PHE B 137 TRP 0.012 0.001 TRP D 71 HIS 0.008 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10539) covalent geometry : angle 0.57554 / 0.29 (14265) hydrogen bonds : bond 0.03605 / 2.43 ( 500) hydrogen bonds : angle 4.60625 / 3.14 ( 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 180 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.9155 (pm20) cc_final: 0.8595 (mp0) REVERT: A 222 GLU cc_start: 0.7196 (tt0) cc_final: 0.6947 (tp30) REVERT: A 241 ASN cc_start: 0.6265 (t0) cc_final: 0.5720 (m-40) REVERT: B 72 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8774 (m-10) REVERT: B 116 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8129 (mm) REVERT: B 156 MET cc_start: 0.8691 (tpp) cc_final: 0.8442 (tpp) REVERT: B 170 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8290 (mm-30) REVERT: B 205 MET cc_start: 0.8841 (mmm) cc_final: 0.8498 (tpp) REVERT: B 225 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6587 (t80) REVERT: C 123 GLU cc_start: 0.5562 (mp0) cc_final: 0.5234 (mp0) REVERT: C 263 ARG cc_start: 0.6187 (mtm-85) cc_final: 0.5568 (mtp85) REVERT: C 274 PHE cc_start: 0.7912 (m-80) cc_final: 0.7572 (m-10) REVERT: C 282 ILE cc_start: 0.8444 (mm) cc_final: 0.8137 (tt) REVERT: C 342 LYS cc_start: 0.8443 (mtmt) cc_final: 0.7924 (mptt) REVERT: C 379 PHE cc_start: 0.8515 (p90) cc_final: 0.8281 (p90) REVERT: D 8 GLU cc_start: 0.8310 (tp30) cc_final: 0.7717 (tp30) REVERT: D 232 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7979 (mt) outliers start: 31 outliers final: 26 residues processed: 169 average time/residue: 0.1008 time to fit residues: 24.6363 Evaluate side-chains 175 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 280 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 122 THR 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 262 VAL 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 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 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: 0.6980 chunk 43 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.135377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110220 restraints weight = 15107.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110473 restraints weight = 10320.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111937 restraints weight = 9396.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114056 restraints weight = 6874.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114313 restraints weight = 5650.880| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3364 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= 0.125 Angle : 0.567 8.241 14265 Z= 0.289 Chirality : 0.042 0.163 1605 Planarity : 0.003 0.046 1735 Dihedral : 5.714 87.191 1346 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.85 % Allowed : 19.54 % Favored : 77.61 % 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: 0.08 (0.25), residues: 1231 helix: 1.08 (0.22), residues: 609 sheet: -0.26 (0.37), residues: 190 loop : -1.23 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 263 TYR 0.015 0.001 TYR C 142 PHE 0.018 0.001 PHE B 137 TRP 0.012 0.001 TRP D 71 HIS 0.008 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (10539) covalent geometry : angle 0.56675 / 0.29 (14265) hydrogen bonds : bond 0.03551 / 2.40 ( 500) hydrogen bonds : angle 4.58678 / 3.12 ( 1437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1560.93 seconds wall clock time: 27 minutes 53.39 seconds (1673.39 seconds total)