Starting phenix.real_space_refine on Sun Apr 5 18:27:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dou_27623/04_2026/8dou_27623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dou_27623/04_2026/8dou_27623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dou_27623/04_2026/8dou_27623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dou_27623/04_2026/8dou_27623.map" model { file = "/net/cci-nas-00/data/ceres_data/8dou_27623/04_2026/8dou_27623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dou_27623/04_2026/8dou_27623.cif" } resolution = 3.54 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= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2287 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 32 5.16 5 C 7090 2.51 5 N 1676 2.21 5 O 1864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10666 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "B" 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: "C" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.46, per 1000 atoms: 0.23 Number of scatterers: 10666 At special positions: 0 Unit cell: (94.08, 101.92, 138.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 4 15.00 O 1864 8.00 N 1676 7.00 C 7090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 449.7 milliseconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 8 sheets defined 51.3% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 17 through 27 removed outlier: 4.214A pdb=" N LEU A 21 " --> pdb=" O PRO A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 99 through 112 removed outlier: 3.757A pdb=" N ASN A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.770A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 removed outlier: 4.071A pdb=" N THR A 141 " --> pdb=" O PRO A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 Processing helix chain 'A' and resid 173 through 190 removed outlier: 3.959A pdb=" N LYS A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 224 through 241 removed outlier: 4.104A pdb=" N ASN A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 22 through 48 removed outlier: 5.195A pdb=" N TRP B 31 " --> pdb=" O TRP B 27 " (cutoff:3.500A) Proline residue: B 32 - end of helix removed outlier: 3.905A pdb=" N ILE B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU B 46 " --> pdb=" O ILE B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 56 through 87 removed outlier: 3.706A pdb=" N TYR B 60 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'B' and resid 101 through 129 removed outlier: 3.772A pdb=" N VAL B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 4.528A pdb=" N LYS B 135 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 163 removed outlier: 4.012A pdb=" N VAL B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 180 Processing helix chain 'B' and resid 188 through 192 removed outlier: 3.603A pdb=" N ILE B 191 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.617A pdb=" N TYR B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 218 Processing helix chain 'B' and resid 223 through 256 Proline residue: B 235 - end of helix removed outlier: 4.586A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.507A pdb=" N LEU C 63 " --> pdb=" O GLY C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 111 removed outlier: 4.437A pdb=" N ILE C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 129 Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.600A pdb=" N TYR C 142 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 159 removed outlier: 4.015A pdb=" N GLU C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 191 removed outlier: 3.984A pdb=" N GLN C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 191 " --> pdb=" O HIS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 206 removed outlier: 4.058A pdb=" N ILE C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 315 through 318 Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 22 through 48 removed outlier: 4.985A pdb=" N TRP D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Proline residue: D 32 - end of helix removed outlier: 3.809A pdb=" N ILE D 42 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER D 44 " --> pdb=" O THR D 40 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N HIS D 45 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU D 46 " --> pdb=" O ILE D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 57 through 84 removed outlier: 3.859A pdb=" N GLY D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Proline residue: D 70 - end of helix removed outlier: 3.593A pdb=" N GLY D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 95 removed outlier: 3.786A pdb=" N THR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS D 94 " --> pdb=" O PHE D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 129 removed outlier: 3.947A pdb=" N VAL D 105 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 139 removed outlier: 4.171A pdb=" N LYS D 135 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR D 138 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 139 " --> pdb=" O TYR D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 163 removed outlier: 3.505A pdb=" N ILE D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 180 Processing helix chain 'D' and resid 188 through 192 removed outlier: 3.541A pdb=" N LEU D 192 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.626A pdb=" N TYR D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.516A pdb=" N VAL D 215 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 256 Proline residue: D 235 - end of helix removed outlier: 5.733A pdb=" N LYS D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASP D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 37 removed outlier: 6.625A pdb=" N LYS A 9 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 2 " --> pdb=" O ILE A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 37 removed outlier: 6.625A pdb=" N LYS A 9 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 77 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 7 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS A 75 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 166 removed outlier: 6.397A pdb=" N PHE A 163 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL A 197 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE A 165 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU A 50 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ALA A 211 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU A 222 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU A 213 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 265 removed outlier: 3.688A pdb=" N ILE A 282 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU A 329 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG C 392 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 371 removed outlier: 8.615A pdb=" N ILE A 363 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LEU A 349 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASN A 365 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N VAL A 347 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS A 367 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 310 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 394 removed outlier: 4.050A pdb=" N ASN A 390 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR C 331 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG A 392 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 329 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS C 327 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY C 326 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 288 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR C 279 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N SER C 266 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE C 281 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU C 264 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU C 283 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL C 262 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP C 285 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY C 269 " --> pdb=" O SER C 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 164 through 165 removed outlier: 3.726A pdb=" N VAL C 197 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU C 50 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE C 212 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLY C 51 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU C 221 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 308 through 313 502 hydrogen bonds defined for protein. 1434 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: 1.48 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1656 1.30 - 1.43: 2980 1.43 - 1.56: 6254 1.56 - 1.69: 6 1.69 - 1.82: 52 Bond restraints: 10948 Sorted by residual: bond pdb=" C HIS B 212 " pdb=" O HIS B 212 " ideal model delta sigma weight residual 1.237 1.168 0.068 1.16e-02 7.43e+03 3.46e+01 bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" N ILE D 211 " pdb=" CA ILE D 211 " ideal model delta sigma weight residual 1.459 1.531 -0.071 1.33e-02 5.65e+03 2.88e+01 bond pdb=" C5 ADP C 501 " pdb=" C6 ADP C 501 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" N LEU D 139 " pdb=" CA LEU D 139 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.16e-02 7.43e+03 1.50e+01 ... (remaining 10943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 14512 1.83 - 3.65: 214 3.65 - 5.48: 61 5.48 - 7.31: 20 7.31 - 9.13: 11 Bond angle restraints: 14818 Sorted by residual: angle pdb=" N THR B 128 " pdb=" CA THR B 128 " pdb=" C THR B 128 " ideal model delta sigma weight residual 111.07 117.99 -6.92 1.07e+00 8.73e-01 4.18e+01 angle pdb=" O PHE B 126 " pdb=" C PHE B 126 " pdb=" N ILE B 127 " ideal model delta sigma weight residual 122.12 116.24 5.88 1.06e+00 8.90e-01 3.08e+01 angle pdb=" C TYR B 114 " pdb=" CA TYR B 114 " pdb=" CB TYR B 114 " ideal model delta sigma weight residual 110.96 119.46 -8.50 1.54e+00 4.22e-01 3.05e+01 angle pdb=" CA TYR B 114 " pdb=" C TYR B 114 " pdb=" O TYR B 114 " ideal model delta sigma weight residual 121.00 115.24 5.76 1.05e+00 9.07e-01 3.01e+01 angle pdb=" C PHE B 126 " pdb=" N ILE B 127 " pdb=" CA ILE B 127 " ideal model delta sigma weight residual 120.72 114.17 6.55 1.22e+00 6.72e-01 2.88e+01 ... (remaining 14813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.15: 6079 27.15 - 54.30: 298 54.30 - 81.44: 13 81.44 - 108.59: 1 108.59 - 135.74: 5 Dihedral angle restraints: 6396 sinusoidal: 2616 harmonic: 3780 Sorted by residual: dihedral pdb=" O2A ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PA ADP C 501 " pdb=" PB ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 75.74 -135.74 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" O2A ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PA ADP A 501 " pdb=" PB ADP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 68.82 -128.82 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" O1B ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PB ADP A 501 " pdb=" PA ADP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 65.56 -125.56 1 2.00e+01 2.50e-03 3.80e+01 ... (remaining 6393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1411 0.058 - 0.116: 220 0.116 - 0.174: 19 0.174 - 0.233: 2 0.233 - 0.291: 2 Chirality restraints: 1654 Sorted by residual: chirality pdb=" CB ILE D 211 " pdb=" CA ILE D 211 " pdb=" CG1 ILE D 211 " pdb=" CG2 ILE D 211 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA THR B 128 " pdb=" N THR B 128 " pdb=" C THR B 128 " pdb=" CB THR B 128 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA TYR B 114 " pdb=" N TYR B 114 " pdb=" C TYR B 114 " pdb=" CB TYR B 114 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.30e-01 ... (remaining 1651 not shown) Planarity restraints: 1816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 139 " -0.018 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C LEU D 139 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU D 139 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE D 140 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 114 " 0.026 2.00e-02 2.50e+03 1.61e-02 5.21e+00 pdb=" CG TYR B 114 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 114 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 114 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 114 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 114 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 114 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 114 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 92 " -0.013 2.00e-02 2.50e+03 1.61e-02 4.51e+00 pdb=" CG PHE B 92 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 92 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 92 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B 92 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 92 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 92 " 0.000 2.00e-02 2.50e+03 ... (remaining 1813 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1828 2.77 - 3.30: 9797 3.30 - 3.83: 16897 3.83 - 4.37: 18279 4.37 - 4.90: 33388 Nonbonded interactions: 80189 Sorted by model distance: nonbonded pdb=" OG SER A 114 " pdb=" OE1 GLU A 117 " model vdw 2.233 3.040 nonbonded pdb=" O PHE A 134 " pdb=" OH TYR A 142 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP C 294 " pdb=" OH TYR C 315 " model vdw 2.264 3.040 nonbonded pdb=" O PHE C 134 " pdb=" OH TYR C 142 " model vdw 2.267 3.040 nonbonded pdb=" O ILE C 154 " pdb=" OG1 THR C 158 " model vdw 2.270 3.040 ... (remaining 80184 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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=0.99 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.580 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 10948 Z= 0.183 Angle : 0.632 9.135 14818 Z= 0.343 Chirality : 0.042 0.291 1654 Planarity : 0.003 0.038 1816 Dihedral : 14.699 135.740 3980 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.34 % Allowed : 0.43 % Favored : 99.22 % 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: 0.61 (0.24), residues: 1292 helix: 1.82 (0.23), residues: 595 sheet: 1.26 (0.43), residues: 170 loop : -1.64 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 116 TYR 0.036 0.001 TYR B 114 PHE 0.037 0.001 PHE B 92 TRP 0.006 0.001 TRP D 181 HIS 0.005 0.000 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00302 (10948) covalent geometry : angle 0.63213 (14818) hydrogen bonds : bond 0.16040 ( 497) hydrogen bonds : angle 6.05912 ( 1434) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 167 time to evaluate : 0.334 Fit side-chains REVERT: A 343 TYR cc_start: 0.7548 (m-80) cc_final: 0.6931 (m-80) REVERT: B 129 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7077 (mt) outliers start: 4 outliers final: 0 residues processed: 170 average time/residue: 0.0839 time to fit residues: 21.4578 Evaluate side-chains 133 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 55 ASN B 218 ASN C 361 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.178178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.148642 restraints weight = 14053.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146813 restraints weight = 18946.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.148875 restraints weight = 18766.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.148727 restraints weight = 12875.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.149024 restraints weight = 14689.149| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10948 Z= 0.187 Angle : 0.645 8.277 14818 Z= 0.323 Chirality : 0.044 0.170 1654 Planarity : 0.004 0.034 1816 Dihedral : 8.067 155.014 1424 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.21 % Allowed : 11.47 % Favored : 87.33 % 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: 0.21 (0.24), residues: 1292 helix: 1.42 (0.22), residues: 597 sheet: 0.56 (0.43), residues: 180 loop : -1.60 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 17 TYR 0.025 0.002 TYR B 243 PHE 0.022 0.002 PHE C 369 TRP 0.016 0.002 TRP B 71 HIS 0.005 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00446 (10948) covalent geometry : angle 0.64502 (14818) hydrogen bonds : bond 0.05629 ( 497) hydrogen bonds : angle 4.81565 ( 1434) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 318 GLU cc_start: 0.7143 (mp0) cc_final: 0.6801 (mp0) REVERT: B 16 ASN cc_start: 0.8793 (p0) cc_final: 0.8477 (p0) REVERT: B 147 MET cc_start: 0.8616 (ptt) cc_final: 0.8352 (ttp) REVERT: B 152 PHE cc_start: 0.7609 (t80) cc_final: 0.7399 (t80) REVERT: B 179 PHE cc_start: 0.8796 (t80) cc_final: 0.8448 (t80) REVERT: B 205 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.5824 (ttm) REVERT: B 211 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8247 (tt) REVERT: C 249 GLN cc_start: 0.6724 (tm-30) cc_final: 0.6372 (tm-30) REVERT: D 156 MET cc_start: 0.8328 (tmm) cc_final: 0.8090 (tpp) outliers start: 14 outliers final: 7 residues processed: 152 average time/residue: 0.0921 time to fit residues: 20.4402 Evaluate side-chains 134 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 357 GLN B 218 ASN C 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.167743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134772 restraints weight = 14140.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.134121 restraints weight = 17764.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.135948 restraints weight = 16404.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.136071 restraints weight = 12485.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136611 restraints weight = 12334.181| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10948 Z= 0.214 Angle : 0.652 7.521 14818 Z= 0.330 Chirality : 0.044 0.144 1654 Planarity : 0.004 0.030 1816 Dihedral : 8.067 175.550 1422 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.59 % Allowed : 15.43 % Favored : 81.98 % 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 (0.24), residues: 1292 helix: 1.36 (0.22), residues: 589 sheet: 0.18 (0.42), residues: 197 loop : -1.91 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 11 TYR 0.024 0.002 TYR B 243 PHE 0.019 0.002 PHE C 369 TRP 0.015 0.002 TRP D 181 HIS 0.005 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00528 (10948) covalent geometry : angle 0.65161 (14818) hydrogen bonds : bond 0.05970 ( 497) hydrogen bonds : angle 4.85367 ( 1434) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7661 (mp0) cc_final: 0.7408 (mp0) REVERT: A 318 GLU cc_start: 0.7312 (mp0) cc_final: 0.6926 (mp0) REVERT: B 16 ASN cc_start: 0.8740 (p0) cc_final: 0.8331 (p0) REVERT: C 249 GLN cc_start: 0.6743 (tm-30) cc_final: 0.6283 (tm-30) REVERT: C 283 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7377 (mt-10) REVERT: D 156 MET cc_start: 0.8401 (tmm) cc_final: 0.8182 (tpp) outliers start: 30 outliers final: 15 residues processed: 165 average time/residue: 0.0930 time to fit residues: 22.4179 Evaluate side-chains 139 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 80 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 0.0980 chunk 48 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 16 ASN B 218 ASN C 187 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.188390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.155121 restraints weight = 14972.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.157842 restraints weight = 12407.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.159241 restraints weight = 8878.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.159363 restraints weight = 6729.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.159864 restraints weight = 6382.834| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3936 r_free = 0.3936 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3935 r_free = 0.3935 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.3935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10948 Z= 0.114 Angle : 0.574 8.114 14818 Z= 0.284 Chirality : 0.041 0.161 1654 Planarity : 0.003 0.027 1816 Dihedral : 7.739 175.714 1422 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.90 % Allowed : 18.36 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.24), residues: 1292 helix: 1.59 (0.22), residues: 590 sheet: 0.62 (0.43), residues: 177 loop : -1.76 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 17 TYR 0.022 0.001 TYR B 243 PHE 0.020 0.001 PHE C 30 TRP 0.008 0.001 TRP B 31 HIS 0.013 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00247 (10948) covalent geometry : angle 0.57371 (14818) hydrogen bonds : bond 0.04334 ( 497) hydrogen bonds : angle 4.48736 ( 1434) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.304 Fit side-chains REVERT: A 102 GLU cc_start: 0.7830 (tp30) cc_final: 0.7457 (tp30) REVERT: B 16 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8134 (p0) REVERT: B 205 MET cc_start: 0.6097 (OUTLIER) cc_final: 0.5539 (ttm) outliers start: 22 outliers final: 12 residues processed: 140 average time/residue: 0.0926 time to fit residues: 18.8640 Evaluate side-chains 138 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.185396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.151132 restraints weight = 14870.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.153105 restraints weight = 12485.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.153894 restraints weight = 10095.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.154487 restraints weight = 7718.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.154654 restraints weight = 6927.601| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3884 r_free = 0.3884 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10948 Z= 0.148 Angle : 0.593 9.343 14818 Z= 0.296 Chirality : 0.042 0.155 1654 Planarity : 0.003 0.036 1816 Dihedral : 7.625 169.409 1422 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.28 % Allowed : 17.50 % Favored : 79.22 % 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 (0.24), residues: 1292 helix: 1.49 (0.22), residues: 598 sheet: 0.11 (0.41), residues: 197 loop : -1.81 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 392 TYR 0.023 0.001 TYR B 243 PHE 0.017 0.001 PHE B 92 TRP 0.012 0.002 TRP D 181 HIS 0.003 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00353 (10948) covalent geometry : angle 0.59332 (14818) hydrogen bonds : bond 0.04927 ( 497) hydrogen bonds : angle 4.50772 ( 1434) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: B 16 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8184 (p0) REVERT: B 205 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5849 (ttm) outliers start: 38 outliers final: 26 residues processed: 154 average time/residue: 0.0861 time to fit residues: 19.9366 Evaluate side-chains 154 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 63 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 HIS B 16 ASN B 218 ASN D 55 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.183065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.149783 restraints weight = 15035.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.151865 restraints weight = 11744.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.152291 restraints weight = 12273.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.152923 restraints weight = 8795.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.153038 restraints weight = 7475.674| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3860 r_free = 0.3860 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10948 Z= 0.167 Angle : 0.612 9.901 14818 Z= 0.307 Chirality : 0.042 0.161 1654 Planarity : 0.004 0.037 1816 Dihedral : 7.590 164.673 1422 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.53 % Allowed : 18.62 % Favored : 77.84 % 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: -0.02 (0.24), residues: 1292 helix: 1.41 (0.22), residues: 598 sheet: 0.03 (0.42), residues: 196 loop : -1.86 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 17 TYR 0.024 0.001 TYR B 243 PHE 0.017 0.001 PHE B 92 TRP 0.012 0.002 TRP D 181 HIS 0.003 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00403 (10948) covalent geometry : angle 0.61206 (14818) hydrogen bonds : bond 0.05236 ( 497) hydrogen bonds : angle 4.55549 ( 1434) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7835 (tp30) cc_final: 0.7422 (tp30) REVERT: A 307 GLN cc_start: 0.8013 (tt0) cc_final: 0.7622 (pt0) REVERT: A 318 GLU cc_start: 0.7212 (mp0) cc_final: 0.6818 (mp0) REVERT: B 205 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5872 (ttm) REVERT: B 211 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8318 (tt) REVERT: C 294 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.6850 (m-30) REVERT: D 156 MET cc_start: 0.8308 (tmm) cc_final: 0.7955 (tpp) outliers start: 41 outliers final: 30 residues processed: 162 average time/residue: 0.0824 time to fit residues: 20.1391 Evaluate side-chains 163 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU 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 142 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 78 optimal weight: 10.0000 chunk 29 optimal weight: 0.0870 chunk 110 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 119 optimal weight: 0.0570 chunk 73 optimal weight: 10.0000 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 218 ASN C 361 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.184506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.152441 restraints weight = 14400.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.154552 restraints weight = 11945.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.154795 restraints weight = 10936.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.155150 restraints weight = 8255.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.155377 restraints weight = 7305.329| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3899 r_free = 0.3899 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3899 r_free = 0.3899 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10948 Z= 0.132 Angle : 0.609 9.883 14818 Z= 0.302 Chirality : 0.042 0.163 1654 Planarity : 0.003 0.028 1816 Dihedral : 7.415 162.899 1422 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.88 % Allowed : 18.79 % Favored : 77.33 % 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: 0.01 (0.24), residues: 1292 helix: 1.46 (0.22), residues: 598 sheet: 0.05 (0.42), residues: 194 loop : -1.88 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 17 TYR 0.023 0.001 TYR B 243 PHE 0.017 0.001 PHE B 92 TRP 0.009 0.001 TRP A 8 HIS 0.003 0.001 HIS C 361 Details of bonding type rmsd covalent geometry : bond 0.00303 (10948) covalent geometry : angle 0.60919 (14818) hydrogen bonds : bond 0.04694 ( 497) hydrogen bonds : angle 4.46167 ( 1434) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 0.326 Fit side-chains REVERT: A 102 GLU cc_start: 0.7800 (tp30) cc_final: 0.7393 (tp30) REVERT: B 205 MET cc_start: 0.6233 (OUTLIER) cc_final: 0.5933 (ttm) REVERT: B 211 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8201 (tt) REVERT: C 294 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.6782 (m-30) REVERT: D 156 MET cc_start: 0.8417 (tmm) cc_final: 0.8033 (tpp) outliers start: 45 outliers final: 29 residues processed: 161 average time/residue: 0.0838 time to fit residues: 19.9784 Evaluate side-chains 157 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU 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 142 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 68 optimal weight: 0.2980 chunk 122 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS B 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.184807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.152143 restraints weight = 14486.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154145 restraints weight = 12755.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.154776 restraints weight = 11897.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.154942 restraints weight = 9077.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.155678 restraints weight = 7775.740| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| r_final: 0.3900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10948 Z= 0.130 Angle : 0.608 8.533 14818 Z= 0.300 Chirality : 0.042 0.164 1654 Planarity : 0.003 0.028 1816 Dihedral : 7.288 162.808 1422 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.71 % Allowed : 18.88 % Favored : 77.41 % 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: -0.00 (0.24), residues: 1292 helix: 1.47 (0.22), residues: 598 sheet: 0.02 (0.42), residues: 194 loop : -1.90 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 392 TYR 0.024 0.001 TYR B 243 PHE 0.018 0.001 PHE C 30 TRP 0.009 0.001 TRP D 181 HIS 0.004 0.001 HIS C 361 Details of bonding type rmsd covalent geometry : bond 0.00300 (10948) covalent geometry : angle 0.60799 (14818) hydrogen bonds : bond 0.04557 ( 497) hydrogen bonds : angle 4.41036 ( 1434) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.291 Fit side-chains REVERT: A 102 GLU cc_start: 0.7814 (tp30) cc_final: 0.7397 (tp30) REVERT: B 137 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7728 (t80) REVERT: B 205 MET cc_start: 0.6232 (OUTLIER) cc_final: 0.5960 (ttm) REVERT: B 211 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8287 (tt) REVERT: C 294 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7139 (m-30) REVERT: D 156 MET cc_start: 0.8408 (tmm) cc_final: 0.8014 (tpp) outliers start: 43 outliers final: 32 residues processed: 160 average time/residue: 0.0835 time to fit residues: 20.1821 Evaluate side-chains 160 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU 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 142 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 17 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.178095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.145697 restraints weight = 14485.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.145833 restraints weight = 13229.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.147238 restraints weight = 14227.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.147749 restraints weight = 9632.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.148113 restraints weight = 9368.278| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 10948 Z= 0.252 Angle : 0.714 8.196 14818 Z= 0.362 Chirality : 0.046 0.170 1654 Planarity : 0.004 0.034 1816 Dihedral : 7.756 169.574 1422 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.05 % Allowed : 18.79 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.24), residues: 1292 helix: 1.08 (0.22), residues: 602 sheet: -0.28 (0.41), residues: 196 loop : -2.11 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 392 TYR 0.028 0.002 TYR B 243 PHE 0.025 0.002 PHE B 85 TRP 0.015 0.002 TRP A 8 HIS 0.005 0.001 HIS D 212 Details of bonding type rmsd covalent geometry : bond 0.00623 (10948) covalent geometry : angle 0.71422 (14818) hydrogen bonds : bond 0.06383 ( 497) hydrogen bonds : angle 4.79453 ( 1434) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 0.324 Fit side-chains REVERT: A 102 GLU cc_start: 0.7958 (tp30) cc_final: 0.7553 (tp30) REVERT: B 85 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.6246 (t80) REVERT: B 137 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7872 (t80) REVERT: B 205 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.6107 (ttm) REVERT: B 211 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8365 (mt) REVERT: C 201 MET cc_start: 0.5896 (mmm) cc_final: 0.5690 (mmm) REVERT: D 136 TYR cc_start: 0.7809 (m-80) cc_final: 0.7565 (m-80) REVERT: D 156 MET cc_start: 0.8468 (tmm) cc_final: 0.8062 (tpp) outliers start: 47 outliers final: 35 residues processed: 168 average time/residue: 0.0803 time to fit residues: 20.4931 Evaluate side-chains 164 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 268 HIS A 357 GLN B 218 ASN D 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.180877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.148283 restraints weight = 14504.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.148894 restraints weight = 12674.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.150467 restraints weight = 12373.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.150951 restraints weight = 9419.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.151482 restraints weight = 9707.653| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3851 r_free = 0.3851 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3851 r_free = 0.3851 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| r_final: 0.3851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10948 Z= 0.177 Angle : 0.664 7.885 14818 Z= 0.334 Chirality : 0.044 0.193 1654 Planarity : 0.004 0.036 1816 Dihedral : 7.743 177.044 1422 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.45 % Allowed : 19.74 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.39 (0.24), residues: 1292 helix: 1.21 (0.22), residues: 598 sheet: -0.43 (0.41), residues: 195 loop : -2.05 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 392 TYR 0.025 0.001 TYR B 243 PHE 0.028 0.002 PHE B 152 TRP 0.012 0.002 TRP A 8 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00429 (10948) covalent geometry : angle 0.66442 (14818) hydrogen bonds : bond 0.05383 ( 497) hydrogen bonds : angle 4.62582 ( 1434) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7899 (tp30) cc_final: 0.7503 (tp30) REVERT: B 85 PHE cc_start: 0.6395 (OUTLIER) cc_final: 0.6167 (t80) REVERT: B 137 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7759 (t80) REVERT: B 211 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8360 (tt) REVERT: D 80 ARG cc_start: 0.8043 (mtm-85) cc_final: 0.7634 (mtm-85) REVERT: D 136 TYR cc_start: 0.7734 (m-80) cc_final: 0.7514 (m-80) REVERT: D 156 MET cc_start: 0.8404 (tmm) cc_final: 0.8077 (tpp) outliers start: 40 outliers final: 32 residues processed: 163 average time/residue: 0.0876 time to fit residues: 21.1618 Evaluate side-chains 167 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 29 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 218 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 = 0.4200 r_free = 0.4200 target = 0.183160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.150153 restraints weight = 14903.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.150719 restraints weight = 12508.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.152863 restraints weight = 11045.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.152796 restraints weight = 8558.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.153218 restraints weight = 7557.817| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| r_final: 0.3859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10948 Z= 0.146 Angle : 0.645 8.451 14818 Z= 0.321 Chirality : 0.043 0.194 1654 Planarity : 0.004 0.032 1816 Dihedral : 7.568 175.094 1422 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.19 % Allowed : 19.91 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1292 helix: 1.34 (0.22), residues: 598 sheet: -0.24 (0.41), residues: 193 loop : -2.05 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 392 TYR 0.024 0.001 TYR B 243 PHE 0.024 0.001 PHE C 30 TRP 0.011 0.002 TRP A 8 HIS 0.004 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00346 (10948) covalent geometry : angle 0.64501 (14818) hydrogen bonds : bond 0.04863 ( 497) hydrogen bonds : angle 4.51583 ( 1434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1573.54 seconds wall clock time: 27 minutes 56.38 seconds (1676.38 seconds total)