Starting phenix.real_space_refine on Thu Jul 2 16:48:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/20zk_67433/07_2026/20zk_67433.cif Found real_map, /net/cci-nas-00/data/ceres_data/20zk_67433/07_2026/20zk_67433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/20zk_67433/07_2026/20zk_67433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/20zk_67433/07_2026/20zk_67433.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/20zk_67433/07_2026/20zk_67433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/20zk_67433/07_2026/20zk_67433.map" } resolution = 2.7 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= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5777 2.51 5 N 1547 2.21 5 O 1689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9076 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1757 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 413 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "D" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2476 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 10, 'TRANS': 301} Chain breaks: 1 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 2.22, per 1000 atoms: 0.24 Number of scatterers: 9076 At special positions: 0 Unit cell: (93.79, 120.35, 123.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1689 8.00 N 1547 7.00 C 5777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.07 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 229 " distance=2.06 Simple disulfide: pdb=" SG CYS R 153 " - pdb=" SG CYS R 236 " distance=2.03 Simple disulfide: pdb=" SG CYS R 393 " - pdb=" SG CYS R 395 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 500.5 milliseconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 16 sheets defined 40.6% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.219A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.273A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.895A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.939A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 22 through 44 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 220 through 224 Processing helix chain 'R' and resid 71 through 103 Processing helix chain 'R' and resid 107 through 139 removed outlier: 3.778A pdb=" N HIS R 114 " --> pdb=" O GLN R 110 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET R 132 " --> pdb=" O LEU R 128 " (cutoff:3.500A) Proline residue: R 133 - end of helix Processing helix chain 'R' and resid 149 through 184 Processing helix chain 'R' and resid 184 through 192 Processing helix chain 'R' and resid 193 through 212 Processing helix chain 'R' and resid 214 through 218 Processing helix chain 'R' and resid 230 through 232 No H-bonds generated for 'chain 'R' and resid 230 through 232' Processing helix chain 'R' and resid 241 through 257 Processing helix chain 'R' and resid 257 through 285 Processing helix chain 'R' and resid 305 through 341 removed outlier: 3.520A pdb=" N VAL R 321 " --> pdb=" O LEU R 317 " (cutoff:3.500A) Proline residue: R 330 - end of helix Processing helix chain 'R' and resid 347 through 377 removed outlier: 3.593A pdb=" N MET R 359 " --> pdb=" O HIS R 355 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER R 369 " --> pdb=" O PHE R 365 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN R 372 " --> pdb=" O SER R 368 " (cutoff:3.500A) Proline residue: R 373 - end of helix Processing helix chain 'R' and resid 380 through 394 removed outlier: 3.898A pdb=" N HIS R 385 " --> pdb=" O ALA R 381 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE R 386 " --> pdb=" O ASN R 382 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.599A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 81 removed outlier: 3.608A pdb=" N ALA B 78 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASP B 101 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LYS B 107 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 123 removed outlier: 6.707A pdb=" N GLY B 133 " --> pdb=" O MET B 119 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N CYS B 121 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA B 131 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR B 123 " --> pdb=" O TYR B 129 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR B 129 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY B 134 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASN B 143 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL B 153 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 164 through 171 removed outlier: 3.507A pdb=" N CYS B 166 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 175 " --> pdb=" O TRP B 187 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASP B 188 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLN B 194 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 205 through 210 removed outlier: 6.777A pdb=" N GLY B 220 " --> pdb=" O MET B 206 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU B 208 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B 218 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU B 210 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU B 216 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 238 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 230 " --> pdb=" O CYS B 236 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS B 236 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 247 through 252 removed outlier: 6.415A pdb=" N CYS B 268 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR B 281 " --> pdb=" O CYS B 268 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 270 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 277 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 291 through 296 removed outlier: 3.583A pdb=" N SER B 293 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP B 316 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ARG B 322 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 333 through 338 removed outlier: 3.515A pdb=" N CYS B 335 " --> pdb=" O GLY B 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.046A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.046A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'D' and resid 146 through 148 removed outlier: 6.433A pdb=" N LEU D 174 " --> pdb=" O TYR D 190 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TYR D 190 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP D 176 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 146 through 148 removed outlier: 3.920A pdb=" N THR D 238 " --> pdb=" O GLN D 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 219 through 223 509 hydrogen bonds defined for protein. 1410 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: 1.72 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1492 1.31 - 1.44: 2555 1.44 - 1.57: 5127 1.57 - 1.69: 1 1.69 - 1.82: 92 Bond restraints: 9267 Sorted by residual: bond pdb=" CA SER D 99 " pdb=" CB SER D 99 " ideal model delta sigma weight residual 1.534 1.442 0.091 1.64e-02 3.72e+03 3.10e+01 bond pdb=" CA SER B 297 " pdb=" CB SER B 297 " ideal model delta sigma weight residual 1.527 1.455 0.072 1.44e-02 4.82e+03 2.48e+01 bond pdb=" CA SER B 116 " pdb=" CB SER B 116 " ideal model delta sigma weight residual 1.532 1.445 0.088 1.79e-02 3.12e+03 2.39e+01 bond pdb=" CA SER B 140 " pdb=" CB SER B 140 " ideal model delta sigma weight residual 1.530 1.460 0.070 1.43e-02 4.89e+03 2.38e+01 bond pdb=" CA SER B 349 " pdb=" CB SER B 349 " ideal model delta sigma weight residual 1.533 1.446 0.087 1.82e-02 3.02e+03 2.29e+01 ... (remaining 9262 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 12225 4.05 - 8.11: 308 8.11 - 12.16: 14 12.16 - 16.21: 4 16.21 - 20.27: 3 Bond angle restraints: 12554 Sorted by residual: angle pdb=" NE ARG A 205 " pdb=" CZ ARG A 205 " pdb=" NH2 ARG A 205 " ideal model delta sigma weight residual 119.20 103.50 15.70 9.00e-01 1.23e+00 3.04e+02 angle pdb=" C TYR L 11 " pdb=" CA TYR L 11 " pdb=" CB TYR L 11 " ideal model delta sigma weight residual 109.56 89.34 20.22 1.65e+00 3.67e-01 1.50e+02 angle pdb=" NE ARG A 205 " pdb=" CZ ARG A 205 " pdb=" NH1 ARG A 205 " ideal model delta sigma weight residual 121.50 131.17 -9.67 1.00e+00 1.00e+00 9.36e+01 angle pdb=" C PHE R 338 " pdb=" CA PHE R 338 " pdb=" CB PHE R 338 " ideal model delta sigma weight residual 110.79 96.77 14.02 1.66e+00 3.63e-01 7.13e+01 angle pdb=" N ARG A 208 " pdb=" CA ARG A 208 " pdb=" CB ARG A 208 " ideal model delta sigma weight residual 110.22 122.31 -12.09 1.54e+00 4.22e-01 6.16e+01 ... (remaining 12549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5136 17.74 - 35.47: 262 35.47 - 53.20: 67 53.20 - 70.94: 21 70.94 - 88.67: 9 Dihedral angle restraints: 5495 sinusoidal: 2128 harmonic: 3367 Sorted by residual: dihedral pdb=" C TYR L 11 " pdb=" N TYR L 11 " pdb=" CA TYR L 11 " pdb=" CB TYR L 11 " ideal model delta harmonic sigma weight residual -122.60 -101.50 -21.10 0 2.50e+00 1.60e-01 7.12e+01 dihedral pdb=" CB CYS R 393 " pdb=" SG CYS R 393 " pdb=" SG CYS R 395 " pdb=" CB CYS R 395 " ideal model delta sinusoidal sigma weight residual -86.00 -157.82 71.82 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" CD ARG A 205 " pdb=" NE ARG A 205 " pdb=" CZ ARG A 205 " pdb=" NH1 ARG A 205 " ideal model delta sinusoidal sigma weight residual 0.00 67.26 -67.26 1 1.00e+01 1.00e-02 5.89e+01 ... (remaining 5492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1048 0.105 - 0.210: 336 0.210 - 0.315: 39 0.315 - 0.419: 7 0.419 - 0.524: 1 Chirality restraints: 1431 Sorted by residual: chirality pdb=" CB VAL D 97 " pdb=" CA VAL D 97 " pdb=" CG1 VAL D 97 " pdb=" CG2 VAL D 97 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.87e+00 chirality pdb=" CA ARG D 191 " pdb=" N ARG D 191 " pdb=" C ARG D 191 " pdb=" CB ARG D 191 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CB VAL B 130 " pdb=" CA VAL B 130 " pdb=" CG1 VAL B 130 " pdb=" CG2 VAL B 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 1428 not shown) Planarity restraints: 1581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 205 " -0.762 9.50e-02 1.11e+02 3.47e-01 1.22e+02 pdb=" NE ARG A 205 " 0.091 2.00e-02 2.50e+03 pdb=" CZ ARG A 205 " -0.113 2.00e-02 2.50e+03 pdb=" NH1 ARG A 205 " 0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG A 205 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 355 " -0.029 2.00e-02 2.50e+03 5.92e-02 3.51e+01 pdb=" C LYS B 355 " 0.102 2.00e-02 2.50e+03 pdb=" O LYS B 355 " -0.039 2.00e-02 2.50e+03 pdb=" N ILE B 356 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 313 " -0.424 9.50e-02 1.11e+02 1.93e-01 3.48e+01 pdb=" NE ARG A 313 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG A 313 " -0.057 2.00e-02 2.50e+03 pdb=" NH1 ARG A 313 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 313 " 0.005 2.00e-02 2.50e+03 ... (remaining 1578 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 735 2.75 - 3.29: 9115 3.29 - 3.82: 15120 3.82 - 4.36: 19343 4.36 - 4.90: 32435 Nonbonded interactions: 76748 Sorted by model distance: nonbonded pdb=" NE2 GLN R 250 " pdb=" OH TYR R 340 " model vdw 2.209 3.120 nonbonded pdb=" N THR B 83 " pdb=" OG1 THR B 83 " model vdw 2.216 2.496 nonbonded pdb=" O PHE A 259 " pdb=" NZ LYS A 317 " model vdw 2.260 3.120 nonbonded pdb=" OG1 THR B 292 " pdb=" O VAL B 333 " model vdw 2.268 3.040 nonbonded pdb=" OG SER A 293 " pdb=" OE1 GLU A 298 " model vdw 2.330 3.040 ... (remaining 76743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.240 Find NCS groups from input model: 0.050 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:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 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 : 0.012 0.091 9271 Z= 0.776 Angle : 1.725 20.269 12562 Z= 1.164 Chirality : 0.098 0.524 1431 Planarity : 0.017 0.347 1581 Dihedral : 12.736 88.674 3311 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.33 % Allowed : 3.43 % Favored : 93.24 % Cbeta Deviations : 0.92 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.23), residues: 1139 helix: 2.09 (0.23), residues: 414 sheet: 1.09 (0.30), residues: 278 loop : -0.11 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.122 0.007 ARG A 205 TYR 0.037 0.007 TYR D 103 PHE 0.037 0.006 PHE R 148 TRP 0.043 0.007 TRP B 357 HIS 0.022 0.004 HIS R 355 Details of bonding type rmsd/Z covalent geometry : bond 0.01193 / 0.78 ( 9267) covalent geometry : angle 1.72234 / 1.16 (12554) SS BOND : bond 0.02331 / 1.18 ( 4) SS BOND : angle 3.99977 / 2.14 ( 8) hydrogen bonds : bond 0.19088 / 12.97 ( 499) hydrogen bonds : angle 7.05249 / 4.93 ( 1410) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.9373 (tt0) cc_final: 0.9138 (tp30) REVERT: A 275 GLU cc_start: 0.9191 (tt0) cc_final: 0.8753 (tm-30) REVERT: B 24 GLN cc_start: 0.9401 (tt0) cc_final: 0.9061 (pp30) REVERT: B 286 ASN cc_start: 0.9296 (m-40) cc_final: 0.9086 (t0) REVERT: C 47 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8654 (mp0) REVERT: C 54 VAL cc_start: 0.8783 (m) cc_final: 0.8546 (p) REVERT: C 58 GLU cc_start: 0.9384 (mt-10) cc_final: 0.8996 (mp0) REVERT: D 147 VAL cc_start: 0.8494 (t) cc_final: 0.7861 (m) REVERT: D 218 ARG cc_start: 0.9225 (mtm110) cc_final: 0.8766 (mtm110) REVERT: D 246 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7632 (pm20) REVERT: R 104 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7535 (tptp) REVERT: R 106 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7533 (mp) REVERT: R 109 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8478 (mm) REVERT: R 122 LEU cc_start: 0.9022 (tp) cc_final: 0.8731 (tp) REVERT: R 126 LEU cc_start: 0.9204 (mt) cc_final: 0.8879 (mt) REVERT: R 135 GLU cc_start: 0.8855 (tt0) cc_final: 0.8516 (tt0) REVERT: R 138 ASN cc_start: 0.8937 (m-40) cc_final: 0.8658 (t160) REVERT: R 142 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.7666 (p) REVERT: R 156 TYR cc_start: 0.8577 (t80) cc_final: 0.8245 (t80) REVERT: R 194 ARG cc_start: 0.8639 (ttm-80) cc_final: 0.8230 (ttm-80) REVERT: L 13 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7590 (tm) outliers start: 33 outliers final: 8 residues processed: 298 average time/residue: 0.6726 time to fit residues: 211.8478 Evaluate side-chains 206 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 254 PRO Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 104 LYS Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 284 GLU Chi-restraints excluded: chain L residue 11 TYR Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.0770 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 347 ASN B 35 GLN B 358 ASN C 18 GLN R 144 HIS R 170 ASN R 223 ASN R 308 GLN R 312 HIS R 332 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.058096 restraints weight = 20433.911| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.46 r_work: 0.2759 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9271 Z= 0.142 Angle : 0.606 7.859 12562 Z= 0.319 Chirality : 0.043 0.142 1431 Planarity : 0.004 0.046 1581 Dihedral : 6.334 63.731 1280 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.53 % Allowed : 14.23 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.24), residues: 1139 helix: 2.69 (0.24), residues: 418 sheet: 1.02 (0.31), residues: 276 loop : -0.24 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 147 TYR 0.019 0.002 TYR D 190 PHE 0.033 0.002 PHE R 338 TRP 0.022 0.002 TRP R 141 HIS 0.009 0.001 HIS R 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 9267) covalent geometry : angle 0.60470 / 0.32 (12554) SS BOND : bond 0.00364 / 0.18 ( 4) SS BOND : angle 1.54017 / 0.86 ( 8) hydrogen bonds : bond 0.04562 / 3.06 ( 499) hydrogen bonds : angle 4.86008 / 3.40 ( 1410) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8853 (m-30) cc_final: 0.8496 (m-30) REVERT: A 53 MET cc_start: 0.8994 (mpp) cc_final: 0.8782 (mpp) REVERT: A 306 GLN cc_start: 0.9303 (mm-40) cc_final: 0.9089 (mm110) REVERT: B 343 MET cc_start: 0.9303 (tpt) cc_final: 0.8943 (tpt) REVERT: C 20 LYS cc_start: 0.9155 (mttt) cc_final: 0.8897 (mtmm) REVERT: C 47 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8373 (mp0) REVERT: D 246 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7809 (pm20) REVERT: R 109 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8271 (mm) REVERT: R 114 HIS cc_start: 0.8680 (m170) cc_final: 0.8468 (m170) REVERT: R 122 LEU cc_start: 0.8950 (tp) cc_final: 0.8606 (tp) REVERT: R 126 LEU cc_start: 0.9040 (mt) cc_final: 0.8683 (mt) REVERT: R 129 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8974 (mm) REVERT: R 142 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8179 (p) REVERT: R 144 HIS cc_start: 0.7347 (m90) cc_final: 0.7045 (m170) REVERT: R 160 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7406 (ttm170) REVERT: R 177 GLU cc_start: 0.8895 (tp30) cc_final: 0.8196 (tp30) REVERT: R 222 GLN cc_start: 0.8480 (tt0) cc_final: 0.7565 (tm-30) REVERT: R 281 GLN cc_start: 0.8336 (mt0) cc_final: 0.8018 (mt0) REVERT: R 369 SER cc_start: 0.9309 (m) cc_final: 0.9020 (p) outliers start: 35 outliers final: 11 residues processed: 230 average time/residue: 0.6584 time to fit residues: 160.4932 Evaluate side-chains 192 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 371 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 71 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 31 GLN B 286 ASN ** R 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 385 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.071915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.053843 restraints weight = 20321.580| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.34 r_work: 0.2657 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9271 Z= 0.283 Angle : 0.646 7.768 12562 Z= 0.344 Chirality : 0.046 0.148 1431 Planarity : 0.004 0.050 1581 Dihedral : 5.266 67.827 1262 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.94 % Allowed : 14.03 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.24), residues: 1139 helix: 2.72 (0.24), residues: 419 sheet: 0.87 (0.30), residues: 276 loop : -0.41 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 102 TYR 0.018 0.002 TYR R 331 PHE 0.014 0.002 PHE B 169 TRP 0.019 0.002 TRP B 100 HIS 0.009 0.001 HIS R 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.28 ( 9267) covalent geometry : angle 0.64466 / 0.34 (12554) SS BOND : bond 0.00583 / 0.28 ( 4) SS BOND : angle 1.53438 / 0.81 ( 8) hydrogen bonds : bond 0.05046 / 3.41 ( 499) hydrogen bonds : angle 4.79465 / 3.33 ( 1410) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.9150 (mpp) cc_final: 0.8778 (mpp) REVERT: A 234 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6564 (mt) REVERT: B 62 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8833 (mt0) REVERT: B 207 SER cc_start: 0.9275 (OUTLIER) cc_final: 0.9055 (p) REVERT: B 233 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8883 (mp0) REVERT: B 235 MET cc_start: 0.9390 (OUTLIER) cc_final: 0.9145 (pmt) REVERT: B 272 ASP cc_start: 0.8681 (t0) cc_final: 0.8477 (t0) REVERT: C 17 GLU cc_start: 0.9192 (tp30) cc_final: 0.8613 (mm-30) REVERT: C 20 LYS cc_start: 0.9249 (mttt) cc_final: 0.9008 (mtmm) REVERT: C 47 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8769 (mp0) REVERT: D 73 ASP cc_start: 0.8835 (t0) cc_final: 0.8497 (t70) REVERT: D 218 ARG cc_start: 0.8536 (mtm110) cc_final: 0.8214 (mpp-170) REVERT: D 220 GLU cc_start: 0.8393 (mp0) cc_final: 0.8067 (mp0) REVERT: D 246 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8043 (pm20) REVERT: R 109 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8250 (mm) REVERT: R 126 LEU cc_start: 0.9092 (mt) cc_final: 0.8818 (mt) REVERT: R 129 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9060 (mm) REVERT: R 142 VAL cc_start: 0.9238 (OUTLIER) cc_final: 0.8997 (p) REVERT: R 160 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7437 (ttm170) REVERT: R 177 GLU cc_start: 0.8981 (tp30) cc_final: 0.8325 (tp30) REVERT: R 198 LYS cc_start: 0.8757 (mttm) cc_final: 0.8555 (mttm) REVERT: R 246 LYS cc_start: 0.9080 (mttt) cc_final: 0.8702 (mtpm) REVERT: R 377 ASN cc_start: 0.7966 (m-40) cc_final: 0.7468 (m110) REVERT: L 9 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.9003 (tptm) REVERT: L 13 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7436 (tm) outliers start: 49 outliers final: 15 residues processed: 215 average time/residue: 0.6506 time to fit residues: 148.2580 Evaluate side-chains 198 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 274 LYS Chi-restraints excluded: chain R residue 371 ILE Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 31 optimal weight: 0.6980 chunk 90 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN R 268 ASN R 308 GLN ** R 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.071942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.053790 restraints weight = 20508.473| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.36 r_work: 0.2654 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9160 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9271 Z= 0.205 Angle : 0.588 7.110 12562 Z= 0.311 Chirality : 0.043 0.146 1431 Planarity : 0.004 0.046 1581 Dihedral : 4.978 69.853 1261 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.63 % Allowed : 16.15 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.24), residues: 1139 helix: 2.75 (0.24), residues: 428 sheet: 0.80 (0.30), residues: 276 loop : -0.37 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 160 TYR 0.021 0.002 TYR R 351 PHE 0.014 0.001 PHE R 383 TRP 0.018 0.001 TRP B 100 HIS 0.004 0.001 HIS R 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 ( 9267) covalent geometry : angle 0.58727 / 0.31 (12554) SS BOND : bond 0.00439 / 0.21 ( 4) SS BOND : angle 1.14881 / 0.60 ( 8) hydrogen bonds : bond 0.04504 / 3.02 ( 499) hydrogen bonds : angle 4.58152 / 3.18 ( 1410) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6675 (mt) REVERT: A 257 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.8888 (ptpp) REVERT: B 62 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8845 (mt0) REVERT: B 207 SER cc_start: 0.9286 (OUTLIER) cc_final: 0.9044 (p) REVERT: B 233 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8778 (mp0) REVERT: B 235 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.9097 (pmt) REVERT: C 17 GLU cc_start: 0.9224 (tp30) cc_final: 0.8725 (mm-30) REVERT: C 47 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8760 (mp0) REVERT: D 73 ASP cc_start: 0.8794 (t0) cc_final: 0.8448 (t70) REVERT: D 76 LYS cc_start: 0.9234 (mtpt) cc_final: 0.9020 (mtmt) REVERT: D 220 GLU cc_start: 0.8460 (mp0) cc_final: 0.8162 (mp0) REVERT: D 246 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8181 (pm20) REVERT: R 109 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8284 (mm) REVERT: R 126 LEU cc_start: 0.9073 (mt) cc_final: 0.8825 (mt) REVERT: R 129 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9060 (mm) REVERT: R 132 MET cc_start: 0.8927 (tpp) cc_final: 0.8506 (tpp) REVERT: R 135 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8706 (tt0) REVERT: R 160 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7466 (ttm170) REVERT: R 219 MET cc_start: 0.8123 (tpp) cc_final: 0.7394 (mmm) REVERT: R 221 GLU cc_start: 0.8813 (tt0) cc_final: 0.8213 (tt0) REVERT: R 246 LYS cc_start: 0.9038 (mttt) cc_final: 0.8633 (mtpm) REVERT: R 377 ASN cc_start: 0.8129 (m-40) cc_final: 0.7802 (m110) REVERT: R 385 HIS cc_start: 0.8653 (t70) cc_final: 0.8395 (t70) outliers start: 36 outliers final: 10 residues processed: 208 average time/residue: 0.6457 time to fit residues: 142.3909 Evaluate side-chains 191 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 208 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN D 77 ASN R 114 HIS R 138 ASN R 250 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.054169 restraints weight = 20352.906| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.36 r_work: 0.2668 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9271 Z= 0.169 Angle : 0.585 9.889 12562 Z= 0.306 Chirality : 0.042 0.177 1431 Planarity : 0.004 0.046 1581 Dihedral : 4.750 66.830 1258 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.73 % Allowed : 17.15 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.25), residues: 1139 helix: 2.89 (0.24), residues: 426 sheet: 0.76 (0.30), residues: 276 loop : -0.34 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 160 TYR 0.017 0.001 TYR D 190 PHE 0.012 0.001 PHE R 383 TRP 0.018 0.001 TRP B 100 HIS 0.012 0.001 HIS R 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 9267) covalent geometry : angle 0.58435 / 0.31 (12554) SS BOND : bond 0.00390 / 0.19 ( 4) SS BOND : angle 1.03474 / 0.54 ( 8) hydrogen bonds : bond 0.04281 / 2.85 ( 499) hydrogen bonds : angle 4.49838 / 3.13 ( 1410) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.9080 (mpp) cc_final: 0.8666 (mpp) REVERT: A 234 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6632 (mp) REVERT: A 257 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.8896 (ptpp) REVERT: B 62 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8759 (mt0) REVERT: B 207 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.9063 (p) REVERT: B 233 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8778 (mp0) REVERT: B 235 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.9149 (pmt) REVERT: C 17 GLU cc_start: 0.9181 (tp30) cc_final: 0.8820 (mm-30) REVERT: C 47 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8732 (mp0) REVERT: D 73 ASP cc_start: 0.8853 (t0) cc_final: 0.8518 (t70) REVERT: D 89 GLU cc_start: 0.8926 (pm20) cc_final: 0.8725 (pp20) REVERT: D 218 ARG cc_start: 0.8538 (mtm110) cc_final: 0.8079 (mpp80) REVERT: D 220 GLU cc_start: 0.8507 (mp0) cc_final: 0.8149 (mp0) REVERT: D 246 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8210 (pm20) REVERT: R 109 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8294 (mm) REVERT: R 126 LEU cc_start: 0.9075 (mt) cc_final: 0.8850 (mt) REVERT: R 129 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9081 (mm) REVERT: R 132 MET cc_start: 0.8897 (tpp) cc_final: 0.8485 (tpp) REVERT: R 135 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8791 (tt0) REVERT: R 160 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7507 (ttm170) REVERT: R 198 LYS cc_start: 0.8783 (mttm) cc_final: 0.8319 (mttp) REVERT: R 246 LYS cc_start: 0.9004 (mttt) cc_final: 0.8706 (mtpm) REVERT: R 281 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8256 (mt0) REVERT: R 344 GLU cc_start: 0.8627 (pm20) cc_final: 0.8403 (pm20) REVERT: R 345 GLN cc_start: 0.8542 (mp10) cc_final: 0.8280 (mp10) REVERT: R 377 ASN cc_start: 0.8139 (m-40) cc_final: 0.7838 (m110) REVERT: L 9 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8990 (tptm) REVERT: L 13 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7373 (tm) outliers start: 37 outliers final: 17 residues processed: 200 average time/residue: 0.5654 time to fit residues: 119.8511 Evaluate side-chains 192 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 281 GLN Chi-restraints excluded: chain R residue 359 MET Chi-restraints excluded: chain R residue 371 ILE Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 269 ASN A 306 GLN R 114 HIS ** R 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.072653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.054813 restraints weight = 20527.513| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.37 r_work: 0.2681 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9271 Z= 0.155 Angle : 0.582 11.519 12562 Z= 0.302 Chirality : 0.042 0.158 1431 Planarity : 0.004 0.045 1581 Dihedral : 4.662 67.190 1258 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.04 % Allowed : 17.76 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.25), residues: 1139 helix: 2.90 (0.24), residues: 426 sheet: 0.71 (0.31), residues: 263 loop : -0.35 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 26 TYR 0.017 0.001 TYR D 190 PHE 0.010 0.001 PHE R 383 TRP 0.017 0.001 TRP B 100 HIS 0.010 0.001 HIS R 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9267) covalent geometry : angle 0.58181 / 0.30 (12554) SS BOND : bond 0.00412 / 0.20 ( 4) SS BOND : angle 1.14680 / 0.59 ( 8) hydrogen bonds : bond 0.04151 / 2.78 ( 499) hydrogen bonds : angle 4.42758 / 3.08 ( 1410) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6692 (mp) REVERT: A 257 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.8906 (ptpp) REVERT: A 325 CYS cc_start: 0.8875 (p) cc_final: 0.8498 (p) REVERT: B 62 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8827 (mt0) REVERT: B 233 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8768 (mp0) REVERT: B 235 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.9129 (pmt) REVERT: C 17 GLU cc_start: 0.9210 (tp30) cc_final: 0.8905 (mm-30) REVERT: C 47 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8726 (mp0) REVERT: D 73 ASP cc_start: 0.8764 (t0) cc_final: 0.8491 (t70) REVERT: D 183 GLN cc_start: 0.9233 (mt0) cc_final: 0.8969 (mt0) REVERT: D 218 ARG cc_start: 0.8527 (mtm110) cc_final: 0.8067 (mpp80) REVERT: D 220 GLU cc_start: 0.8553 (mp0) cc_final: 0.8162 (mp0) REVERT: R 66 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.6747 (tm) REVERT: R 67 ASP cc_start: 0.8554 (t70) cc_final: 0.8132 (m-30) REVERT: R 126 LEU cc_start: 0.9090 (mt) cc_final: 0.8870 (mt) REVERT: R 129 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9058 (mm) REVERT: R 132 MET cc_start: 0.8885 (tpp) cc_final: 0.8448 (tpp) REVERT: R 135 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8767 (tt0) REVERT: R 160 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7473 (ttm170) REVERT: R 246 LYS cc_start: 0.8931 (tttt) cc_final: 0.8576 (tttp) REVERT: R 281 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8261 (mt0) REVERT: R 345 GLN cc_start: 0.8530 (mp10) cc_final: 0.8220 (mp10) REVERT: R 377 ASN cc_start: 0.8199 (m-40) cc_final: 0.7911 (m110) REVERT: R 385 HIS cc_start: 0.8672 (t70) cc_final: 0.8404 (t70) REVERT: L 9 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8964 (tptm) REVERT: L 13 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7403 (tm) outliers start: 40 outliers final: 16 residues processed: 201 average time/residue: 0.5318 time to fit residues: 113.6629 Evaluate side-chains 194 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 281 GLN Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 359 MET Chi-restraints excluded: chain R residue 371 ILE Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 306 GLN R 114 HIS ** R 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 382 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.072690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.054783 restraints weight = 20400.023| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.38 r_work: 0.2696 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9147 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9271 Z= 0.139 Angle : 0.604 11.688 12562 Z= 0.308 Chirality : 0.042 0.175 1431 Planarity : 0.004 0.045 1581 Dihedral : 4.352 66.984 1254 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.03 % Allowed : 19.58 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.25), residues: 1139 helix: 2.89 (0.24), residues: 428 sheet: 0.67 (0.31), residues: 263 loop : -0.32 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 160 TYR 0.016 0.001 TYR D 190 PHE 0.010 0.001 PHE A 189 TRP 0.016 0.001 TRP B 100 HIS 0.013 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 9267) covalent geometry : angle 0.60330 / 0.31 (12554) SS BOND : bond 0.00367 / 0.18 ( 4) SS BOND : angle 0.98007 / 0.52 ( 8) hydrogen bonds : bond 0.04037 / 2.69 ( 499) hydrogen bonds : angle 4.38843 / 3.06 ( 1410) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8801 (mttp) REVERT: A 234 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6773 (mp) REVERT: A 257 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.8875 (ptpp) REVERT: A 325 CYS cc_start: 0.8874 (p) cc_final: 0.8490 (p) REVERT: B 62 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8813 (mt0) REVERT: B 233 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8764 (mp0) REVERT: B 235 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.9140 (pmt) REVERT: C 17 GLU cc_start: 0.9209 (tp30) cc_final: 0.8914 (mm-30) REVERT: C 47 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8714 (mp0) REVERT: D 183 GLN cc_start: 0.9225 (mt0) cc_final: 0.8977 (mt0) REVERT: D 218 ARG cc_start: 0.8496 (mtm110) cc_final: 0.8035 (mpp80) REVERT: D 220 GLU cc_start: 0.8577 (mp0) cc_final: 0.8180 (mp0) REVERT: R 66 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.6561 (tm) REVERT: R 67 ASP cc_start: 0.8546 (t70) cc_final: 0.7975 (m-30) REVERT: R 126 LEU cc_start: 0.9094 (mt) cc_final: 0.8875 (mt) REVERT: R 129 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9067 (mm) REVERT: R 132 MET cc_start: 0.8859 (tpp) cc_final: 0.8437 (tpp) REVERT: R 144 HIS cc_start: 0.7018 (m90) cc_final: 0.6607 (m170) REVERT: R 219 MET cc_start: 0.8152 (tpp) cc_final: 0.7485 (mmm) REVERT: R 222 GLN cc_start: 0.8676 (tt0) cc_final: 0.8313 (tt0) REVERT: R 246 LYS cc_start: 0.8899 (tttt) cc_final: 0.8592 (tttp) REVERT: R 281 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8268 (mt0) REVERT: R 377 ASN cc_start: 0.8233 (m-40) cc_final: 0.8000 (m110) REVERT: R 385 HIS cc_start: 0.8744 (t70) cc_final: 0.8479 (t70) REVERT: L 9 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8956 (tptm) REVERT: L 13 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7386 (tm) outliers start: 30 outliers final: 14 residues processed: 198 average time/residue: 0.5645 time to fit residues: 118.6782 Evaluate side-chains 194 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain R residue 281 GLN Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 371 ILE Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 306 GLN R 114 HIS R 382 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.073059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.055242 restraints weight = 20314.738| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.36 r_work: 0.2711 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9139 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9271 Z= 0.132 Angle : 0.603 13.244 12562 Z= 0.310 Chirality : 0.042 0.156 1431 Planarity : 0.004 0.045 1581 Dihedral : 4.315 66.742 1254 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.03 % Allowed : 19.98 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.25), residues: 1139 helix: 2.86 (0.25), residues: 431 sheet: 0.71 (0.31), residues: 261 loop : -0.34 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 160 TYR 0.016 0.001 TYR D 190 PHE 0.010 0.001 PHE A 189 TRP 0.016 0.001 TRP B 100 HIS 0.013 0.001 HIS R 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9267) covalent geometry : angle 0.60291 / 0.31 (12554) SS BOND : bond 0.00360 / 0.18 ( 4) SS BOND : angle 0.98578 / 0.52 ( 8) hydrogen bonds : bond 0.03884 / 2.60 ( 499) hydrogen bonds : angle 4.33162 / 3.02 ( 1410) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8808 (mttp) REVERT: A 234 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6696 (mp) REVERT: A 257 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.8892 (ptpp) REVERT: A 325 CYS cc_start: 0.8884 (p) cc_final: 0.8509 (p) REVERT: B 62 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8801 (mt0) REVERT: B 233 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8753 (mp0) REVERT: B 235 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.9154 (pmt) REVERT: C 17 GLU cc_start: 0.9187 (tp30) cc_final: 0.8815 (mm-30) REVERT: C 20 LYS cc_start: 0.9172 (mtmm) cc_final: 0.8306 (mtmm) REVERT: C 47 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8700 (mp0) REVERT: D 183 GLN cc_start: 0.9201 (mt0) cc_final: 0.8990 (mt0) REVERT: D 218 ARG cc_start: 0.8482 (mtm110) cc_final: 0.8048 (mpp80) REVERT: D 220 GLU cc_start: 0.8559 (mp0) cc_final: 0.8210 (mp0) REVERT: D 238 THR cc_start: 0.9315 (m) cc_final: 0.8971 (p) REVERT: R 66 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.6786 (tm) REVERT: R 67 ASP cc_start: 0.8520 (t70) cc_final: 0.8041 (m-30) REVERT: R 126 LEU cc_start: 0.9097 (mt) cc_final: 0.8869 (mt) REVERT: R 129 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9042 (mm) REVERT: R 132 MET cc_start: 0.8839 (tpp) cc_final: 0.8412 (tpp) REVERT: R 144 HIS cc_start: 0.6932 (m90) cc_final: 0.6525 (m170) REVERT: R 206 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7850 (mm) REVERT: R 219 MET cc_start: 0.8220 (tpp) cc_final: 0.7968 (tpp) REVERT: R 222 GLN cc_start: 0.8693 (tt0) cc_final: 0.8307 (tt0) REVERT: R 246 LYS cc_start: 0.8901 (tttt) cc_final: 0.8617 (tttp) REVERT: R 377 ASN cc_start: 0.8274 (m-40) cc_final: 0.8059 (m110) REVERT: R 385 HIS cc_start: 0.8745 (t70) cc_final: 0.8497 (t70) REVERT: L 9 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8963 (tptm) outliers start: 30 outliers final: 13 residues processed: 193 average time/residue: 0.5246 time to fit residues: 107.8845 Evaluate side-chains 186 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain R residue 371 ILE Chi-restraints excluded: chain L residue 9 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 306 GLN R 114 HIS R 281 GLN R 382 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.072384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.054669 restraints weight = 20489.546| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.37 r_work: 0.2694 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9152 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9271 Z= 0.157 Angle : 0.644 11.860 12562 Z= 0.325 Chirality : 0.042 0.231 1431 Planarity : 0.004 0.046 1581 Dihedral : 4.369 70.175 1254 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.93 % Allowed : 20.69 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.25), residues: 1139 helix: 2.84 (0.25), residues: 430 sheet: 0.68 (0.31), residues: 263 loop : -0.38 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 160 TYR 0.016 0.001 TYR D 190 PHE 0.010 0.001 PHE A 189 TRP 0.015 0.001 TRP B 100 HIS 0.010 0.001 HIS R 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 9267) covalent geometry : angle 0.64342 / 0.32 (12554) SS BOND : bond 0.00366 / 0.18 ( 4) SS BOND : angle 0.99692 / 0.53 ( 8) hydrogen bonds : bond 0.04011 / 2.69 ( 499) hydrogen bonds : angle 4.36284 / 3.04 ( 1410) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8820 (mttp) REVERT: A 234 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6697 (mp) REVERT: A 257 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.8918 (ptpp) REVERT: A 325 CYS cc_start: 0.8906 (p) cc_final: 0.8535 (p) REVERT: B 62 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8759 (mt0) REVERT: B 233 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8747 (mp0) REVERT: B 235 MET cc_start: 0.9414 (OUTLIER) cc_final: 0.9134 (pmt) REVERT: C 17 GLU cc_start: 0.9200 (tp30) cc_final: 0.8851 (mm-30) REVERT: C 20 LYS cc_start: 0.9192 (mtmm) cc_final: 0.8377 (mtmm) REVERT: C 47 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8729 (mp0) REVERT: D 183 GLN cc_start: 0.9221 (mt0) cc_final: 0.9007 (mt0) REVERT: D 218 ARG cc_start: 0.8497 (mtm110) cc_final: 0.8056 (mpp80) REVERT: D 220 GLU cc_start: 0.8525 (mp0) cc_final: 0.8119 (mp0) REVERT: R 66 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.6872 (tm) REVERT: R 67 ASP cc_start: 0.8629 (t70) cc_final: 0.8182 (m-30) REVERT: R 126 LEU cc_start: 0.9111 (mt) cc_final: 0.8882 (mt) REVERT: R 129 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9047 (mm) REVERT: R 132 MET cc_start: 0.8845 (tpp) cc_final: 0.8416 (tpp) REVERT: R 144 HIS cc_start: 0.6877 (m90) cc_final: 0.6444 (m170) REVERT: R 206 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7857 (mm) REVERT: R 219 MET cc_start: 0.8240 (tpp) cc_final: 0.7499 (mmm) REVERT: R 222 GLN cc_start: 0.8682 (tt0) cc_final: 0.8285 (tt0) REVERT: R 246 LYS cc_start: 0.8860 (tttt) cc_final: 0.8591 (tttp) REVERT: R 377 ASN cc_start: 0.8257 (m-40) cc_final: 0.8030 (m110) REVERT: R 385 HIS cc_start: 0.8768 (t70) cc_final: 0.8532 (t70) REVERT: L 9 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8973 (tptm) outliers start: 29 outliers final: 15 residues processed: 183 average time/residue: 0.5600 time to fit residues: 108.9646 Evaluate side-chains 189 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 141 TRP Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain R residue 371 ILE Chi-restraints excluded: chain L residue 9 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 111 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 306 GLN R 114 HIS R 382 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.072765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.055038 restraints weight = 20583.640| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.38 r_work: 0.2704 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9271 Z= 0.139 Angle : 0.636 11.458 12562 Z= 0.322 Chirality : 0.042 0.220 1431 Planarity : 0.004 0.050 1581 Dihedral : 4.341 69.368 1254 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.72 % Allowed : 21.29 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.25), residues: 1139 helix: 2.82 (0.25), residues: 430 sheet: 0.73 (0.31), residues: 261 loop : -0.37 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 160 TYR 0.014 0.001 TYR D 190 PHE 0.010 0.001 PHE A 189 TRP 0.016 0.001 TRP B 100 HIS 0.010 0.001 HIS R 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9267) covalent geometry : angle 0.63592 / 0.32 (12554) SS BOND : bond 0.00357 / 0.18 ( 4) SS BOND : angle 0.97422 / 0.52 ( 8) hydrogen bonds : bond 0.03934 / 2.63 ( 499) hydrogen bonds : angle 4.34537 / 3.03 ( 1410) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8801 (mttp) REVERT: A 234 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6696 (mp) REVERT: A 257 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.8891 (ptpp) REVERT: A 325 CYS cc_start: 0.8916 (p) cc_final: 0.8545 (p) REVERT: B 62 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8767 (mt0) REVERT: B 233 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8758 (mp0) REVERT: B 235 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.9147 (pmt) REVERT: C 17 GLU cc_start: 0.9201 (tp30) cc_final: 0.8852 (mm-30) REVERT: C 20 LYS cc_start: 0.9239 (mtmm) cc_final: 0.8374 (mtmm) REVERT: C 47 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8704 (mp0) REVERT: D 183 GLN cc_start: 0.9222 (mt0) cc_final: 0.9013 (mt0) REVERT: D 218 ARG cc_start: 0.8539 (mtm110) cc_final: 0.8084 (mpp80) REVERT: D 219 LEU cc_start: 0.9296 (mt) cc_final: 0.9073 (tt) REVERT: D 220 GLU cc_start: 0.8518 (mp0) cc_final: 0.8138 (mp0) REVERT: R 66 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.6901 (tm) REVERT: R 67 ASP cc_start: 0.8607 (t70) cc_final: 0.8213 (m-30) REVERT: R 126 LEU cc_start: 0.9107 (mt) cc_final: 0.8892 (mt) REVERT: R 129 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9032 (mm) REVERT: R 132 MET cc_start: 0.8798 (tpp) cc_final: 0.8404 (tpp) REVERT: R 144 HIS cc_start: 0.6848 (m90) cc_final: 0.6396 (m90) REVERT: R 206 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7835 (mm) REVERT: R 219 MET cc_start: 0.8261 (tpp) cc_final: 0.7555 (mmm) REVERT: R 222 GLN cc_start: 0.8689 (tt0) cc_final: 0.8216 (tt0) REVERT: R 246 LYS cc_start: 0.8827 (tttt) cc_final: 0.8572 (tttp) REVERT: R 385 HIS cc_start: 0.8769 (t70) cc_final: 0.8536 (t70) REVERT: L 9 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8936 (tptm) outliers start: 27 outliers final: 10 residues processed: 183 average time/residue: 0.5322 time to fit residues: 103.5944 Evaluate side-chains 177 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain L residue 9 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN R 114 HIS ** R 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 281 GLN R 377 ASN R 382 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.077066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.059313 restraints weight = 20431.935| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.38 r_work: 0.2697 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9271 Z= 0.156 Angle : 0.658 14.469 12562 Z= 0.331 Chirality : 0.042 0.212 1431 Planarity : 0.004 0.045 1581 Dihedral : 4.377 69.953 1254 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.42 % Allowed : 21.59 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.25), residues: 1139 helix: 2.79 (0.25), residues: 430 sheet: 0.69 (0.31), residues: 263 loop : -0.38 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 160 TYR 0.014 0.001 TYR R 331 PHE 0.010 0.001 PHE A 189 TRP 0.015 0.001 TRP B 100 HIS 0.009 0.001 HIS R 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 9267) covalent geometry : angle 0.65817 / 0.33 (12554) SS BOND : bond 0.00368 / 0.18 ( 4) SS BOND : angle 0.98348 / 0.52 ( 8) hydrogen bonds : bond 0.04065 / 2.68 ( 499) hydrogen bonds : angle 4.37241 / 3.06 ( 1410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3795.91 seconds wall clock time: 65 minutes 29.18 seconds (3929.18 seconds total)