Starting phenix.real_space_refine on Tue Feb 3 23:18:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jxe_61860/02_2026/9jxe_61860.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jxe_61860/02_2026/9jxe_61860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jxe_61860/02_2026/9jxe_61860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jxe_61860/02_2026/9jxe_61860.map" model { file = "/net/cci-nas-00/data/ceres_data/9jxe_61860/02_2026/9jxe_61860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jxe_61860/02_2026/9jxe_61860.cif" } resolution = 3.85 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= 0.004 sd= 0.052 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 34 5.16 5 C 5068 2.51 5 N 1217 2.21 5 O 1258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7577 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3132 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 361} Chain breaks: 1 Chain: "B" Number of atoms: 4445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4445 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 515} Chain breaks: 4 Time building chain proxies: 1.37, per 1000 atoms: 0.18 Number of scatterers: 7577 At special positions: 0 Unit cell: (100.225, 105.5, 126.6, 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 34 16.00 O 1258 8.00 N 1217 7.00 C 5068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 262.5 milliseconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1736 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 230 through 258 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 272 through 296 removed outlier: 4.312A pdb=" N LEU A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.330A pdb=" N ILE A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.956A pdb=" N ASN A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.830A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 removed outlier: 4.591A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 403 through 420 removed outlier: 4.150A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 removed outlier: 3.550A pdb=" N ILE A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A 452 " --> pdb=" O ARG A 448 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 472 through 503 removed outlier: 4.457A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 Processing helix chain 'A' and resid 555 through 581 removed outlier: 4.239A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 564 " --> pdb=" O TYR A 560 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 618 Proline residue: A 598 - end of helix Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.737A pdb=" N HIS B 6 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 9 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS B 10 " --> pdb=" O HIS B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 19 removed outlier: 3.518A pdb=" N TYR B 19 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 34 removed outlier: 3.893A pdb=" N ASP B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 removed outlier: 4.227A pdb=" N GLU B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 55' Processing helix chain 'B' and resid 56 through 64 removed outlier: 3.570A pdb=" N PHE B 59 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR B 61 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS B 62 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 63 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS B 64 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 93 removed outlier: 4.590A pdb=" N ILE B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 88 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 168 removed outlier: 3.716A pdb=" N ALA B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 143 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE B 153 " --> pdb=" O GLN B 149 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG B 157 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 161 " --> pdb=" O ARG B 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE B 166 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B 167 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 181 removed outlier: 3.797A pdb=" N ASP B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N HIS B 179 " --> pdb=" O TRP B 175 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 181 " --> pdb=" O VAL B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 removed outlier: 3.516A pdb=" N TYR B 186 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N CYS B 188 " --> pdb=" O PHE B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.903A pdb=" N GLN B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 201 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 258 Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 272 through 294 removed outlier: 3.820A pdb=" N PHE B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU B 278 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 336 removed outlier: 3.618A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 367 through 383 removed outlier: 3.563A pdb=" N THR B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 387 Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.504A pdb=" N PHE B 394 " --> pdb=" O GLY B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 4.030A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 471 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 475 through 503 removed outlier: 4.069A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 Processing helix chain 'B' and resid 555 through 581 removed outlier: 4.177A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 564 " --> pdb=" O TYR B 560 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 575 " --> pdb=" O PHE B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 618 removed outlier: 3.936A pdb=" N ILE B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) Proline residue: B 598 - end of helix 473 hydrogen bonds defined for protein. 1404 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: 0.78 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2255 1.34 - 1.46: 2141 1.46 - 1.58: 3371 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 7815 Sorted by residual: bond pdb=" N ALA A 229 " pdb=" CA ALA A 229 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 bond pdb=" CB VAL A 246 " pdb=" CG1 VAL A 246 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CB VAL B 246 " pdb=" CG1 VAL B 246 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.54e+00 bond pdb=" CG1 ILE B 406 " pdb=" CD1 ILE B 406 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.33e+00 ... (remaining 7810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 10345 1.67 - 3.33: 230 3.33 - 5.00: 31 5.00 - 6.66: 4 6.66 - 8.33: 2 Bond angle restraints: 10612 Sorted by residual: angle pdb=" CB MET B 408 " pdb=" CG MET B 408 " pdb=" SD MET B 408 " ideal model delta sigma weight residual 112.70 121.03 -8.33 3.00e+00 1.11e-01 7.71e+00 angle pdb=" C ARG B 611 " pdb=" N LEU B 612 " pdb=" CA LEU B 612 " ideal model delta sigma weight residual 120.31 116.64 3.67 1.52e+00 4.33e-01 5.83e+00 angle pdb=" CA GLN B 92 " pdb=" CB GLN B 92 " pdb=" CG GLN B 92 " ideal model delta sigma weight residual 114.10 118.42 -4.32 2.00e+00 2.50e-01 4.66e+00 angle pdb=" CA LEU A 396 " pdb=" CB LEU A 396 " pdb=" CG LEU A 396 " ideal model delta sigma weight residual 116.30 109.57 6.73 3.50e+00 8.16e-02 3.70e+00 angle pdb=" C PHE A 487 " pdb=" CA PHE A 487 " pdb=" CB PHE A 487 " ideal model delta sigma weight residual 110.88 107.89 2.99 1.57e+00 4.06e-01 3.64e+00 ... (remaining 10607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 3772 17.67 - 35.34: 496 35.34 - 53.01: 159 53.01 - 70.67: 21 70.67 - 88.34: 9 Dihedral angle restraints: 4457 sinusoidal: 1772 harmonic: 2685 Sorted by residual: dihedral pdb=" CA ILE A 269 " pdb=" C ILE A 269 " pdb=" N ARG A 270 " pdb=" CA ARG A 270 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ILE A 269 " pdb=" CA ILE A 269 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE B 54 " pdb=" C PHE B 54 " pdb=" N GLU B 55 " pdb=" CA GLU B 55 " ideal model delta harmonic sigma weight residual -180.00 -162.84 -17.16 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 4454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 759 0.031 - 0.062: 289 0.062 - 0.093: 93 0.093 - 0.123: 13 0.123 - 0.154: 5 Chirality restraints: 1159 Sorted by residual: chirality pdb=" CA PRO B 267 " pdb=" N PRO B 267 " pdb=" C PRO B 267 " pdb=" CB PRO B 267 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ILE A 551 " pdb=" N ILE A 551 " pdb=" C ILE A 551 " pdb=" CB ILE A 551 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE B 342 " pdb=" N ILE B 342 " pdb=" C ILE B 342 " pdb=" CB ILE B 342 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1156 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 454 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.62e+00 pdb=" N PRO B 455 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 455 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 455 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 379 " -0.012 2.00e-02 2.50e+03 1.25e-02 2.75e+00 pdb=" CG PHE A 379 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 379 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 379 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 379 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 379 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 379 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 264 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C SER B 264 " -0.027 2.00e-02 2.50e+03 pdb=" O SER B 264 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE B 265 " 0.009 2.00e-02 2.50e+03 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 46 2.51 - 3.11: 6155 3.11 - 3.70: 11944 3.70 - 4.30: 15632 4.30 - 4.90: 25666 Nonbonded interactions: 59443 Sorted by model distance: nonbonded pdb=" O SER A 578 " pdb=" OG SER A 581 " model vdw 1.910 3.040 nonbonded pdb=" O VAL B 478 " pdb=" OH TYR B 524 " model vdw 2.167 3.040 nonbonded pdb=" NH2 ARG B 548 " pdb=" OE1 GLU B 613 " model vdw 2.183 3.120 nonbonded pdb=" OE2 GLU B 318 " pdb=" OH TYR B 367 " model vdw 2.251 3.040 nonbonded pdb=" O TYR B 148 " pdb=" ND2 ASN B 152 " model vdw 2.252 3.120 ... (remaining 59438 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.970 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7815 Z= 0.208 Angle : 0.612 8.328 10612 Z= 0.341 Chirality : 0.036 0.154 1159 Planarity : 0.004 0.054 1298 Dihedral : 17.676 88.343 2721 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.37 % Allowed : 27.61 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.29), residues: 892 helix: 1.17 (0.21), residues: 647 sheet: None (None), residues: 0 loop : -1.37 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 465 TYR 0.019 0.001 TYR A 524 PHE 0.029 0.002 PHE A 379 TRP 0.012 0.001 TRP B 292 HIS 0.005 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 7815) covalent geometry : angle 0.61150 (10612) hydrogen bonds : bond 0.12370 ( 473) hydrogen bonds : angle 4.98415 ( 1404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 0.281 Fit side-chains REVERT: A 246 VAL cc_start: 0.8326 (p) cc_final: 0.7447 (m) REVERT: A 248 ASN cc_start: 0.8332 (m-40) cc_final: 0.8116 (m-40) REVERT: A 314 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7924 (mm-40) REVERT: B 368 TYR cc_start: 0.7931 (p90) cc_final: 0.7631 (p90) outliers start: 3 outliers final: 2 residues processed: 118 average time/residue: 0.0563 time to fit residues: 9.6087 Evaluate side-chains 108 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 579 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 20.0000 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.0570 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.170846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.133863 restraints weight = 14444.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.134972 restraints weight = 7861.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.137746 restraints weight = 5412.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.138038 restraints weight = 4034.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.138766 restraints weight = 4023.220| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7815 Z= 0.151 Angle : 0.601 7.827 10612 Z= 0.309 Chirality : 0.040 0.174 1159 Planarity : 0.004 0.047 1298 Dihedral : 4.414 25.350 1001 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.23 % Allowed : 27.24 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.29), residues: 892 helix: 1.19 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -1.39 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 308 TYR 0.018 0.001 TYR A 345 PHE 0.020 0.001 PHE B 379 TRP 0.006 0.001 TRP A 266 HIS 0.004 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7815) covalent geometry : angle 0.60103 (10612) hydrogen bonds : bond 0.04875 ( 473) hydrogen bonds : angle 4.04579 ( 1404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.280 Fit side-chains REVERT: A 246 VAL cc_start: 0.8484 (p) cc_final: 0.7535 (m) REVERT: A 314 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7770 (mm-40) REVERT: A 452 GLN cc_start: 0.8831 (tm130) cc_final: 0.8441 (tm-30) REVERT: A 489 MET cc_start: 0.7910 (tpp) cc_final: 0.7592 (tpp) REVERT: A 517 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.8125 (t80) REVERT: B 153 PHE cc_start: 0.6650 (t80) cc_final: 0.5388 (t80) REVERT: B 157 ARG cc_start: 0.7924 (ptt180) cc_final: 0.7659 (ptt180) REVERT: B 189 LYS cc_start: 0.6770 (mmtm) cc_final: 0.6509 (mmmt) REVERT: B 355 MET cc_start: 0.8815 (mtt) cc_final: 0.8485 (mtt) outliers start: 26 outliers final: 16 residues processed: 132 average time/residue: 0.0562 time to fit residues: 10.7973 Evaluate side-chains 125 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain B residue 488 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 46 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 44 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 HIS B 10 HIS ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.171281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.134967 restraints weight = 14260.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.136208 restraints weight = 7479.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.138731 restraints weight = 5174.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.141247 restraints weight = 3850.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.141557 restraints weight = 3342.059| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7815 Z= 0.138 Angle : 0.583 7.406 10612 Z= 0.295 Chirality : 0.039 0.183 1159 Planarity : 0.004 0.058 1298 Dihedral : 4.180 15.756 997 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.48 % Allowed : 27.11 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.29), residues: 892 helix: 1.16 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.40 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 308 TYR 0.015 0.001 TYR A 524 PHE 0.016 0.001 PHE B 605 TRP 0.011 0.001 TRP B 266 HIS 0.012 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7815) covalent geometry : angle 0.58342 (10612) hydrogen bonds : bond 0.04448 ( 473) hydrogen bonds : angle 3.86782 ( 1404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.225 Fit side-chains REVERT: A 246 VAL cc_start: 0.8375 (p) cc_final: 0.7383 (m) REVERT: A 314 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7687 (mm-40) REVERT: A 452 GLN cc_start: 0.8861 (tm130) cc_final: 0.8471 (tm-30) REVERT: A 517 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8193 (t80) REVERT: B 189 LYS cc_start: 0.6908 (mmtm) cc_final: 0.6660 (mmmt) outliers start: 36 outliers final: 20 residues processed: 141 average time/residue: 0.0558 time to fit residues: 11.4942 Evaluate side-chains 128 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain B residue 6 HIS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain B residue 335 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 53 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 0.0010 chunk 60 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 55 optimal weight: 0.0870 chunk 80 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 0.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.170253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.133402 restraints weight = 15019.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.137548 restraints weight = 7090.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.139937 restraints weight = 4501.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.141656 restraints weight = 3485.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.142469 restraints weight = 2936.334| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7815 Z= 0.127 Angle : 0.592 11.702 10612 Z= 0.292 Chirality : 0.039 0.194 1159 Planarity : 0.004 0.063 1298 Dihedral : 4.118 14.762 997 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.73 % Allowed : 28.36 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.29), residues: 892 helix: 1.20 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.60 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 308 TYR 0.020 0.001 TYR A 345 PHE 0.013 0.001 PHE A 605 TRP 0.009 0.001 TRP B 266 HIS 0.010 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7815) covalent geometry : angle 0.59161 (10612) hydrogen bonds : bond 0.04157 ( 473) hydrogen bonds : angle 3.77093 ( 1404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7700 (mm-40) REVERT: A 452 GLN cc_start: 0.8657 (tm130) cc_final: 0.8418 (tm-30) REVERT: A 517 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.8058 (t80) REVERT: B 157 ARG cc_start: 0.7959 (ptt180) cc_final: 0.7662 (ptt180) outliers start: 30 outliers final: 17 residues processed: 132 average time/residue: 0.0645 time to fit residues: 11.9994 Evaluate side-chains 127 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 406 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 74 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 64 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.0370 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.168690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.134519 restraints weight = 14925.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.135344 restraints weight = 7470.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.138061 restraints weight = 5239.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.140088 restraints weight = 3820.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.140371 restraints weight = 3415.941| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7815 Z= 0.136 Angle : 0.591 9.270 10612 Z= 0.290 Chirality : 0.039 0.202 1159 Planarity : 0.004 0.065 1298 Dihedral : 4.115 15.978 997 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.73 % Allowed : 27.86 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.29), residues: 892 helix: 1.26 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.52 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 308 TYR 0.017 0.001 TYR B 412 PHE 0.024 0.001 PHE B 357 TRP 0.010 0.001 TRP B 266 HIS 0.010 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7815) covalent geometry : angle 0.59104 (10612) hydrogen bonds : bond 0.04191 ( 473) hydrogen bonds : angle 3.72942 ( 1404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7696 (mm-40) REVERT: A 517 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8243 (t80) REVERT: B 157 ARG cc_start: 0.8053 (ptt180) cc_final: 0.7731 (ptt180) outliers start: 38 outliers final: 23 residues processed: 141 average time/residue: 0.0587 time to fit residues: 11.9020 Evaluate side-chains 131 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 579 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 12 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.171397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.131847 restraints weight = 14432.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.135897 restraints weight = 7106.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.138528 restraints weight = 4681.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.139665 restraints weight = 3651.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.141032 restraints weight = 3225.890| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7815 Z= 0.143 Angle : 0.612 10.163 10612 Z= 0.298 Chirality : 0.040 0.210 1159 Planarity : 0.004 0.066 1298 Dihedral : 4.087 14.430 997 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.60 % Allowed : 28.73 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.29), residues: 892 helix: 1.28 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.47 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 308 TYR 0.022 0.001 TYR A 345 PHE 0.017 0.001 PHE B 605 TRP 0.009 0.001 TRP B 266 HIS 0.007 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7815) covalent geometry : angle 0.61157 (10612) hydrogen bonds : bond 0.04218 ( 473) hydrogen bonds : angle 3.70086 ( 1404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7704 (mm-40) REVERT: A 383 THR cc_start: 0.8056 (p) cc_final: 0.7717 (p) REVERT: A 517 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8174 (t80) REVERT: B 157 ARG cc_start: 0.8059 (ptt180) cc_final: 0.7807 (ptt180) outliers start: 37 outliers final: 23 residues processed: 144 average time/residue: 0.0610 time to fit residues: 12.7875 Evaluate side-chains 136 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain B residue 335 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 58 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 38 optimal weight: 0.0060 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.171166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.134422 restraints weight = 14818.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.138487 restraints weight = 7152.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.140987 restraints weight = 4581.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.142607 restraints weight = 3525.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.143223 restraints weight = 2995.966| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7815 Z= 0.132 Angle : 0.647 14.020 10612 Z= 0.307 Chirality : 0.040 0.216 1159 Planarity : 0.004 0.065 1298 Dihedral : 4.071 14.916 997 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.98 % Allowed : 29.10 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.29), residues: 892 helix: 1.27 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.43 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 308 TYR 0.014 0.001 TYR A 524 PHE 0.024 0.001 PHE B 357 TRP 0.007 0.001 TRP B 266 HIS 0.006 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7815) covalent geometry : angle 0.64738 (10612) hydrogen bonds : bond 0.04077 ( 473) hydrogen bonds : angle 3.65339 ( 1404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7713 (mm-40) REVERT: A 383 THR cc_start: 0.8050 (p) cc_final: 0.7751 (p) REVERT: A 517 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8180 (t80) REVERT: B 157 ARG cc_start: 0.7981 (ptt180) cc_final: 0.7734 (ptt180) REVERT: B 266 TRP cc_start: 0.7975 (m-10) cc_final: 0.7714 (m-10) REVERT: B 326 LEU cc_start: 0.8329 (mt) cc_final: 0.8090 (tp) outliers start: 32 outliers final: 20 residues processed: 139 average time/residue: 0.0663 time to fit residues: 12.9542 Evaluate side-chains 131 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 579 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.169885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.132967 restraints weight = 14865.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.136926 restraints weight = 7151.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.139412 restraints weight = 4605.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.140545 restraints weight = 3546.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.141726 restraints weight = 3105.453| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7815 Z= 0.140 Angle : 0.634 12.333 10612 Z= 0.304 Chirality : 0.040 0.226 1159 Planarity : 0.004 0.065 1298 Dihedral : 4.101 14.637 997 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.61 % Allowed : 29.48 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.29), residues: 892 helix: 1.25 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -1.45 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 293 TYR 0.024 0.001 TYR A 345 PHE 0.031 0.001 PHE A 379 TRP 0.014 0.001 TRP A 534 HIS 0.005 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7815) covalent geometry : angle 0.63355 (10612) hydrogen bonds : bond 0.04117 ( 473) hydrogen bonds : angle 3.67152 ( 1404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7738 (mm-40) REVERT: A 492 PHE cc_start: 0.7855 (m-80) cc_final: 0.7631 (m-10) REVERT: A 517 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8169 (t80) REVERT: B 157 ARG cc_start: 0.7983 (ptt180) cc_final: 0.7746 (ptt180) REVERT: B 266 TRP cc_start: 0.7982 (m-10) cc_final: 0.7721 (m-10) REVERT: B 326 LEU cc_start: 0.8347 (mt) cc_final: 0.8108 (tp) outliers start: 29 outliers final: 19 residues processed: 136 average time/residue: 0.0635 time to fit residues: 12.3521 Evaluate side-chains 129 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 579 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN A 499 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.168978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.134353 restraints weight = 14832.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.135911 restraints weight = 7593.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.137946 restraints weight = 5255.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.140538 restraints weight = 3960.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.140788 restraints weight = 3516.004| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7815 Z= 0.161 Angle : 0.662 11.914 10612 Z= 0.318 Chirality : 0.041 0.228 1159 Planarity : 0.004 0.064 1298 Dihedral : 4.135 14.744 997 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.48 % Allowed : 30.10 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.29), residues: 892 helix: 1.20 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.43 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 308 TYR 0.016 0.001 TYR B 412 PHE 0.027 0.001 PHE A 510 TRP 0.010 0.001 TRP A 534 HIS 0.005 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 7815) covalent geometry : angle 0.66159 (10612) hydrogen bonds : bond 0.04331 ( 473) hydrogen bonds : angle 3.71901 ( 1404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7739 (mm-40) REVERT: A 452 GLN cc_start: 0.8527 (tm130) cc_final: 0.8326 (tm-30) REVERT: A 517 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8369 (t80) REVERT: B 157 ARG cc_start: 0.7911 (ptt180) cc_final: 0.7699 (ptt180) REVERT: B 266 TRP cc_start: 0.8009 (m-10) cc_final: 0.7752 (m-10) REVERT: B 355 MET cc_start: 0.8797 (mtt) cc_final: 0.8303 (mtt) outliers start: 28 outliers final: 19 residues processed: 132 average time/residue: 0.0604 time to fit residues: 11.3881 Evaluate side-chains 130 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 454 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 12 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.0370 chunk 55 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN B 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.170700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.136520 restraints weight = 14813.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.137915 restraints weight = 7367.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.140558 restraints weight = 5168.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.142641 restraints weight = 3784.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.143008 restraints weight = 3342.086| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7815 Z= 0.133 Angle : 0.648 11.707 10612 Z= 0.309 Chirality : 0.041 0.229 1159 Planarity : 0.004 0.062 1298 Dihedral : 4.122 14.520 997 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.74 % Allowed : 31.22 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.29), residues: 892 helix: 1.28 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -1.40 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 308 TYR 0.022 0.001 TYR A 345 PHE 0.022 0.001 PHE A 510 TRP 0.009 0.001 TRP A 534 HIS 0.005 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7815) covalent geometry : angle 0.64849 (10612) hydrogen bonds : bond 0.04112 ( 473) hydrogen bonds : angle 3.68092 ( 1404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7723 (mm-40) REVERT: A 379 PHE cc_start: 0.8498 (t80) cc_final: 0.8231 (t80) REVERT: A 452 GLN cc_start: 0.8521 (tm130) cc_final: 0.8274 (tm-30) REVERT: A 517 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8469 (t80) REVERT: B 157 ARG cc_start: 0.8071 (ptt180) cc_final: 0.7813 (ptt180) REVERT: B 266 TRP cc_start: 0.7961 (m-10) cc_final: 0.7748 (m-10) REVERT: B 326 LEU cc_start: 0.8238 (mt) cc_final: 0.7978 (tp) outliers start: 22 outliers final: 19 residues processed: 130 average time/residue: 0.0561 time to fit residues: 10.5356 Evaluate side-chains 131 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 454 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 67 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 78 optimal weight: 0.0670 chunk 59 optimal weight: 0.7980 chunk 73 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.170861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.133540 restraints weight = 14675.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.137543 restraints weight = 7151.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.140042 restraints weight = 4646.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.141390 restraints weight = 3595.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.142444 restraints weight = 3103.511| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7815 Z= 0.133 Angle : 0.655 11.334 10612 Z= 0.311 Chirality : 0.040 0.224 1159 Planarity : 0.004 0.060 1298 Dihedral : 4.104 14.772 997 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.86 % Allowed : 31.47 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.29), residues: 892 helix: 1.18 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.51 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 308 TYR 0.023 0.001 TYR A 345 PHE 0.015 0.001 PHE B 492 TRP 0.008 0.001 TRP A 534 HIS 0.005 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7815) covalent geometry : angle 0.65514 (10612) hydrogen bonds : bond 0.04059 ( 473) hydrogen bonds : angle 3.67753 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1069.82 seconds wall clock time: 19 minutes 10.89 seconds (1150.89 seconds total)