Starting phenix.real_space_refine on Thu Mar 5 03:13:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nb8_12257/03_2026/7nb8_12257.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nb8_12257/03_2026/7nb8_12257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nb8_12257/03_2026/7nb8_12257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nb8_12257/03_2026/7nb8_12257.map" model { file = "/net/cci-nas-00/data/ceres_data/7nb8_12257/03_2026/7nb8_12257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nb8_12257/03_2026/7nb8_12257.cif" } resolution = 4.4 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 ------------------------------------------------------------------------------- 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= 0.007 sd= 0.019 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 5906 2.51 5 N 1596 2.21 5 O 1815 1.98 5 H 9185 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18570 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6636 Classifications: {'peptide': 428} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "B" Number of atoms: 6588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6588 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "K" Number of atoms: 5280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 5280 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 3, 'TRANS': 319} Chain breaks: 5 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.87, per 1000 atoms: 0.15 Number of scatterers: 18570 At special positions: 0 Unit cell: (98.69, 105.64, 113.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 60 16.00 P 6 15.00 Mg 2 11.99 O 1815 8.00 N 1596 7.00 C 5906 6.00 H 9185 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 551.9 milliseconds 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 50.9% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.166A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.615A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.611A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 161 removed outlier: 3.516A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.547A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 239 Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 296 through 301 removed outlier: 6.178A pdb=" N ALA A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.657A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.544A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.947A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 435 removed outlier: 4.035A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.579A pdb=" N GLY B 13 " --> pdb=" O ALA B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.020A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 79 removed outlier: 3.681A pdb=" N GLY B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 107 through 126 removed outlier: 3.556A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.585A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.118A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.546A pdb=" N GLN B 280 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.619A pdb=" N MET B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 3.881A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 4.052A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 38 Processing helix chain 'K' and resid 57 through 61 Processing helix chain 'K' and resid 78 through 86 Processing helix chain 'K' and resid 86 through 95 Processing helix chain 'K' and resid 111 through 116 Processing helix chain 'K' and resid 156 through 177 Processing helix chain 'K' and resid 239 through 252 removed outlier: 3.937A pdb=" N LYS K 252 " --> pdb=" O CYS K 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 308 Processing helix chain 'K' and resid 314 through 339 removed outlier: 3.607A pdb=" N SER K 326 " --> pdb=" O ASN K 322 " (cutoff:3.500A) Processing helix chain 'K' and resid 343 through 348 Processing helix chain 'K' and resid 349 through 355 Processing helix chain 'K' and resid 356 through 359 Processing helix chain 'K' and resid 374 through 376 No H-bonds generated for 'chain 'K' and resid 374 through 376' Processing helix chain 'K' and resid 377 through 394 removed outlier: 3.901A pdb=" N ALA K 391 " --> pdb=" O TYR K 387 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS K 392 " --> pdb=" O VAL K 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.964A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 57 removed outlier: 6.825A pdb=" N LYS A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 248 removed outlier: 6.398A pdb=" N ILE A 355 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N LYS A 352 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS A 315 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASN A 356 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR A 319 " --> pdb=" O ASN A 356 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.979A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 11.158A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.323A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'K' and resid 71 through 73 removed outlier: 6.690A pdb=" N ASN K 99 " --> pdb=" O LYS K 364 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N PHE K 366 " --> pdb=" O ASN K 99 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR K 101 " --> pdb=" O PHE K 366 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL K 368 " --> pdb=" O THR K 101 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE K 103 " --> pdb=" O VAL K 368 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR K 370 " --> pdb=" O PHE K 103 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR K 105 " --> pdb=" O THR K 370 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N CYS K 100 " --> pdb=" O ASN K 295 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL K 297 " --> pdb=" O CYS K 100 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU K 102 " --> pdb=" O VAL K 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 71 through 73 removed outlier: 6.690A pdb=" N ASN K 99 " --> pdb=" O LYS K 364 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N PHE K 366 " --> pdb=" O ASN K 99 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR K 101 " --> pdb=" O PHE K 366 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL K 368 " --> pdb=" O THR K 101 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE K 103 " --> pdb=" O VAL K 368 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR K 370 " --> pdb=" O PHE K 103 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR K 105 " --> pdb=" O THR K 370 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N CYS K 100 " --> pdb=" O ASN K 295 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL K 297 " --> pdb=" O CYS K 100 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU K 102 " --> pdb=" O VAL K 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 45 through 48 Processing sheet with id=AA9, first strand: chain 'K' and resid 216 through 217 Processing sheet with id=AB1, first strand: chain 'K' and resid 256 through 257 496 hydrogen bonds defined for protein. 1362 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: 4.35 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 9156 1.13 - 1.31: 1734 1.31 - 1.49: 4057 1.49 - 1.67: 3708 1.67 - 1.85: 95 Bond restraints: 18750 Sorted by residual: bond pdb=" CB ASP B 67 " pdb=" CG ASP B 67 " ideal model delta sigma weight residual 1.516 1.846 -0.330 2.50e-02 1.60e+03 1.74e+02 bond pdb=" CB ASP A 69 " pdb=" CG ASP A 69 " ideal model delta sigma weight residual 1.516 1.779 -0.263 2.50e-02 1.60e+03 1.10e+02 bond pdb=" NH2 ARG A 243 " pdb="HH22 ARG A 243 " ideal model delta sigma weight residual 0.860 1.053 -0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" NH1 ARG B 213 " pdb="HH11 ARG B 213 " ideal model delta sigma weight residual 0.860 1.048 -0.188 2.00e-02 2.50e+03 8.86e+01 bond pdb=" NH1 ARG A 156 " pdb="HH12 ARG A 156 " ideal model delta sigma weight residual 0.860 1.047 -0.187 2.00e-02 2.50e+03 8.71e+01 ... (remaining 18745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 30177 3.14 - 6.28: 2975 6.28 - 9.42: 584 9.42 - 12.57: 24 12.57 - 15.71: 27 Bond angle restraints: 33787 Sorted by residual: angle pdb=" N VAL A 260 " pdb=" CA VAL A 260 " pdb=" C VAL A 260 " ideal model delta sigma weight residual 107.56 116.86 -9.30 9.10e-01 1.21e+00 1.04e+02 angle pdb=" CA ASP B 249 " pdb=" CB ASP B 249 " pdb=" CG ASP B 249 " ideal model delta sigma weight residual 112.60 120.22 -7.62 1.00e+00 1.00e+00 5.81e+01 angle pdb=" CA ASP A 205 " pdb=" CB ASP A 205 " pdb=" CG ASP A 205 " ideal model delta sigma weight residual 112.60 119.88 -7.28 1.00e+00 1.00e+00 5.30e+01 angle pdb=" N TYR K 185 " pdb=" CA TYR K 185 " pdb=" C TYR K 185 " ideal model delta sigma weight residual 113.50 101.67 11.83 1.65e+00 3.67e-01 5.14e+01 angle pdb=" N SER K 320 " pdb=" CA SER K 320 " pdb=" C SER K 320 " ideal model delta sigma weight residual 111.28 103.50 7.78 1.09e+00 8.42e-01 5.09e+01 ... (remaining 33782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.42: 8652 33.42 - 66.84: 187 66.84 - 100.26: 16 100.26 - 133.68: 1 133.68 - 167.09: 2 Dihedral angle restraints: 8858 sinusoidal: 4848 harmonic: 4010 Sorted by residual: dihedral pdb=" O3B GTP A 500 " pdb=" O3A GTP A 500 " pdb=" PB GTP A 500 " pdb=" PA GTP A 500 " ideal model delta sinusoidal sigma weight residual 291.08 123.98 167.09 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C8 GTP A 500 " pdb=" C1' GTP A 500 " pdb=" N9 GTP A 500 " pdb=" O4' GTP A 500 " ideal model delta sinusoidal sigma weight residual 104.59 -45.21 149.80 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" CD2 HIS A 192 " pdb=" CG HIS A 192 " pdb=" ND1 HIS A 192 " pdb=" HD1 HIS A 192 " ideal model delta harmonic sigma weight residual 180.00 150.26 29.74 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 8855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 968 0.086 - 0.172: 380 0.172 - 0.258: 80 0.258 - 0.344: 13 0.344 - 0.429: 2 Chirality restraints: 1443 Sorted by residual: chirality pdb=" C3' G2P B 500 " pdb=" C2' G2P B 500 " pdb=" C4' G2P B 500 " pdb=" O3' G2P B 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CA ILE K 378 " pdb=" N ILE K 378 " pdb=" C ILE K 378 " pdb=" CB ILE K 378 " both_signs ideal model delta sigma weight residual False 2.43 2.05 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA PHE K 159 " pdb=" N PHE K 159 " pdb=" C PHE K 159 " pdb=" CB PHE K 159 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1440 not shown) Planarity restraints: 2793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP A 500 " -0.891 2.00e-02 2.50e+03 3.92e-01 4.62e+03 pdb=" C2 GTP A 500 " 0.207 2.00e-02 2.50e+03 pdb=" C4 GTP A 500 " 0.450 2.00e-02 2.50e+03 pdb=" C5 GTP A 500 " 0.075 2.00e-02 2.50e+03 pdb=" C6 GTP A 500 " -0.185 2.00e-02 2.50e+03 pdb=" C8 GTP A 500 " 0.152 2.00e-02 2.50e+03 pdb=" N1 GTP A 500 " -0.435 2.00e-02 2.50e+03 pdb=" N2 GTP A 500 " -0.074 2.00e-02 2.50e+03 pdb=" N3 GTP A 500 " 0.693 2.00e-02 2.50e+03 pdb=" N7 GTP A 500 " 0.160 2.00e-02 2.50e+03 pdb=" N9 GTP A 500 " 0.056 2.00e-02 2.50e+03 pdb=" O6 GTP A 500 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 192 " -0.113 2.00e-02 2.50e+03 1.09e-01 2.69e+02 pdb=" CG HIS A 192 " -0.042 2.00e-02 2.50e+03 pdb=" ND1 HIS A 192 " -0.093 2.00e-02 2.50e+03 pdb=" CD2 HIS A 192 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS A 192 " -0.057 2.00e-02 2.50e+03 pdb=" NE2 HIS A 192 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 HIS A 192 " 0.253 2.00e-02 2.50e+03 pdb=" HD2 HIS A 192 " 0.085 2.00e-02 2.50e+03 pdb=" HE1 HIS A 192 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 307 " 0.095 2.00e-02 2.50e+03 1.05e-01 2.50e+02 pdb=" CG HIS B 307 " 0.062 2.00e-02 2.50e+03 pdb=" ND1 HIS B 307 " 0.102 2.00e-02 2.50e+03 pdb=" CD2 HIS B 307 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 HIS B 307 " 0.051 2.00e-02 2.50e+03 pdb=" NE2 HIS B 307 " -0.027 2.00e-02 2.50e+03 pdb=" HD1 HIS B 307 " -0.245 2.00e-02 2.50e+03 pdb=" HD2 HIS B 307 " -0.086 2.00e-02 2.50e+03 pdb=" HE1 HIS B 307 " 0.073 2.00e-02 2.50e+03 ... (remaining 2790 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.87: 345 1.87 - 2.56: 17507 2.56 - 3.24: 60075 3.24 - 3.92: 77326 3.92 - 4.60: 120260 Nonbonded interactions: 275513 Sorted by model distance: nonbonded pdb=" HG1 THR B 166 " pdb=" HG1 THR B 196 " model vdw 1.193 2.100 nonbonded pdb=" HG1 THR B 107 " pdb=" H GLU B 108 " model vdw 1.240 2.100 nonbonded pdb=" H TYR K 185 " pdb=" H ASP K 186 " model vdw 1.281 2.100 nonbonded pdb=" OE1 GLU B 343 " pdb=" H GLU B 343 " model vdw 1.319 2.450 nonbonded pdb=" H ARG B 309 " pdb=" HG1 THR B 372 " model vdw 1.573 2.100 ... (remaining 275508 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: 0.020 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: 0.090 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.320 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 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 : 0.018 0.330 9565 Z= 0.984 Angle : 1.788 15.385 12951 Z= 1.186 Chirality : 0.093 0.429 1443 Planarity : 0.014 0.392 1668 Dihedral : 12.102 167.095 3570 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.85 % Favored : 96.81 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % Favored : 99.52 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.24), residues: 1159 helix: 0.18 (0.22), residues: 488 sheet: 0.19 (0.39), residues: 189 loop : -0.05 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 241 TYR 0.046 0.009 TYR A 108 PHE 0.042 0.006 PHE K 103 TRP 0.029 0.007 TRP B 21 HIS 0.012 0.003 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.01827 ( 9565) covalent geometry : angle 1.78785 (12951) hydrogen bonds : bond 0.18037 ( 466) hydrogen bonds : angle 7.87357 ( 1362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 516 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8950 (tp) cc_final: 0.8165 (tp) REVERT: A 96 LYS cc_start: 0.7976 (mttt) cc_final: 0.7036 (mtmt) REVERT: A 110 ILE cc_start: 0.8726 (mm) cc_final: 0.8430 (tp) REVERT: A 189 LEU cc_start: 0.9547 (mt) cc_final: 0.9277 (mt) REVERT: A 235 VAL cc_start: 0.9340 (t) cc_final: 0.8948 (p) REVERT: A 292 THR cc_start: 0.8703 (m) cc_final: 0.8227 (p) REVERT: A 295 CYS cc_start: 0.8700 (m) cc_final: 0.7927 (m) REVERT: A 377 MET cc_start: 0.7876 (ttm) cc_final: 0.6741 (tmm) REVERT: A 417 GLU cc_start: 0.8836 (mt-10) cc_final: 0.7391 (tt0) REVERT: B 135 LEU cc_start: 0.7416 (mp) cc_final: 0.7191 (mp) REVERT: B 150 LEU cc_start: 0.9107 (tp) cc_final: 0.8738 (tt) REVERT: B 267 MET cc_start: 0.7961 (mtt) cc_final: 0.7705 (mmm) REVERT: B 350 LYS cc_start: 0.8757 (tptp) cc_final: 0.8548 (tptp) REVERT: B 366 THR cc_start: 0.7809 (m) cc_final: 0.7111 (p) REVERT: B 377 LEU cc_start: 0.8661 (tp) cc_final: 0.8039 (tp) REVERT: B 407 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7452 (mt-10) REVERT: K 227 LEU cc_start: 0.7593 (tp) cc_final: 0.7295 (tp) REVERT: K 246 ILE cc_start: 0.8788 (mt) cc_final: 0.8531 (tp) REVERT: K 295 ASN cc_start: 0.7346 (m-40) cc_final: 0.7136 (m110) outliers start: 1 outliers final: 1 residues processed: 517 average time/residue: 0.2902 time to fit residues: 192.3394 Evaluate side-chains 304 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 309 HIS B 134 GLN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 188 ASN ** K 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.078110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.065441 restraints weight = 100123.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.069035 restraints weight = 42709.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.071259 restraints weight = 22259.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.072694 restraints weight = 13192.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.073665 restraints weight = 8637.477| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9565 Z= 0.221 Angle : 0.734 8.719 12951 Z= 0.419 Chirality : 0.047 0.288 1443 Planarity : 0.006 0.059 1668 Dihedral : 10.925 172.175 1324 Min Nonbonded Distance : 1.594 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.02 % Favored : 96.89 % Rotamer: Outliers : 0.10 % Allowed : 1.75 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.31 (0.25), residues: 1159 helix: 0.52 (0.22), residues: 488 sheet: -0.20 (0.37), residues: 210 loop : 0.31 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 267 TYR 0.021 0.002 TYR K 88 PHE 0.013 0.002 PHE K 103 TRP 0.006 0.001 TRP B 21 HIS 0.005 0.002 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9565) covalent geometry : angle 0.73365 (12951) hydrogen bonds : bond 0.07484 ( 466) hydrogen bonds : angle 6.16362 ( 1362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 337 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.9299 (tp) cc_final: 0.8492 (tp) REVERT: A 35 GLN cc_start: 0.8989 (mt0) cc_final: 0.8602 (mp10) REVERT: A 76 ASP cc_start: 0.8339 (m-30) cc_final: 0.8058 (m-30) REVERT: A 96 LYS cc_start: 0.7726 (mttt) cc_final: 0.6861 (mtmt) REVERT: A 110 ILE cc_start: 0.8675 (mm) cc_final: 0.8377 (tp) REVERT: A 157 LEU cc_start: 0.9205 (mt) cc_final: 0.8728 (tp) REVERT: A 182 VAL cc_start: 0.8004 (m) cc_final: 0.7801 (m) REVERT: A 237 SER cc_start: 0.9176 (m) cc_final: 0.8768 (p) REVERT: A 243 ARG cc_start: 0.8028 (mtm110) cc_final: 0.7825 (mtm-85) REVERT: A 255 PHE cc_start: 0.8602 (t80) cc_final: 0.8174 (t80) REVERT: A 302 MET cc_start: 0.8956 (mtp) cc_final: 0.8562 (mtm) REVERT: A 313 MET cc_start: 0.8416 (mmm) cc_final: 0.8056 (mmm) REVERT: A 341 ILE cc_start: 0.7962 (mm) cc_final: 0.7695 (mm) REVERT: A 377 MET cc_start: 0.7462 (ttm) cc_final: 0.6369 (tmm) REVERT: A 378 LEU cc_start: 0.9189 (mt) cc_final: 0.8918 (mp) REVERT: A 415 GLU cc_start: 0.7910 (pp20) cc_final: 0.7240 (tm-30) REVERT: B 161 ASP cc_start: 0.9248 (t0) cc_final: 0.8926 (t70) REVERT: B 211 CYS cc_start: 0.9287 (t) cc_final: 0.8968 (p) REVERT: B 300 MET cc_start: 0.8566 (mtt) cc_final: 0.8153 (mtm) REVERT: K 52 VAL cc_start: 0.8967 (t) cc_final: 0.7768 (t) REVERT: K 88 TYR cc_start: 0.8929 (t80) cc_final: 0.8687 (t80) REVERT: K 272 PHE cc_start: 0.8095 (t80) cc_final: 0.7612 (t80) REVERT: K 386 ASP cc_start: 0.8188 (t0) cc_final: 0.7905 (t0) outliers start: 1 outliers final: 0 residues processed: 338 average time/residue: 0.2630 time to fit residues: 117.5475 Evaluate side-chains 263 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 1 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 76 optimal weight: 0.5980 chunk 92 optimal weight: 30.0000 chunk 105 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.076569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.064204 restraints weight = 101064.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.067676 restraints weight = 42870.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.069823 restraints weight = 22207.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.071215 restraints weight = 13131.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072031 restraints weight = 8539.226| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.6483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9565 Z= 0.176 Angle : 0.621 6.705 12951 Z= 0.350 Chirality : 0.044 0.219 1443 Planarity : 0.005 0.052 1668 Dihedral : 10.558 173.054 1324 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.49 (0.25), residues: 1159 helix: 0.78 (0.23), residues: 490 sheet: -0.28 (0.37), residues: 207 loop : 0.35 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 347 TYR 0.033 0.002 TYR B 422 PHE 0.018 0.002 PHE K 166 TRP 0.009 0.001 TRP A 21 HIS 0.008 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9565) covalent geometry : angle 0.62145 (12951) hydrogen bonds : bond 0.06093 ( 466) hydrogen bonds : angle 5.70435 ( 1362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.9360 (tp) cc_final: 0.9094 (tp) REVERT: A 35 GLN cc_start: 0.9062 (mt0) cc_final: 0.8809 (mp10) REVERT: A 53 PHE cc_start: 0.7823 (m-10) cc_final: 0.7564 (m-10) REVERT: A 70 LEU cc_start: 0.7508 (mt) cc_final: 0.7242 (mp) REVERT: A 96 LYS cc_start: 0.7610 (mttt) cc_final: 0.6933 (mtmt) REVERT: A 109 THR cc_start: 0.8039 (m) cc_final: 0.7512 (p) REVERT: A 110 ILE cc_start: 0.8703 (mm) cc_final: 0.8497 (tp) REVERT: A 237 SER cc_start: 0.8983 (m) cc_final: 0.8637 (p) REVERT: A 243 ARG cc_start: 0.7740 (mtm110) cc_final: 0.7213 (mtm110) REVERT: A 295 CYS cc_start: 0.8928 (m) cc_final: 0.8322 (m) REVERT: A 313 MET cc_start: 0.8382 (mmm) cc_final: 0.8092 (mmm) REVERT: A 339 ARG cc_start: 0.8306 (tpp80) cc_final: 0.7989 (tpp-160) REVERT: A 352 LYS cc_start: 0.1709 (mmtt) cc_final: 0.1365 (mmtm) REVERT: A 420 GLU cc_start: 0.8336 (pm20) cc_final: 0.8111 (mp0) REVERT: B 12 CYS cc_start: 0.7177 (t) cc_final: 0.6780 (t) REVERT: B 147 MET cc_start: 0.8410 (tpp) cc_final: 0.8193 (tpp) REVERT: B 257 MET cc_start: 0.8836 (mmm) cc_final: 0.8592 (tpp) REVERT: B 300 MET cc_start: 0.8527 (mtt) cc_final: 0.8178 (mtm) REVERT: K 88 TYR cc_start: 0.8820 (t80) cc_final: 0.8513 (t80) REVERT: K 332 ARG cc_start: 0.9376 (ttm110) cc_final: 0.9079 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2565 time to fit residues: 101.2406 Evaluate side-chains 236 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 114 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 56 optimal weight: 30.0000 chunk 100 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 84 optimal weight: 50.0000 chunk 99 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.074439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.062291 restraints weight = 102910.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.065636 restraints weight = 43217.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.067718 restraints weight = 22427.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069022 restraints weight = 13236.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.069858 restraints weight = 8672.274| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.7070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9565 Z= 0.160 Angle : 0.575 6.852 12951 Z= 0.319 Chirality : 0.043 0.206 1443 Planarity : 0.004 0.043 1668 Dihedral : 10.324 177.808 1324 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.29 % Rotamer: Outliers : 0.10 % Allowed : 0.68 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.34 (0.25), residues: 1159 helix: 0.82 (0.23), residues: 496 sheet: -0.47 (0.36), residues: 207 loop : 0.11 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 347 TYR 0.013 0.002 TYR K 197 PHE 0.013 0.001 PHE A 149 TRP 0.009 0.001 TRP A 346 HIS 0.005 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9565) covalent geometry : angle 0.57544 (12951) hydrogen bonds : bond 0.05379 ( 466) hydrogen bonds : angle 5.37863 ( 1362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 277 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.9093 (mt0) cc_final: 0.8810 (mp10) REVERT: A 70 LEU cc_start: 0.7655 (mt) cc_final: 0.7227 (mp) REVERT: A 71 GLU cc_start: 0.8097 (tt0) cc_final: 0.7622 (pt0) REVERT: A 96 LYS cc_start: 0.7501 (mttt) cc_final: 0.6964 (mtmt) REVERT: A 101 ASN cc_start: 0.8280 (t0) cc_final: 0.7726 (t0) REVERT: A 109 THR cc_start: 0.8084 (m) cc_final: 0.7542 (p) REVERT: A 295 CYS cc_start: 0.8871 (m) cc_final: 0.8324 (m) REVERT: A 313 MET cc_start: 0.8092 (mmm) cc_final: 0.7692 (mmt) REVERT: A 352 LYS cc_start: 0.1623 (mmtt) cc_final: 0.1231 (mmtm) REVERT: A 413 MET cc_start: 0.6136 (ttt) cc_final: 0.5587 (ttt) REVERT: B 6 HIS cc_start: 0.8490 (t-170) cc_final: 0.8200 (t-170) REVERT: B 12 CYS cc_start: 0.7136 (t) cc_final: 0.6765 (t) REVERT: B 108 GLU cc_start: 0.8614 (mp0) cc_final: 0.8408 (mp0) REVERT: B 257 MET cc_start: 0.8840 (mmm) cc_final: 0.8543 (mmt) REVERT: B 267 MET cc_start: 0.8185 (mtt) cc_final: 0.7923 (mpp) REVERT: B 325 GLU cc_start: 0.9132 (tp30) cc_final: 0.8818 (tp30) REVERT: K 88 TYR cc_start: 0.8678 (t80) cc_final: 0.8403 (t80) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.2468 time to fit residues: 91.1686 Evaluate side-chains 231 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 5 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 60 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 84 optimal weight: 40.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.073432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.061206 restraints weight = 103069.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.064463 restraints weight = 43787.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.066551 restraints weight = 23138.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.067836 restraints weight = 13820.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.068720 restraints weight = 9188.582| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.7459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9565 Z= 0.167 Angle : 0.561 8.026 12951 Z= 0.312 Chirality : 0.042 0.207 1443 Planarity : 0.004 0.042 1668 Dihedral : 10.191 176.288 1324 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1159 helix: 0.79 (0.22), residues: 502 sheet: -0.58 (0.36), residues: 207 loop : -0.01 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 276 TYR 0.036 0.002 TYR K 346 PHE 0.012 0.001 PHE K 366 TRP 0.008 0.001 TRP B 21 HIS 0.005 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9565) covalent geometry : angle 0.56107 (12951) hydrogen bonds : bond 0.05147 ( 466) hydrogen bonds : angle 5.27045 ( 1362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5928 (ptm) cc_final: 0.5602 (ptm) REVERT: A 35 GLN cc_start: 0.9053 (mt0) cc_final: 0.8724 (mp10) REVERT: A 36 MET cc_start: 0.8270 (ptm) cc_final: 0.7808 (ppp) REVERT: A 71 GLU cc_start: 0.8109 (tt0) cc_final: 0.7708 (tt0) REVERT: A 76 ASP cc_start: 0.8476 (m-30) cc_final: 0.8258 (m-30) REVERT: A 96 LYS cc_start: 0.7742 (mttt) cc_final: 0.7184 (mtmt) REVERT: A 101 ASN cc_start: 0.8340 (t0) cc_final: 0.7979 (t0) REVERT: A 109 THR cc_start: 0.7992 (m) cc_final: 0.7663 (p) REVERT: A 182 VAL cc_start: 0.7961 (m) cc_final: 0.7687 (m) REVERT: A 295 CYS cc_start: 0.8960 (m) cc_final: 0.8373 (m) REVERT: A 313 MET cc_start: 0.8376 (mmm) cc_final: 0.7904 (mmt) REVERT: A 352 LYS cc_start: 0.1704 (mmtt) cc_final: 0.1212 (mmtm) REVERT: B 12 CYS cc_start: 0.7348 (t) cc_final: 0.7126 (t) REVERT: B 19 LYS cc_start: 0.9235 (mmmt) cc_final: 0.8865 (mmmm) REVERT: B 267 MET cc_start: 0.8211 (mtt) cc_final: 0.7910 (mpp) REVERT: B 325 GLU cc_start: 0.9110 (tp30) cc_final: 0.8547 (tp30) REVERT: B 350 LYS cc_start: 0.9076 (tmtt) cc_final: 0.8700 (tmtt) REVERT: K 88 TYR cc_start: 0.8579 (t80) cc_final: 0.8247 (t80) REVERT: K 246 ILE cc_start: 0.9173 (mt) cc_final: 0.8786 (tp) REVERT: K 295 ASN cc_start: 0.8590 (m110) cc_final: 0.8284 (m110) REVERT: K 339 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8572 (tm-30) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2323 time to fit residues: 85.1418 Evaluate side-chains 222 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 65 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 104 optimal weight: 30.0000 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.070396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.058585 restraints weight = 105105.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.061696 restraints weight = 44561.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.063623 restraints weight = 23531.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.064924 restraints weight = 14131.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.065665 restraints weight = 9343.938| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.7951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9565 Z= 0.221 Angle : 0.605 5.800 12951 Z= 0.339 Chirality : 0.042 0.213 1443 Planarity : 0.005 0.046 1668 Dihedral : 10.006 173.805 1324 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.19 (0.24), residues: 1159 helix: 0.54 (0.22), residues: 503 sheet: -0.82 (0.36), residues: 209 loop : -0.34 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 276 TYR 0.034 0.002 TYR B 422 PHE 0.025 0.002 PHE B 265 TRP 0.009 0.001 TRP B 21 HIS 0.010 0.002 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 9565) covalent geometry : angle 0.60517 (12951) hydrogen bonds : bond 0.05203 ( 466) hydrogen bonds : angle 5.31707 ( 1362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.8358 (ptm) cc_final: 0.7801 (ppp) REVERT: A 76 ASP cc_start: 0.8568 (m-30) cc_final: 0.8325 (m-30) REVERT: A 96 LYS cc_start: 0.7864 (mttt) cc_final: 0.7241 (mtmt) REVERT: A 101 ASN cc_start: 0.8397 (t0) cc_final: 0.8146 (t0) REVERT: A 109 THR cc_start: 0.8007 (m) cc_final: 0.7726 (p) REVERT: A 182 VAL cc_start: 0.8045 (m) cc_final: 0.7790 (m) REVERT: A 237 SER cc_start: 0.9022 (m) cc_final: 0.8676 (p) REVERT: A 295 CYS cc_start: 0.9147 (m) cc_final: 0.8522 (m) REVERT: A 313 MET cc_start: 0.8525 (mmm) cc_final: 0.8019 (mmt) REVERT: A 352 LYS cc_start: 0.1742 (mmtt) cc_final: 0.1483 (mmtt) REVERT: A 376 CYS cc_start: 0.8832 (t) cc_final: 0.8187 (t) REVERT: A 398 MET cc_start: 0.8045 (mmm) cc_final: 0.7426 (mtt) REVERT: A 413 MET cc_start: 0.6469 (ttt) cc_final: 0.5855 (ttt) REVERT: B 19 LYS cc_start: 0.9260 (mmmt) cc_final: 0.8871 (mmmm) REVERT: B 20 PHE cc_start: 0.9070 (t80) cc_final: 0.8849 (t80) REVERT: B 257 MET cc_start: 0.8826 (mmm) cc_final: 0.8521 (mmt) REVERT: B 267 MET cc_start: 0.8273 (mtt) cc_final: 0.7992 (mpp) REVERT: B 325 GLU cc_start: 0.9192 (tp30) cc_final: 0.8672 (tp30) REVERT: K 88 TYR cc_start: 0.8571 (t80) cc_final: 0.8214 (t80) REVERT: K 295 ASN cc_start: 0.8789 (m110) cc_final: 0.8471 (m110) REVERT: K 332 ARG cc_start: 0.9212 (ttm110) cc_final: 0.8998 (ttp80) REVERT: K 348 ASP cc_start: 0.7570 (m-30) cc_final: 0.6807 (m-30) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2280 time to fit residues: 81.3419 Evaluate side-chains 213 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 9.9990 chunk 59 optimal weight: 0.4980 chunk 72 optimal weight: 30.0000 chunk 67 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS K 107 GLN K 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.071166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.059285 restraints weight = 105518.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.062443 restraints weight = 44468.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.064398 restraints weight = 23274.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.065657 restraints weight = 13981.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.066416 restraints weight = 9290.840| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.8222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9565 Z= 0.152 Angle : 0.554 6.606 12951 Z= 0.305 Chirality : 0.042 0.211 1443 Planarity : 0.004 0.046 1668 Dihedral : 9.720 171.232 1324 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.24), residues: 1159 helix: 0.76 (0.22), residues: 511 sheet: -0.66 (0.36), residues: 206 loop : -0.30 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 2 TYR 0.026 0.002 TYR K 346 PHE 0.013 0.001 PHE K 187 TRP 0.008 0.001 TRP B 21 HIS 0.012 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9565) covalent geometry : angle 0.55355 (12951) hydrogen bonds : bond 0.04894 ( 466) hydrogen bonds : angle 5.09658 ( 1362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.8524 (m-30) cc_final: 0.8266 (m-30) REVERT: A 96 LYS cc_start: 0.7883 (mttt) cc_final: 0.7238 (mtmt) REVERT: A 109 THR cc_start: 0.7986 (m) cc_final: 0.7719 (p) REVERT: A 129 CYS cc_start: 0.7760 (p) cc_final: 0.7537 (p) REVERT: A 182 VAL cc_start: 0.7959 (m) cc_final: 0.7708 (m) REVERT: A 237 SER cc_start: 0.8979 (m) cc_final: 0.8545 (p) REVERT: A 295 CYS cc_start: 0.9149 (m) cc_final: 0.8482 (m) REVERT: A 313 MET cc_start: 0.8516 (mmm) cc_final: 0.8240 (mmm) REVERT: A 315 CYS cc_start: 0.9036 (t) cc_final: 0.8642 (t) REVERT: A 376 CYS cc_start: 0.8737 (t) cc_final: 0.7998 (t) REVERT: A 398 MET cc_start: 0.8043 (mmm) cc_final: 0.7500 (mtt) REVERT: B 20 PHE cc_start: 0.9099 (t80) cc_final: 0.8894 (t80) REVERT: B 200 TYR cc_start: 0.7513 (m-80) cc_final: 0.7267 (m-10) REVERT: B 257 MET cc_start: 0.8842 (mmm) cc_final: 0.8561 (mmt) REVERT: B 266 PHE cc_start: 0.8476 (m-10) cc_final: 0.8071 (m-10) REVERT: B 267 MET cc_start: 0.8232 (mtt) cc_final: 0.7823 (mpp) REVERT: B 325 GLU cc_start: 0.9122 (tp30) cc_final: 0.8511 (tp30) REVERT: K 88 TYR cc_start: 0.8471 (t80) cc_final: 0.8153 (t80) REVERT: K 204 LEU cc_start: 0.8361 (tp) cc_final: 0.8131 (tp) REVERT: K 295 ASN cc_start: 0.8746 (m110) cc_final: 0.8369 (m110) REVERT: K 332 ARG cc_start: 0.9188 (ttm110) cc_final: 0.8979 (ttp80) REVERT: K 339 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8371 (tm-30) REVERT: K 348 ASP cc_start: 0.7759 (m-30) cc_final: 0.6952 (m-30) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.2355 time to fit residues: 84.9052 Evaluate side-chains 219 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 72 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 overall best weight: 11.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS K 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.067982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.056514 restraints weight = 108346.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.059557 restraints weight = 45948.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.061459 restraints weight = 24222.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.062712 restraints weight = 14512.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.063510 restraints weight = 9589.103| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.8726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 9565 Z= 0.259 Angle : 0.641 6.514 12951 Z= 0.359 Chirality : 0.043 0.228 1443 Planarity : 0.005 0.061 1668 Dihedral : 9.903 169.251 1324 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.69 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.51 (0.24), residues: 1159 helix: 0.22 (0.21), residues: 515 sheet: -0.89 (0.36), residues: 206 loop : -0.52 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 264 TYR 0.036 0.002 TYR A 432 PHE 0.015 0.002 PHE B 92 TRP 0.014 0.002 TRP A 388 HIS 0.009 0.002 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 9565) covalent geometry : angle 0.64137 (12951) hydrogen bonds : bond 0.05108 ( 466) hydrogen bonds : angle 5.41764 ( 1362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.8628 (m-30) cc_final: 0.8376 (m-30) REVERT: A 96 LYS cc_start: 0.7881 (mttt) cc_final: 0.7282 (mtmt) REVERT: A 101 ASN cc_start: 0.8619 (t0) cc_final: 0.8293 (t0) REVERT: A 109 THR cc_start: 0.8088 (m) cc_final: 0.7807 (p) REVERT: A 182 VAL cc_start: 0.8055 (m) cc_final: 0.7811 (m) REVERT: A 237 SER cc_start: 0.8964 (m) cc_final: 0.8616 (p) REVERT: A 295 CYS cc_start: 0.9167 (m) cc_final: 0.8503 (m) REVERT: A 313 MET cc_start: 0.8586 (mmm) cc_final: 0.8135 (mmt) REVERT: A 315 CYS cc_start: 0.9031 (t) cc_final: 0.8694 (t) REVERT: A 376 CYS cc_start: 0.8718 (t) cc_final: 0.8012 (t) REVERT: A 398 MET cc_start: 0.8242 (mmm) cc_final: 0.7625 (mtt) REVERT: B 20 PHE cc_start: 0.9179 (t80) cc_final: 0.8972 (t80) REVERT: B 179 VAL cc_start: 0.8951 (m) cc_final: 0.8553 (p) REVERT: B 257 MET cc_start: 0.8709 (mmm) cc_final: 0.8480 (mmt) REVERT: B 267 MET cc_start: 0.8255 (mtt) cc_final: 0.7884 (mpp) REVERT: B 325 GLU cc_start: 0.9182 (tp30) cc_final: 0.8653 (tp30) REVERT: K 88 TYR cc_start: 0.8449 (t80) cc_final: 0.8046 (t80) REVERT: K 204 LEU cc_start: 0.8531 (tp) cc_final: 0.8290 (tp) REVERT: K 295 ASN cc_start: 0.8723 (m110) cc_final: 0.8483 (m110) REVERT: K 304 ASN cc_start: 0.8882 (t0) cc_final: 0.8653 (t0) REVERT: K 339 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8456 (tm-30) REVERT: K 348 ASP cc_start: 0.7629 (m-30) cc_final: 0.6986 (m-30) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2314 time to fit residues: 74.8710 Evaluate side-chains 205 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 102 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.069425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.057716 restraints weight = 106469.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.060795 restraints weight = 45347.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.062683 restraints weight = 23889.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.063924 restraints weight = 14392.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.064735 restraints weight = 9584.445| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.8832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9565 Z= 0.160 Angle : 0.573 6.388 12951 Z= 0.315 Chirality : 0.043 0.213 1443 Planarity : 0.005 0.054 1668 Dihedral : 9.682 165.704 1324 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.24), residues: 1159 helix: 0.68 (0.22), residues: 510 sheet: -0.92 (0.36), residues: 206 loop : -0.50 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 2 TYR 0.044 0.002 TYR K 193 PHE 0.041 0.002 PHE K 272 TRP 0.008 0.001 TRP B 21 HIS 0.010 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9565) covalent geometry : angle 0.57312 (12951) hydrogen bonds : bond 0.04804 ( 466) hydrogen bonds : angle 5.16680 ( 1362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 CYS cc_start: 0.8509 (m) cc_final: 0.8305 (m) REVERT: A 76 ASP cc_start: 0.8504 (m-30) cc_final: 0.8221 (m-30) REVERT: A 96 LYS cc_start: 0.7845 (mttt) cc_final: 0.7237 (mtmt) REVERT: A 101 ASN cc_start: 0.8584 (t0) cc_final: 0.8159 (t0) REVERT: A 109 THR cc_start: 0.8006 (m) cc_final: 0.7745 (p) REVERT: A 182 VAL cc_start: 0.7967 (m) cc_final: 0.7680 (m) REVERT: A 237 SER cc_start: 0.8957 (m) cc_final: 0.8594 (p) REVERT: A 295 CYS cc_start: 0.9128 (m) cc_final: 0.8442 (m) REVERT: A 313 MET cc_start: 0.8562 (mmm) cc_final: 0.8113 (mmt) REVERT: A 315 CYS cc_start: 0.9055 (t) cc_final: 0.8644 (t) REVERT: A 339 ARG cc_start: 0.8407 (tpp-160) cc_final: 0.7809 (tpp-160) REVERT: A 349 THR cc_start: 0.8832 (p) cc_final: 0.8630 (p) REVERT: A 376 CYS cc_start: 0.8451 (t) cc_final: 0.7482 (t) REVERT: A 398 MET cc_start: 0.8153 (mmm) cc_final: 0.7557 (mtt) REVERT: B 20 PHE cc_start: 0.9122 (t80) cc_final: 0.8920 (t80) REVERT: B 22 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8410 (tm-30) REVERT: B 179 VAL cc_start: 0.8957 (m) cc_final: 0.8529 (p) REVERT: B 257 MET cc_start: 0.8628 (mmm) cc_final: 0.8302 (mmt) REVERT: B 266 PHE cc_start: 0.8416 (m-10) cc_final: 0.8178 (m-10) REVERT: B 267 MET cc_start: 0.8170 (mtt) cc_final: 0.7653 (mpp) REVERT: B 325 GLU cc_start: 0.9098 (tp30) cc_final: 0.8459 (tp30) REVERT: B 404 ASP cc_start: 0.8601 (t0) cc_final: 0.8396 (t0) REVERT: K 88 TYR cc_start: 0.8363 (t80) cc_final: 0.8038 (t80) REVERT: K 204 LEU cc_start: 0.8374 (tp) cc_final: 0.8072 (tp) REVERT: K 295 ASN cc_start: 0.8820 (m110) cc_final: 0.8554 (m110) REVERT: K 304 ASN cc_start: 0.8867 (t0) cc_final: 0.8627 (t0) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.2210 time to fit residues: 74.8582 Evaluate side-chains 215 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 chunk 88 optimal weight: 0.0050 chunk 93 optimal weight: 40.0000 chunk 61 optimal weight: 8.9990 chunk 40 optimal weight: 30.0000 chunk 94 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN K 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.069642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.057820 restraints weight = 106505.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.060961 restraints weight = 45455.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.062931 restraints weight = 23924.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.064133 restraints weight = 14300.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.064963 restraints weight = 9617.741| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.8966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9565 Z= 0.142 Angle : 0.557 6.283 12951 Z= 0.304 Chirality : 0.042 0.204 1443 Planarity : 0.004 0.044 1668 Dihedral : 9.356 164.059 1324 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.03 (0.24), residues: 1159 helix: 0.90 (0.22), residues: 510 sheet: -0.83 (0.37), residues: 191 loop : -0.45 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 2 TYR 0.023 0.002 TYR K 193 PHE 0.040 0.001 PHE K 272 TRP 0.008 0.001 TRP A 346 HIS 0.009 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9565) covalent geometry : angle 0.55673 (12951) hydrogen bonds : bond 0.04588 ( 466) hydrogen bonds : angle 5.09064 ( 1362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 CYS cc_start: 0.8526 (m) cc_final: 0.8290 (m) REVERT: A 96 LYS cc_start: 0.7863 (mttt) cc_final: 0.7103 (mtmt) REVERT: A 101 ASN cc_start: 0.8590 (t0) cc_final: 0.8092 (t0) REVERT: A 109 THR cc_start: 0.8063 (m) cc_final: 0.7803 (p) REVERT: A 182 VAL cc_start: 0.7952 (m) cc_final: 0.7601 (m) REVERT: A 215 ARG cc_start: 0.8658 (ttp80) cc_final: 0.8443 (ttp80) REVERT: A 237 SER cc_start: 0.9008 (m) cc_final: 0.8624 (p) REVERT: A 295 CYS cc_start: 0.9109 (m) cc_final: 0.8411 (m) REVERT: A 313 MET cc_start: 0.8563 (mmm) cc_final: 0.8115 (mmt) REVERT: A 315 CYS cc_start: 0.9012 (t) cc_final: 0.8619 (t) REVERT: A 339 ARG cc_start: 0.8445 (tpp-160) cc_final: 0.7874 (tpp-160) REVERT: A 376 CYS cc_start: 0.8706 (t) cc_final: 0.7864 (t) REVERT: A 398 MET cc_start: 0.8145 (mmm) cc_final: 0.7531 (mtt) REVERT: B 19 LYS cc_start: 0.9315 (mmmm) cc_final: 0.9075 (mmmm) REVERT: B 22 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8373 (tm-30) REVERT: B 74 ASP cc_start: 0.9166 (t0) cc_final: 0.8940 (t0) REVERT: B 179 VAL cc_start: 0.8933 (m) cc_final: 0.8510 (p) REVERT: B 257 MET cc_start: 0.8628 (mmm) cc_final: 0.8355 (mmt) REVERT: B 266 PHE cc_start: 0.8374 (m-10) cc_final: 0.8167 (m-10) REVERT: B 267 MET cc_start: 0.8180 (mtt) cc_final: 0.7763 (mpp) REVERT: B 325 GLU cc_start: 0.9112 (tp30) cc_final: 0.8481 (tp30) REVERT: K 88 TYR cc_start: 0.8359 (t80) cc_final: 0.8037 (t80) REVERT: K 204 LEU cc_start: 0.8350 (tp) cc_final: 0.7984 (tp) REVERT: K 295 ASN cc_start: 0.8670 (m110) cc_final: 0.8323 (m110) REVERT: K 339 GLU cc_start: 0.9207 (pt0) cc_final: 0.8856 (tm-30) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2224 time to fit residues: 75.9403 Evaluate side-chains 209 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 76 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN K 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.069300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.057762 restraints weight = 107021.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.060778 restraints weight = 46048.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.062669 restraints weight = 24361.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.063819 restraints weight = 14582.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.064598 restraints weight = 9830.459| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.9167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9565 Z= 0.169 Angle : 0.572 6.251 12951 Z= 0.318 Chirality : 0.042 0.203 1443 Planarity : 0.004 0.043 1668 Dihedral : 9.233 159.185 1324 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.11 (0.24), residues: 1159 helix: 0.77 (0.22), residues: 515 sheet: -0.93 (0.36), residues: 200 loop : -0.50 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 254 TYR 0.030 0.002 TYR A 172 PHE 0.034 0.002 PHE K 272 TRP 0.026 0.002 TRP B 21 HIS 0.012 0.002 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9565) covalent geometry : angle 0.57173 (12951) hydrogen bonds : bond 0.04711 ( 466) hydrogen bonds : angle 5.12665 ( 1362) =============================================================================== Job complete usr+sys time: 2966.96 seconds wall clock time: 51 minutes 59.21 seconds (3119.21 seconds total)