Starting phenix.real_space_refine on Sat Jul 4 05:32:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nb8_12257/07_2026/7nb8_12257.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nb8_12257/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7nb8_12257/07_2026/7nb8_12257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nb8_12257/07_2026/7nb8_12257.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7nb8_12257/07_2026/7nb8_12257.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nb8_12257/07_2026/7nb8_12257.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nb8_12257/07_2026/7nb8_12257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nb8_12257/07_2026/7nb8_12257.map" } 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-6108/lib/python3.11/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: 3.40, per 1000 atoms: 0.18 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: 1.87 Conformation dependent library (CDL) restraints added in 640.7 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: 0.48 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: 4.46 Time building geometry restraints manager: 2.50 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: 8632 33.42 - 66.84: 181 66.84 - 100.26: 14 100.26 - 133.68: 1 133.68 - 167.09: 2 Dihedral angle restraints: 8830 sinusoidal: 4820 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 8827 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: 0.010 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: 0.130 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.020 Process input model: 19.580 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 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 : 11.876 167.095 3542 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/Z covalent geometry : bond 0.01827 / 0.98 ( 9565) covalent geometry : angle 1.78785 / 1.19 (12951) hydrogen bonds : bond 0.18037 / 12.06 ( 466) hydrogen bonds : angle 7.87357 / 5.59 ( 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 : 0.645 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: A 23 LEU cc_start: 0.8950 (tp) cc_final: 0.8150 (tp) REVERT: A 96 LYS cc_start: 0.7976 (mttt) cc_final: 0.7023 (mtmt) REVERT: A 110 ILE cc_start: 0.8726 (mm) cc_final: 0.8432 (tp) REVERT: A 132 LEU cc_start: 0.8982 (tp) cc_final: 0.8490 (tp) REVERT: A 139 HIS cc_start: 0.7696 (p-80) cc_final: 0.7461 (p90) REVERT: A 189 LEU cc_start: 0.9547 (mt) cc_final: 0.9279 (mt) REVERT: A 235 VAL cc_start: 0.9340 (t) cc_final: 0.8964 (p) REVERT: A 292 THR cc_start: 0.8703 (m) cc_final: 0.8226 (p) REVERT: A 295 CYS cc_start: 0.8700 (m) cc_final: 0.7892 (m) REVERT: A 377 MET cc_start: 0.7876 (ttm) cc_final: 0.6758 (tmm) REVERT: A 417 GLU cc_start: 0.8836 (mt-10) cc_final: 0.7382 (tt0) REVERT: B 135 LEU cc_start: 0.7416 (mp) cc_final: 0.7198 (mp) REVERT: B 150 LEU cc_start: 0.9107 (tp) cc_final: 0.8732 (tt) REVERT: B 267 MET cc_start: 0.7961 (mtt) cc_final: 0.7686 (mmm) REVERT: B 350 LYS cc_start: 0.8757 (tptp) cc_final: 0.8541 (tptp) REVERT: B 377 LEU cc_start: 0.8661 (tp) cc_final: 0.8054 (tp) REVERT: B 407 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7443 (mt-10) REVERT: K 227 LEU cc_start: 0.7593 (tp) cc_final: 0.7336 (tp) outliers start: 1 outliers final: 1 residues processed: 517 average time/residue: 0.3030 time to fit residues: 203.4131 Evaluate side-chains 302 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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: 10.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 ASN A 309 HIS ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS K 188 ASN ** K 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.078284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.065312 restraints weight = 99864.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.069066 restraints weight = 41873.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.071388 restraints weight = 21490.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.072862 restraints weight = 12568.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.073815 restraints weight = 8147.388| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9565 Z= 0.226 Angle : 0.738 8.897 12951 Z= 0.427 Chirality : 0.047 0.236 1443 Planarity : 0.006 0.060 1668 Dihedral : 10.215 171.635 1296 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.67 % Favored : 97.24 % 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: 0.37 (0.25), residues: 1159 helix: 0.57 (0.22), residues: 488 sheet: -0.16 (0.37), residues: 210 loop : 0.33 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 347 TYR 0.022 0.002 TYR K 88 PHE 0.018 0.002 PHE A 149 TRP 0.008 0.001 TRP B 21 HIS 0.005 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.23 ( 9565) covalent geometry : angle 0.73801 / 0.43 (12951) hydrogen bonds : bond 0.07846 / 5.30 ( 466) hydrogen bonds : angle 6.21739 / 4.40 ( 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 344 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 343 time to evaluate : 0.537 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: A 35 GLN cc_start: 0.9012 (mt0) cc_final: 0.8611 (mp10) REVERT: A 76 ASP cc_start: 0.8438 (m-30) cc_final: 0.8168 (m-30) REVERT: A 96 LYS cc_start: 0.7646 (mttt) cc_final: 0.6806 (mtmt) REVERT: A 110 ILE cc_start: 0.8614 (mm) cc_final: 0.8327 (tp) REVERT: A 157 LEU cc_start: 0.9172 (mt) cc_final: 0.8730 (tp) REVERT: A 172 TYR cc_start: 0.5827 (m-80) cc_final: 0.5176 (m-80) REVERT: A 237 SER cc_start: 0.9186 (m) cc_final: 0.8768 (p) REVERT: A 255 PHE cc_start: 0.8608 (t80) cc_final: 0.8180 (t80) REVERT: A 301 GLN cc_start: 0.8316 (mm110) cc_final: 0.8061 (mm110) REVERT: A 302 MET cc_start: 0.8976 (mtp) cc_final: 0.8517 (mtm) REVERT: A 313 MET cc_start: 0.8403 (mmm) cc_final: 0.8044 (mmm) REVERT: A 341 ILE cc_start: 0.7968 (mm) cc_final: 0.7720 (mm) REVERT: A 377 MET cc_start: 0.7472 (ttm) cc_final: 0.6395 (tmm) REVERT: A 378 LEU cc_start: 0.9170 (mt) cc_final: 0.8949 (mp) REVERT: A 415 GLU cc_start: 0.7848 (pp20) cc_final: 0.7217 (tm-30) REVERT: B 161 ASP cc_start: 0.9273 (t0) cc_final: 0.8941 (t70) REVERT: B 211 CYS cc_start: 0.9307 (t) cc_final: 0.8915 (p) REVERT: B 300 MET cc_start: 0.8444 (mtt) cc_final: 0.8098 (mtm) REVERT: K 52 VAL cc_start: 0.9003 (t) cc_final: 0.8171 (t) REVERT: K 69 PHE cc_start: 0.8061 (m-80) cc_final: 0.7814 (m-80) REVERT: K 88 TYR cc_start: 0.9023 (t80) cc_final: 0.8785 (t80) REVERT: K 191 ILE cc_start: 0.9392 (pt) cc_final: 0.9178 (mm) REVERT: K 246 ILE cc_start: 0.9178 (mt) cc_final: 0.8902 (tp) REVERT: K 272 PHE cc_start: 0.8170 (t80) cc_final: 0.7567 (t80) REVERT: K 296 LEU cc_start: 0.9170 (mt) cc_final: 0.8962 (mt) REVERT: K 386 ASP cc_start: 0.8175 (t0) cc_final: 0.7905 (t0) outliers start: 1 outliers final: 0 residues processed: 344 average time/residue: 0.2681 time to fit residues: 123.5815 Evaluate side-chains 255 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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: 9.9990 chunk 20 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 93 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN B 190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.075428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.063204 restraints weight = 102244.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.066696 restraints weight = 43692.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.068874 restraints weight = 22754.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.070199 restraints weight = 13394.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.071103 restraints weight = 8796.594| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.6424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9565 Z= 0.200 Angle : 0.630 6.900 12951 Z= 0.358 Chirality : 0.044 0.223 1443 Planarity : 0.005 0.053 1668 Dihedral : 9.944 176.519 1296 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.19 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: 0.61 (0.23), residues: 491 sheet: -0.25 (0.37), residues: 207 loop : 0.27 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 243 TYR 0.036 0.002 TYR B 422 PHE 0.017 0.002 PHE K 166 TRP 0.009 0.001 TRP B 21 HIS 0.008 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.20 ( 9565) covalent geometry : angle 0.62986 / 0.36 (12951) hydrogen bonds : bond 0.06286 / 4.25 ( 466) hydrogen bonds : angle 5.77627 / 4.05 ( 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 296 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.515 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: A 23 LEU cc_start: 0.9310 (tp) cc_final: 0.9093 (tp) REVERT: A 35 GLN cc_start: 0.9028 (mt0) cc_final: 0.8799 (mp10) REVERT: A 53 PHE cc_start: 0.7817 (m-10) cc_final: 0.7612 (m-10) REVERT: A 70 LEU cc_start: 0.7546 (mt) cc_final: 0.7303 (mp) REVERT: A 96 LYS cc_start: 0.7608 (mttt) cc_final: 0.6959 (mtmt) REVERT: A 109 THR cc_start: 0.8151 (m) cc_final: 0.7595 (p) REVERT: A 110 ILE cc_start: 0.8744 (mm) cc_final: 0.8533 (tp) REVERT: A 237 SER cc_start: 0.9037 (m) cc_final: 0.8681 (p) REVERT: A 295 CYS cc_start: 0.8908 (m) cc_final: 0.8383 (m) REVERT: A 301 GLN cc_start: 0.8444 (mm110) cc_final: 0.8236 (mm110) REVERT: A 313 MET cc_start: 0.8412 (mmm) cc_final: 0.8122 (mmm) REVERT: A 352 LYS cc_start: 0.1845 (mmtt) cc_final: 0.1486 (mmtm) REVERT: A 413 MET cc_start: 0.5937 (ttt) cc_final: 0.5367 (ttt) REVERT: A 420 GLU cc_start: 0.8306 (pm20) cc_final: 0.8102 (mp0) REVERT: B 12 CYS cc_start: 0.7314 (t) cc_final: 0.7010 (t) REVERT: B 181 GLU cc_start: 0.8795 (tt0) cc_final: 0.8576 (tt0) REVERT: B 299 MET cc_start: 0.8636 (mmp) cc_final: 0.8326 (mmm) REVERT: B 300 MET cc_start: 0.8539 (mtt) cc_final: 0.8230 (mtm) REVERT: K 88 TYR cc_start: 0.8762 (t80) cc_final: 0.8464 (t80) REVERT: K 295 ASN cc_start: 0.8423 (m110) cc_final: 0.7946 (m110) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.2646 time to fit residues: 105.3493 Evaluate side-chains 230 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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: 0.8980 chunk 66 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 100 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 84 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 HIS ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.074913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.062686 restraints weight = 103298.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.066075 restraints weight = 43719.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.068202 restraints weight = 22669.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.069492 restraints weight = 13409.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.070365 restraints weight = 8874.024| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.6959 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= 0.155 Angle : 0.579 8.671 12951 Z= 0.321 Chirality : 0.043 0.207 1443 Planarity : 0.005 0.043 1668 Dihedral : 9.739 178.329 1296 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: 0.32 (0.25), residues: 1159 helix: 0.78 (0.23), residues: 496 sheet: -0.35 (0.37), residues: 209 loop : 0.05 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 276 TYR 0.040 0.002 TYR A 172 PHE 0.017 0.002 PHE A 141 TRP 0.013 0.001 TRP A 346 HIS 0.005 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 ( 9565) covalent geometry : angle 0.57869 / 0.32 (12951) hydrogen bonds : bond 0.05654 / 3.83 ( 466) hydrogen bonds : angle 5.41580 / 3.79 ( 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 277 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.504 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: A 35 GLN cc_start: 0.9153 (mt0) cc_final: 0.8838 (mp10) REVERT: A 70 LEU cc_start: 0.7574 (mt) cc_final: 0.7013 (mp) REVERT: A 71 GLU cc_start: 0.7999 (tt0) cc_final: 0.7581 (tt0) REVERT: A 76 ASP cc_start: 0.8277 (m-30) cc_final: 0.8025 (m-30) REVERT: A 96 LYS cc_start: 0.7509 (mttt) cc_final: 0.6911 (mtmt) REVERT: A 101 ASN cc_start: 0.8301 (t0) cc_final: 0.7543 (t0) REVERT: A 109 THR cc_start: 0.8020 (m) cc_final: 0.7489 (p) REVERT: A 139 HIS cc_start: 0.8167 (p-80) cc_final: 0.7927 (p-80) REVERT: A 202 PHE cc_start: 0.8814 (m-80) cc_final: 0.8325 (m-80) REVERT: A 203 MET cc_start: 0.8263 (mmm) cc_final: 0.8043 (mmp) REVERT: A 209 ILE cc_start: 0.9272 (mm) cc_final: 0.9066 (mm) REVERT: A 295 CYS cc_start: 0.8811 (m) cc_final: 0.8327 (m) REVERT: A 302 MET cc_start: 0.8743 (mtp) cc_final: 0.8236 (mtt) REVERT: A 313 MET cc_start: 0.8092 (mmm) cc_final: 0.7671 (mmt) REVERT: A 413 MET cc_start: 0.6104 (ttt) cc_final: 0.5550 (ttt) REVERT: B 12 CYS cc_start: 0.7300 (t) cc_final: 0.7069 (t) REVERT: B 266 PHE cc_start: 0.8476 (m-80) cc_final: 0.8029 (m-80) REVERT: B 300 MET cc_start: 0.8479 (mtt) cc_final: 0.8178 (mtm) REVERT: B 325 GLU cc_start: 0.9125 (tp30) cc_final: 0.8709 (tp30) REVERT: B 350 LYS cc_start: 0.8948 (tmtt) cc_final: 0.8673 (tmtt) REVERT: K 52 VAL cc_start: 0.8949 (t) cc_final: 0.8229 (t) REVERT: K 69 PHE cc_start: 0.8106 (m-80) cc_final: 0.7506 (m-80) REVERT: K 88 TYR cc_start: 0.8785 (t80) cc_final: 0.8477 (t80) REVERT: K 339 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8639 (tm-30) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.2491 time to fit residues: 94.6788 Evaluate side-chains 238 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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: 2.9990 chunk 92 optimal weight: 30.0000 chunk 60 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 111 optimal weight: 0.8980 chunk 100 optimal weight: 20.0000 chunk 84 optimal weight: 40.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.074201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.061969 restraints weight = 103280.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.065354 restraints weight = 44521.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.067462 restraints weight = 23475.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.068861 restraints weight = 14014.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.069653 restraints weight = 9139.323| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.7331 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= 0.157 Angle : 0.567 6.921 12951 Z= 0.315 Chirality : 0.042 0.206 1443 Planarity : 0.005 0.047 1668 Dihedral : 9.612 174.221 1296 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 0.30 (0.25), residues: 1159 helix: 0.80 (0.23), residues: 501 sheet: -0.41 (0.37), residues: 205 loop : 0.01 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 241 TYR 0.021 0.002 TYR B 422 PHE 0.015 0.001 PHE B 265 TRP 0.008 0.001 TRP B 21 HIS 0.014 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 ( 9565) covalent geometry : angle 0.56656 / 0.31 (12951) hydrogen bonds : bond 0.05287 / 3.57 ( 466) hydrogen bonds : angle 5.30212 / 3.70 ( 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 272 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.517 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: A 35 GLN cc_start: 0.9095 (mt0) cc_final: 0.8788 (mp10) REVERT: A 70 LEU cc_start: 0.7536 (mt) cc_final: 0.7208 (mp) REVERT: A 71 GLU cc_start: 0.8005 (tt0) cc_final: 0.7661 (tt0) REVERT: A 96 LYS cc_start: 0.7674 (mttt) cc_final: 0.7144 (mtmt) REVERT: A 101 ASN cc_start: 0.8317 (t0) cc_final: 0.7945 (t0) REVERT: A 109 THR cc_start: 0.7913 (m) cc_final: 0.7599 (p) REVERT: A 139 HIS cc_start: 0.8292 (p-80) cc_final: 0.8009 (p-80) REVERT: A 182 VAL cc_start: 0.7972 (m) cc_final: 0.7640 (m) REVERT: A 202 PHE cc_start: 0.8337 (m-80) cc_final: 0.7940 (m-80) REVERT: A 203 MET cc_start: 0.7424 (mmm) cc_final: 0.7019 (tpp) REVERT: A 295 CYS cc_start: 0.8927 (m) cc_final: 0.8419 (m) REVERT: A 313 MET cc_start: 0.8311 (mmm) cc_final: 0.8098 (mmm) REVERT: A 352 LYS cc_start: 0.2466 (mmtm) cc_final: 0.2234 (mmtm) REVERT: A 398 MET cc_start: 0.7495 (mtp) cc_final: 0.7158 (mtt) REVERT: A 413 MET cc_start: 0.6263 (ttt) cc_final: 0.5609 (ttt) REVERT: B 12 CYS cc_start: 0.7257 (t) cc_final: 0.7055 (t) REVERT: B 20 PHE cc_start: 0.9072 (t80) cc_final: 0.8754 (t80) REVERT: B 266 PHE cc_start: 0.8426 (m-80) cc_final: 0.8004 (m-80) REVERT: B 325 GLU cc_start: 0.9126 (tp30) cc_final: 0.8498 (tp30) REVERT: B 350 LYS cc_start: 0.8958 (tmtt) cc_final: 0.8680 (tmtt) REVERT: K 52 VAL cc_start: 0.8909 (t) cc_final: 0.8356 (t) REVERT: K 69 PHE cc_start: 0.8092 (m-80) cc_final: 0.7520 (m-80) REVERT: K 88 TYR cc_start: 0.8599 (t80) cc_final: 0.8309 (t80) REVERT: K 246 ILE cc_start: 0.9165 (mt) cc_final: 0.8781 (tp) REVERT: K 272 PHE cc_start: 0.8264 (t80) cc_final: 0.7954 (t80) REVERT: K 295 ASN cc_start: 0.8403 (m110) cc_final: 0.8011 (m110) REVERT: K 339 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8589 (tm-30) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.2475 time to fit residues: 92.3585 Evaluate side-chains 228 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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: 9.9990 chunk 114 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 104 optimal weight: 30.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.071511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.059487 restraints weight = 105250.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.062801 restraints weight = 44440.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.064830 restraints weight = 23128.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.066159 restraints weight = 13775.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.067044 restraints weight = 9079.913| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.7821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9565 Z= 0.196 Angle : 0.593 6.176 12951 Z= 0.328 Chirality : 0.042 0.212 1443 Planarity : 0.005 0.046 1668 Dihedral : 9.287 173.699 1296 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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 (0.25), residues: 1159 helix: 0.58 (0.22), residues: 512 sheet: -0.48 (0.38), residues: 205 loop : -0.19 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 306 TYR 0.029 0.002 TYR B 422 PHE 0.017 0.002 PHE B 265 TRP 0.011 0.001 TRP B 21 HIS 0.015 0.002 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.20 ( 9565) covalent geometry : angle 0.59350 / 0.33 (12951) hydrogen bonds : bond 0.05149 / 3.44 ( 466) hydrogen bonds : angle 5.24698 / 3.64 ( 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 255 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.420 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: A 69 ASP cc_start: 0.7736 (t0) cc_final: 0.7218 (t70) REVERT: A 71 GLU cc_start: 0.7907 (tt0) cc_final: 0.7640 (tt0) REVERT: A 76 ASP cc_start: 0.8572 (m-30) cc_final: 0.8358 (m-30) REVERT: A 96 LYS cc_start: 0.7810 (mttt) cc_final: 0.7220 (mtmt) REVERT: A 101 ASN cc_start: 0.8381 (t0) cc_final: 0.8002 (t0) REVERT: A 182 VAL cc_start: 0.7995 (m) cc_final: 0.7731 (m) REVERT: A 205 ASP cc_start: 0.8538 (t70) cc_final: 0.8121 (t0) REVERT: A 295 CYS cc_start: 0.8998 (m) cc_final: 0.8391 (m) REVERT: A 313 MET cc_start: 0.8443 (mmm) cc_final: 0.8195 (mmm) REVERT: A 398 MET cc_start: 0.7782 (mtp) cc_final: 0.7335 (mtt) REVERT: A 413 MET cc_start: 0.6473 (ttt) cc_final: 0.5831 (ttt) REVERT: B 266 PHE cc_start: 0.8416 (m-80) cc_final: 0.8165 (m-80) REVERT: B 267 MET cc_start: 0.8242 (mtt) cc_final: 0.7927 (mpp) REVERT: B 325 GLU cc_start: 0.9115 (tp30) cc_final: 0.8549 (tp30) REVERT: K 88 TYR cc_start: 0.8550 (t80) cc_final: 0.8236 (t80) REVERT: K 295 ASN cc_start: 0.8659 (m110) cc_final: 0.8318 (m110) REVERT: K 339 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8617 (tm-30) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.2492 time to fit residues: 87.8950 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 : 0.552 ------------------------------------------------------------------------------- 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: 10.0000 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 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 = 0.3439 r_free = 0.3439 target = 0.071813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059861 restraints weight = 104918.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.063117 restraints weight = 44827.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.065119 restraints weight = 23507.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.066420 restraints weight = 14056.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.067258 restraints weight = 9346.738| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.8155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 9565 Z= 0.168 Angle : 0.564 6.227 12951 Z= 0.311 Chirality : 0.042 0.211 1443 Planarity : 0.004 0.044 1668 Dihedral : 9.118 173.372 1296 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 0.07 (0.24), residues: 1159 helix: 0.67 (0.22), residues: 513 sheet: -0.46 (0.38), residues: 202 loop : -0.26 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 320 TYR 0.032 0.002 TYR A 432 PHE 0.011 0.001 PHE K 366 TRP 0.009 0.001 TRP A 388 HIS 0.008 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 ( 9565) covalent geometry : angle 0.56384 / 0.31 (12951) hydrogen bonds : bond 0.05034 / 3.39 ( 466) hydrogen bonds : angle 5.08851 / 3.52 ( 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 255 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.506 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: A 76 ASP cc_start: 0.8609 (m-30) cc_final: 0.8399 (m-30) REVERT: A 96 LYS cc_start: 0.7855 (mttt) cc_final: 0.7274 (mtmt) REVERT: A 101 ASN cc_start: 0.8349 (t0) cc_final: 0.8049 (t0) REVERT: A 182 VAL cc_start: 0.8014 (m) cc_final: 0.7714 (m) REVERT: A 205 ASP cc_start: 0.8584 (t70) cc_final: 0.8126 (t0) REVERT: A 237 SER cc_start: 0.9060 (m) cc_final: 0.8660 (p) REVERT: A 295 CYS cc_start: 0.8987 (m) cc_final: 0.8448 (m) REVERT: A 313 MET cc_start: 0.8448 (mmm) cc_final: 0.8131 (mmm) REVERT: A 315 CYS cc_start: 0.9060 (t) cc_final: 0.8667 (t) REVERT: A 376 CYS cc_start: 0.8745 (t) cc_final: 0.8513 (t) REVERT: A 398 MET cc_start: 0.7805 (mtp) cc_final: 0.7381 (mtt) REVERT: B 6 HIS cc_start: 0.8370 (t-170) cc_final: 0.8031 (t-170) REVERT: B 179 VAL cc_start: 0.8967 (m) cc_final: 0.8663 (p) REVERT: B 266 PHE cc_start: 0.8376 (m-80) cc_final: 0.8142 (m-80) REVERT: B 267 MET cc_start: 0.8213 (mtt) cc_final: 0.7855 (mpp) REVERT: B 325 GLU cc_start: 0.9129 (tp30) cc_final: 0.8522 (tp30) REVERT: K 88 TYR cc_start: 0.8490 (t80) cc_final: 0.8183 (t80) REVERT: K 204 LEU cc_start: 0.8341 (tp) cc_final: 0.8140 (tp) REVERT: K 246 ILE cc_start: 0.9130 (mt) cc_final: 0.8752 (tp) REVERT: K 272 PHE cc_start: 0.8228 (t80) cc_final: 0.7793 (t80) REVERT: K 295 ASN cc_start: 0.8683 (m110) cc_final: 0.8384 (m110) REVERT: K 339 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8571 (tm-30) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.2459 time to fit residues: 86.2599 Evaluate side-chains 217 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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: 5.9990 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 overall best weight: 9.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 HIS K 317 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 = 0.3404 r_free = 0.3404 target = 0.070287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.058413 restraints weight = 106199.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.061589 restraints weight = 45737.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.063565 restraints weight = 24060.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.064821 restraints weight = 14491.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.065657 restraints weight = 9721.374| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.8499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9565 Z= 0.226 Angle : 0.602 5.937 12951 Z= 0.338 Chirality : 0.042 0.211 1443 Planarity : 0.005 0.049 1668 Dihedral : 9.008 168.990 1296 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.16 (0.24), residues: 1159 helix: 0.49 (0.22), residues: 511 sheet: -0.74 (0.38), residues: 193 loop : -0.31 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 276 TYR 0.019 0.002 TYR A 172 PHE 0.013 0.002 PHE K 366 TRP 0.023 0.002 TRP B 21 HIS 0.012 0.002 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.23 ( 9565) covalent geometry : angle 0.60167 / 0.34 (12951) hydrogen bonds : bond 0.05181 / 3.49 ( 466) hydrogen bonds : angle 5.21598 / 3.62 ( 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 248 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.506 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: A 76 ASP cc_start: 0.8649 (m-30) cc_final: 0.8407 (m-30) REVERT: A 96 LYS cc_start: 0.7822 (mttt) cc_final: 0.7270 (mtmt) REVERT: A 139 HIS cc_start: 0.8692 (p-80) cc_final: 0.7685 (p90) REVERT: A 182 VAL cc_start: 0.8031 (m) cc_final: 0.7799 (m) REVERT: A 203 MET cc_start: 0.8584 (tpp) cc_final: 0.8146 (mmp) REVERT: A 205 ASP cc_start: 0.8648 (t70) cc_final: 0.8178 (t0) REVERT: A 218 ASP cc_start: 0.8567 (t0) cc_final: 0.8337 (t0) REVERT: A 237 SER cc_start: 0.9009 (m) cc_final: 0.8714 (p) REVERT: A 295 CYS cc_start: 0.9173 (m) cc_final: 0.8551 (m) REVERT: A 313 MET cc_start: 0.8506 (mmm) cc_final: 0.8199 (mmm) REVERT: A 315 CYS cc_start: 0.9011 (t) cc_final: 0.8684 (t) REVERT: A 376 CYS cc_start: 0.8825 (t) cc_final: 0.8227 (t) REVERT: A 398 MET cc_start: 0.7978 (mtp) cc_final: 0.7572 (mtt) REVERT: A 413 MET cc_start: 0.6738 (ttt) cc_final: 0.6046 (ttt) REVERT: B 179 VAL cc_start: 0.9091 (m) cc_final: 0.8763 (p) REVERT: B 266 PHE cc_start: 0.8263 (m-80) cc_final: 0.8042 (m-80) REVERT: B 267 MET cc_start: 0.8234 (mtt) cc_final: 0.7847 (mpp) REVERT: B 293 MET cc_start: 0.7927 (mmm) cc_final: 0.7710 (mmm) REVERT: B 325 GLU cc_start: 0.9156 (tp30) cc_final: 0.8605 (tp30) REVERT: K 88 TYR cc_start: 0.8412 (t80) cc_final: 0.8098 (t80) REVERT: K 295 ASN cc_start: 0.8722 (m110) cc_final: 0.8381 (m-40) REVERT: K 339 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8510 (tm-30) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2475 time to fit residues: 84.3237 Evaluate side-chains 211 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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: 10.0000 chunk 113 optimal weight: 30.0000 chunk 68 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 overall best weight: 7.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 107 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 = 0.3403 r_free = 0.3403 target = 0.070330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.058407 restraints weight = 106758.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.061533 restraints weight = 45799.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.063457 restraints weight = 24183.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.064712 restraints weight = 14616.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.065554 restraints weight = 9853.048| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.8732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9565 Z= 0.178 Angle : 0.576 5.963 12951 Z= 0.322 Chirality : 0.042 0.208 1443 Planarity : 0.005 0.056 1668 Dihedral : 8.885 166.222 1296 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % 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 : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.25), residues: 1159 helix: 0.62 (0.22), residues: 512 sheet: -0.95 (0.37), residues: 199 loop : -0.31 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 64 TYR 0.020 0.002 TYR A 172 PHE 0.013 0.001 PHE K 272 TRP 0.015 0.002 TRP B 21 HIS 0.007 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 ( 9565) covalent geometry : angle 0.57631 / 0.32 (12951) hydrogen bonds : bond 0.04918 / 3.30 ( 466) hydrogen bonds : angle 5.15186 / 3.57 ( 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 245 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.520 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: 0.8668 (m) cc_final: 0.8459 (m) REVERT: A 76 ASP cc_start: 0.8712 (m-30) cc_final: 0.8469 (m-30) REVERT: A 96 LYS cc_start: 0.7793 (mttt) cc_final: 0.7229 (mtmt) REVERT: A 101 ASN cc_start: 0.8510 (t0) cc_final: 0.8138 (t0) REVERT: A 182 VAL cc_start: 0.8032 (m) cc_final: 0.7793 (m) REVERT: A 237 SER cc_start: 0.9019 (m) cc_final: 0.8695 (p) REVERT: A 267 PHE cc_start: 0.9097 (m-80) cc_final: 0.8693 (m-80) REVERT: A 295 CYS cc_start: 0.9144 (m) cc_final: 0.8604 (m) REVERT: A 313 MET cc_start: 0.8469 (mmm) cc_final: 0.7981 (mmt) REVERT: A 315 CYS cc_start: 0.8989 (t) cc_final: 0.8708 (t) REVERT: A 376 CYS cc_start: 0.8846 (t) cc_final: 0.8192 (t) REVERT: A 377 MET cc_start: 0.7973 (ttm) cc_final: 0.7580 (tmm) REVERT: B 22 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8313 (tm-30) REVERT: B 74 ASP cc_start: 0.9140 (t0) cc_final: 0.8932 (t0) REVERT: B 179 VAL cc_start: 0.9052 (m) cc_final: 0.8743 (p) REVERT: B 267 MET cc_start: 0.8241 (mtt) cc_final: 0.7835 (mpp) REVERT: B 293 MET cc_start: 0.7972 (mmm) cc_final: 0.7758 (mmm) REVERT: B 325 GLU cc_start: 0.9135 (tp30) cc_final: 0.8553 (tp30) REVERT: K 26 VAL cc_start: 0.8979 (p) cc_final: 0.8766 (p) REVERT: K 52 VAL cc_start: 0.8913 (t) cc_final: 0.7909 (t) REVERT: K 69 PHE cc_start: 0.8129 (m-80) cc_final: 0.7673 (m-80) REVERT: K 88 TYR cc_start: 0.8293 (t80) cc_final: 0.8002 (t80) REVERT: K 204 LEU cc_start: 0.8493 (tp) cc_final: 0.8169 (tp) REVERT: K 295 ASN cc_start: 0.8727 (m110) cc_final: 0.8397 (m-40) REVERT: K 304 ASN cc_start: 0.8730 (t0) cc_final: 0.8509 (t0) REVERT: K 339 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8488 (tm-30) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.2377 time to fit residues: 80.8000 Evaluate side-chains 212 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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: 2.9990 chunk 45 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 93 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 chunk 40 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 ASN K 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.071265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.059106 restraints weight = 105558.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.062297 restraints weight = 45322.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.064268 restraints weight = 23908.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.065527 restraints weight = 14413.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.066383 restraints weight = 9683.626| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.8909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9565 Z= 0.148 Angle : 0.580 6.291 12951 Z= 0.322 Chirality : 0.043 0.231 1443 Planarity : 0.005 0.101 1668 Dihedral : 8.632 161.335 1296 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % 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: 0.01 (0.25), residues: 1159 helix: 0.85 (0.23), residues: 511 sheet: -0.96 (0.37), residues: 189 loop : -0.35 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 390 TYR 0.055 0.002 TYR K 193 PHE 0.051 0.002 PHE K 272 TRP 0.011 0.001 TRP B 21 HIS 0.017 0.002 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 9565) covalent geometry : angle 0.58030 / 0.32 (12951) hydrogen bonds : bond 0.04807 / 3.20 ( 466) hydrogen bonds : angle 5.02982 / 3.49 ( 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 245 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.537 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: A 96 LYS cc_start: 0.7806 (mttt) cc_final: 0.7231 (mtmt) REVERT: A 101 ASN cc_start: 0.8503 (t0) cc_final: 0.8063 (t0) REVERT: A 182 VAL cc_start: 0.8001 (m) cc_final: 0.7696 (m) REVERT: A 205 ASP cc_start: 0.8520 (t0) cc_final: 0.8287 (t0) REVERT: A 237 SER cc_start: 0.9074 (m) cc_final: 0.8754 (p) REVERT: A 295 CYS cc_start: 0.9128 (m) cc_final: 0.8580 (m) REVERT: A 313 MET cc_start: 0.8469 (mmm) cc_final: 0.7976 (mmt) REVERT: A 315 CYS cc_start: 0.8989 (t) cc_final: 0.8681 (t) REVERT: A 376 CYS cc_start: 0.8795 (t) cc_final: 0.8056 (t) REVERT: A 377 MET cc_start: 0.7997 (ttm) cc_final: 0.7400 (tmm) REVERT: A 398 MET cc_start: 0.8040 (mtp) cc_final: 0.7540 (mtt) REVERT: B 179 VAL cc_start: 0.9056 (m) cc_final: 0.8739 (p) REVERT: B 267 MET cc_start: 0.8101 (mtt) cc_final: 0.7693 (mpp) REVERT: B 293 MET cc_start: 0.8029 (mmm) cc_final: 0.7779 (mmm) REVERT: B 325 GLU cc_start: 0.9131 (tp30) cc_final: 0.8511 (tp30) REVERT: B 367 PHE cc_start: 0.8988 (t80) cc_final: 0.8770 (t80) REVERT: K 26 VAL cc_start: 0.8943 (p) cc_final: 0.8709 (p) REVERT: K 52 VAL cc_start: 0.8928 (t) cc_final: 0.7972 (t) REVERT: K 69 PHE cc_start: 0.8079 (m-80) cc_final: 0.7625 (m-80) REVERT: K 88 TYR cc_start: 0.8294 (t80) cc_final: 0.8008 (t80) REVERT: K 204 LEU cc_start: 0.8249 (tp) cc_final: 0.7967 (tp) REVERT: K 295 ASN cc_start: 0.8745 (m110) cc_final: 0.8490 (m110) REVERT: K 304 ASN cc_start: 0.8671 (t0) cc_final: 0.8428 (t0) REVERT: K 339 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8441 (tm-30) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.2302 time to fit residues: 79.7111 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 : 0.525 ------------------------------------------------------------------------------- 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: 5.9990 chunk 45 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.071096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.058917 restraints weight = 105755.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.062116 restraints weight = 45403.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.064103 restraints weight = 23871.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.065414 restraints weight = 14370.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.066277 restraints weight = 9532.289| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.9042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9565 Z= 0.140 Angle : 0.550 7.333 12951 Z= 0.304 Chirality : 0.042 0.210 1443 Planarity : 0.005 0.053 1668 Dihedral : 8.318 155.016 1296 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.16 (0.25), residues: 1159 helix: 1.01 (0.23), residues: 507 sheet: -0.93 (0.37), residues: 194 loop : -0.29 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 390 TYR 0.029 0.002 TYR K 193 PHE 0.048 0.002 PHE K 272 TRP 0.010 0.001 TRP A 21 HIS 0.006 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 9565) covalent geometry : angle 0.55019 / 0.30 (12951) hydrogen bonds : bond 0.04565 / 3.03 ( 466) hydrogen bonds : angle 4.91356 / 3.39 ( 1362) =============================================================================== Job complete usr+sys time: 3238.41 seconds wall clock time: 56 minutes 19.91 seconds (3379.91 seconds total)