Starting phenix.real_space_refine on Fri Jul 3 08:44:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pxi_71970/07_2026/9pxi_71970_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pxi_71970/07_2026/9pxi_71970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pxi_71970/07_2026/9pxi_71970_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pxi_71970/07_2026/9pxi_71970_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pxi_71970/07_2026/9pxi_71970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pxi_71970/07_2026/9pxi_71970.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 8083 2.51 5 N 2211 2.21 5 O 2481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 12801 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1727 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "C" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 341 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 8, 'TRANS': 35} Chain: "B" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2666 Classifications: {'peptide': 355} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 343} Chain: "A" Number of atoms: 5491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5491 Classifications: {'peptide': 700} Link IDs: {'PTRANS': 27, 'TRANS': 672} Chain breaks: 1 Chain: "E" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 713 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "F" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1863 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 14, 'TRANS': 223} Time building chain proxies: 2.46, per 1000 atoms: 0.19 Number of scatterers: 12801 At special positions: 0 Unit cell: (105, 144.75, 170.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 2481 8.00 N 2211 7.00 C 8083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 737 " - pdb=" SG CYS A 745 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 558.6 milliseconds 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2972 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 21 sheets defined 20.2% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 46 through 59 removed outlier: 3.655A pdb=" N SER D 59 " --> pdb=" O LYS D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 81 removed outlier: 4.530A pdb=" N GLN D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 98 removed outlier: 4.088A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 119 removed outlier: 3.658A pdb=" N ALA D 107 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASP D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 127 removed outlier: 3.751A pdb=" N LEU D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 134 removed outlier: 3.625A pdb=" N LYS D 133 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG D 134 " --> pdb=" O MET D 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 130 through 134' Processing helix chain 'D' and resid 136 through 153 removed outlier: 3.556A pdb=" N PHE D 143 " --> pdb=" O ALA D 139 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU D 145 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE D 146 " --> pdb=" O SER D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 188 removed outlier: 3.547A pdb=" N TYR D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 204 removed outlier: 3.673A pdb=" N ALA D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 225 Processing helix chain 'D' and resid 226 through 241 removed outlier: 3.576A pdb=" N THR D 232 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN D 240 " --> pdb=" O THR D 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 125 through 143 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 214 through 231 Processing helix chain 'A' and resid 279 through 287 removed outlier: 3.796A pdb=" N VAL A 283 " --> pdb=" O PRO A 279 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 313 Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.766A pdb=" N LEU A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 392 removed outlier: 4.361A pdb=" N GLY A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 544 through 555 removed outlier: 3.595A pdb=" N TYR A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.723A pdb=" N ASN A 641 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 753 Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.939A pdb=" N GLN E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 57 Processing helix chain 'F' and resid 83 through 89 removed outlier: 3.746A pdb=" N GLU F 89 " --> pdb=" O PHE F 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 41 through 48 removed outlier: 5.585A pdb=" N LYS B 43 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR B 378 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TRP B 45 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.016A pdb=" N GLN B 82 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B 88 " --> pdb=" O GLN B 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 103 through 104 removed outlier: 5.881A pdb=" N ASP B 122 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS B 128 " --> pdb=" O ASP B 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 143 through 144 removed outlier: 5.902A pdb=" N ASP B 162 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLN B 168 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 179 through 181 removed outlier: 6.377A pdb=" N THR B 180 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE A 239 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASN A 260 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE A 176 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N ILE A 255 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N HIS A 178 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL A 257 " --> pdb=" O HIS A 178 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASN A 180 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE A 259 " --> pdb=" O ASN A 180 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL A 182 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 188 through 190 removed outlier: 5.848A pdb=" N ASP B 207 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 238 through 241 removed outlier: 7.216A pdb=" N GLY B 252 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU B 269 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA B 254 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN B 267 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA B 256 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 279 removed outlier: 3.865A pdb=" N TRP B 304 " --> pdb=" O GLY B 294 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP B 296 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N SER B 302 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 318 through 320 removed outlier: 5.319A pdb=" N SER B 337 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE B 343 " --> pdb=" O SER B 337 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 92 through 99 removed outlier: 4.643A pdb=" N ILE A 93 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU A 164 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N SER A 95 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE A 166 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU A 97 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 168 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU A 99 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 266 through 274 removed outlier: 6.282A pdb=" N THR A 266 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL A 336 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ARG A 268 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 12.967A pdb=" N PHE A 338 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 10.484A pdb=" N VAL A 270 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 12.568A pdb=" N VAL A 340 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N LEU A 272 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 347 through 354 removed outlier: 7.491A pdb=" N VAL A 413 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE A 351 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N TYR A 415 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A 353 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL A 417 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN A 414 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL A 399 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER A 416 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A 397 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU A 418 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 423 through 428 removed outlier: 3.611A pdb=" N GLY A 458 " --> pdb=" O ASN A 469 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N THR A 493 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL A 507 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N PHE A 599 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS A 621 " --> pdb=" O GLY A 705 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 710 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR A 723 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 501 through 502 removed outlier: 6.530A pdb=" N ASP A 501 " --> pdb=" O ILE F 236 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 35 removed outlier: 7.275A pdb=" N ARG E 90 " --> pdb=" O GLY E 106 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLY E 106 " --> pdb=" O ARG E 90 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER E 92 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU E 104 " --> pdb=" O SER E 92 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE E 94 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN E 100 " --> pdb=" O ASN E 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.910A pdb=" N ALA F 56 " --> pdb=" O ILE F 11 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL F 57 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN F 63 " --> pdb=" O VAL F 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AB9, first strand: chain 'F' and resid 91 through 94 removed outlier: 8.349A pdb=" N PHE F 100 " --> pdb=" O THR F 223 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N THR F 223 " --> pdb=" O PHE F 100 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE F 102 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU F 215 " --> pdb=" O LYS F 108 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY F 110 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU F 213 " --> pdb=" O GLY F 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 94 removed outlier: 8.349A pdb=" N PHE F 100 " --> pdb=" O THR F 223 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N THR F 223 " --> pdb=" O PHE F 100 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE F 102 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU F 215 " --> pdb=" O LYS F 108 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY F 110 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU F 213 " --> pdb=" O GLY F 110 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR F 223 " --> pdb=" O GLY F 227 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 131 through 132 removed outlier: 3.873A pdb=" N TRP F 193 " --> pdb=" O ILE F 185 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LYS F 187 " --> pdb=" O ALA F 191 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ALA F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 137 through 139 removed outlier: 6.672A pdb=" N GLN F 157 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL F 163 " --> pdb=" O GLN F 157 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4295 1.34 - 1.46: 2639 1.46 - 1.58: 6082 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 13066 Sorted by residual: bond pdb=" N ILE E 30 " pdb=" CA ILE E 30 " ideal model delta sigma weight residual 1.455 1.416 0.039 1.38e-02 5.25e+03 8.00e+00 bond pdb=" CA GLU F 59 " pdb=" C GLU F 59 " ideal model delta sigma weight residual 1.530 1.506 0.024 1.23e-02 6.61e+03 3.90e+00 bond pdb=" N ARG B 312 " pdb=" CA ARG B 312 " ideal model delta sigma weight residual 1.454 1.478 -0.023 1.40e-02 5.10e+03 2.81e+00 bond pdb=" CA ILE E 30 " pdb=" CB ILE E 30 " ideal model delta sigma weight residual 1.543 1.517 0.026 1.62e-02 3.81e+03 2.60e+00 bond pdb=" CA TYR A 505 " pdb=" CB TYR A 505 " ideal model delta sigma weight residual 1.532 1.508 0.024 1.68e-02 3.54e+03 2.06e+00 ... (remaining 13061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 17244 1.56 - 3.13: 407 3.13 - 4.69: 64 4.69 - 6.25: 12 6.25 - 7.81: 6 Bond angle restraints: 17733 Sorted by residual: angle pdb=" N LYS F 187 " pdb=" CA LYS F 187 " pdb=" C LYS F 187 " ideal model delta sigma weight residual 108.34 100.53 7.81 1.64e+00 3.72e-01 2.27e+01 angle pdb=" N ARG F 144 " pdb=" CA ARG F 144 " pdb=" C ARG F 144 " ideal model delta sigma weight residual 108.34 115.56 -7.22 1.64e+00 3.72e-01 1.94e+01 angle pdb=" N ALA F 56 " pdb=" CA ALA F 56 " pdb=" C ALA F 56 " ideal model delta sigma weight residual 107.80 114.10 -6.30 1.73e+00 3.34e-01 1.33e+01 angle pdb=" N ASP F 150 " pdb=" CA ASP F 150 " pdb=" C ASP F 150 " ideal model delta sigma weight residual 113.20 108.82 4.38 1.21e+00 6.83e-01 1.31e+01 angle pdb=" N ASN F 33 " pdb=" CA ASN F 33 " pdb=" C ASN F 33 " ideal model delta sigma weight residual 111.39 116.08 -4.69 1.38e+00 5.25e-01 1.16e+01 ... (remaining 17728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7112 17.90 - 35.80: 543 35.80 - 53.70: 93 53.70 - 71.59: 17 71.59 - 89.49: 14 Dihedral angle restraints: 7779 sinusoidal: 3096 harmonic: 4683 Sorted by residual: dihedral pdb=" CB CYS A 737 " pdb=" SG CYS A 737 " pdb=" SG CYS A 745 " pdb=" CB CYS A 745 " ideal model delta sinusoidal sigma weight residual -86.00 -2.84 -83.16 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CA GLU A 197 " pdb=" C GLU A 197 " pdb=" N LEU A 198 " pdb=" CA LEU A 198 " ideal model delta harmonic sigma weight residual 180.00 160.42 19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLN F 157 " pdb=" C GLN F 157 " pdb=" N ILE F 158 " pdb=" CA ILE F 158 " ideal model delta harmonic sigma weight residual 180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 7776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1205 0.032 - 0.063: 460 0.063 - 0.095: 153 0.095 - 0.126: 121 0.126 - 0.158: 12 Chirality restraints: 1951 Sorted by residual: chirality pdb=" CA ILE A 778 " pdb=" N ILE A 778 " pdb=" C ILE A 778 " pdb=" CB ILE A 778 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA VAL B 325 " pdb=" N VAL B 325 " pdb=" C VAL B 325 " pdb=" CB VAL B 325 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA ILE F 185 " pdb=" N ILE F 185 " pdb=" C ILE F 185 " pdb=" CB ILE F 185 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 1948 not shown) Planarity restraints: 2331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 504 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.28e+00 pdb=" C SER A 504 " -0.043 2.00e-02 2.50e+03 pdb=" O SER A 504 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR A 505 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 776 " -0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO A 777 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 777 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 777 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 55 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO C 56 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 56 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 56 " -0.027 5.00e-02 4.00e+02 ... (remaining 2328 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2420 2.77 - 3.30: 11875 3.30 - 3.84: 20503 3.84 - 4.37: 23615 4.37 - 4.90: 41874 Nonbonded interactions: 100287 Sorted by model distance: nonbonded pdb=" OG SER F 19 " pdb=" OD1 ASN F 21 " model vdw 2.241 3.040 nonbonded pdb=" OE2 GLU A 546 " pdb=" OG1 THR A 739 " model vdw 2.261 3.040 nonbonded pdb=" OD2 ASP F 105 " pdb=" OH TYR F 204 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR A 265 " pdb=" OD1 ASP A 329 " model vdw 2.274 3.040 nonbonded pdb=" O GLY F 181 " pdb=" OG1 THR F 197 " model vdw 2.278 3.040 ... (remaining 100282 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.710 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13067 Z= 0.155 Angle : 0.595 7.813 17735 Z= 0.331 Chirality : 0.044 0.158 1951 Planarity : 0.004 0.049 2331 Dihedral : 13.412 89.491 4804 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.21), residues: 1626 helix: 2.03 (0.32), residues: 275 sheet: 0.62 (0.23), residues: 507 loop : -1.14 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 369 TYR 0.015 0.001 TYR D 183 PHE 0.024 0.001 PHE B 35 TRP 0.025 0.001 TRP B 364 HIS 0.003 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (13066) covalent geometry : angle 0.59408 / 0.33 (17733) SS BOND : bond 0.00087 / 0.05 ( 1) SS BOND : angle 2.33933 / 1.25 ( 2) hydrogen bonds : bond 0.11287 / 7.44 ( 508) hydrogen bonds : angle 5.52174 / 3.99 ( 1425) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 140 ARG cc_start: 0.6398 (tpt90) cc_final: 0.5423 (mtt90) REVERT: D 153 PHE cc_start: 0.7534 (m-80) cc_final: 0.7299 (m-80) REVERT: D 157 ARG cc_start: 0.7763 (ptp-110) cc_final: 0.7556 (ptp-110) REVERT: D 206 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6655 (mm-30) REVERT: B 178 VAL cc_start: 0.8584 (t) cc_final: 0.8347 (m) REVERT: B 217 GLN cc_start: 0.6257 (tm130) cc_final: 0.5387 (tm-30) REVERT: B 338 GLN cc_start: 0.5221 (tt0) cc_final: 0.4960 (pm20) REVERT: B 360 VAL cc_start: 0.7075 (t) cc_final: 0.6419 (t) REVERT: B 365 MET cc_start: 0.6788 (ppp) cc_final: 0.5746 (mtp) REVERT: A 226 ARG cc_start: 0.5995 (mtp85) cc_final: 0.5693 (mtm-85) REVERT: A 251 LYS cc_start: 0.8053 (tptp) cc_final: 0.7822 (ttmt) REVERT: A 285 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7602 (mtm180) REVERT: A 694 GLU cc_start: 0.6932 (tp30) cc_final: 0.6654 (tt0) REVERT: A 750 THR cc_start: 0.8089 (p) cc_final: 0.7876 (p) REVERT: A 779 LYS cc_start: 0.6296 (tptp) cc_final: 0.5808 (ttpt) REVERT: F 44 ILE cc_start: 0.5140 (pt) cc_final: 0.4704 (mp) REVERT: F 63 ASN cc_start: 0.6553 (m-40) cc_final: 0.6250 (m110) REVERT: F 109 TRP cc_start: 0.8312 (t60) cc_final: 0.7959 (t60) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.4254 time to fit residues: 113.5373 Evaluate side-chains 157 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 188 GLN D 205 GLN B 58 ASN B 217 GLN B 287 GLN A 469 ASN E 71 ASN E 100 GLN F 46 ASN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.237144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.140257 restraints weight = 14906.779| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.52 r_work: 0.3530 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13067 Z= 0.116 Angle : 0.561 8.122 17735 Z= 0.291 Chirality : 0.045 0.171 1951 Planarity : 0.004 0.047 2331 Dihedral : 4.223 20.669 1809 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.89 % Allowed : 10.56 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.21), residues: 1626 helix: 1.84 (0.32), residues: 282 sheet: 0.48 (0.22), residues: 518 loop : -1.11 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.026 0.001 TYR F 91 PHE 0.010 0.001 PHE A 726 TRP 0.011 0.001 TRP B 364 HIS 0.008 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13066) covalent geometry : angle 0.56127 / 0.29 (17733) SS BOND : bond 0.00901 / 0.47 ( 1) SS BOND : angle 1.08796 / 0.57 ( 2) hydrogen bonds : bond 0.03837 / 2.55 ( 508) hydrogen bonds : angle 4.78726 / 3.42 ( 1425) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: D 140 ARG cc_start: 0.7028 (tpt90) cc_final: 0.6019 (mtt90) REVERT: D 145 GLU cc_start: 0.7604 (mp0) cc_final: 0.6862 (mp0) REVERT: D 153 PHE cc_start: 0.7472 (m-80) cc_final: 0.7170 (m-80) REVERT: D 157 ARG cc_start: 0.8086 (ptp-110) cc_final: 0.7872 (ptp-110) REVERT: D 206 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7123 (mm-30) REVERT: D 239 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7420 (tm) REVERT: B 77 ARG cc_start: 0.6302 (ttp80) cc_final: 0.5682 (ttp80) REVERT: B 168 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6858 (tt0) REVERT: B 178 VAL cc_start: 0.8436 (t) cc_final: 0.8221 (m) REVERT: B 217 GLN cc_start: 0.5769 (tm-30) cc_final: 0.5073 (tm-30) REVERT: B 360 VAL cc_start: 0.6924 (t) cc_final: 0.6178 (t) REVERT: B 365 MET cc_start: 0.6800 (ppp) cc_final: 0.5905 (mtp) REVERT: B 366 TYR cc_start: 0.5199 (m-80) cc_final: 0.3960 (m-80) REVERT: A 271 LYS cc_start: 0.8275 (ptpp) cc_final: 0.7623 (ptpt) REVERT: A 285 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.8049 (mtm180) REVERT: A 443 ILE cc_start: 0.7763 (mp) cc_final: 0.7250 (pt) REVERT: A 694 GLU cc_start: 0.7870 (tp30) cc_final: 0.7572 (tt0) REVERT: A 779 LYS cc_start: 0.7162 (tptp) cc_final: 0.6634 (ttpt) REVERT: F 23 LYS cc_start: 0.5178 (ptmt) cc_final: 0.4803 (tptt) REVERT: F 109 TRP cc_start: 0.7510 (t60) cc_final: 0.7072 (t60) outliers start: 26 outliers final: 8 residues processed: 184 average time/residue: 0.4355 time to fit residues: 88.5164 Evaluate side-chains 164 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain F residue 139 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 41 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 ASN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN A 151 ASN A 469 ASN E 54 GLN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 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 = 0.4566 r_free = 0.4566 target = 0.232635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.145640 restraints weight = 14918.906| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 3.26 r_work: 0.3434 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13067 Z= 0.239 Angle : 0.651 8.860 17735 Z= 0.341 Chirality : 0.048 0.196 1951 Planarity : 0.005 0.048 2331 Dihedral : 4.595 21.547 1809 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.48 % Allowed : 13.04 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1626 helix: 1.32 (0.32), residues: 279 sheet: 0.36 (0.22), residues: 516 loop : -1.20 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 365 TYR 0.019 0.002 TYR D 176 PHE 0.027 0.002 PHE A 726 TRP 0.013 0.001 TRP B 215 HIS 0.008 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.24 (13066) covalent geometry : angle 0.65104 / 0.34 (17733) SS BOND : bond 0.00373 / 0.20 ( 1) SS BOND : angle 2.36124 / 1.24 ( 2) hydrogen bonds : bond 0.05155 / 3.41 ( 508) hydrogen bonds : angle 5.05879 / 3.61 ( 1425) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 69 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6500 (tm-30) REVERT: D 140 ARG cc_start: 0.7161 (tpt90) cc_final: 0.6022 (mtt90) REVERT: D 141 ASP cc_start: 0.8351 (t0) cc_final: 0.8133 (t0) REVERT: D 145 GLU cc_start: 0.7991 (mp0) cc_final: 0.7095 (mp0) REVERT: D 153 PHE cc_start: 0.7538 (m-80) cc_final: 0.7155 (m-80) REVERT: D 157 ARG cc_start: 0.8217 (ptp-110) cc_final: 0.7999 (ptp-110) REVERT: D 206 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7380 (mm-30) REVERT: B 77 ARG cc_start: 0.6491 (ttp80) cc_final: 0.6026 (ttp80) REVERT: B 193 MET cc_start: 0.5025 (tpt) cc_final: 0.4441 (tpp) REVERT: B 217 GLN cc_start: 0.5891 (tm-30) cc_final: 0.5067 (tm-30) REVERT: A 271 LYS cc_start: 0.8254 (ptpp) cc_final: 0.7790 (ptpt) REVERT: A 285 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7973 (mtm180) REVERT: A 344 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7396 (mtpt) REVERT: A 694 GLU cc_start: 0.8156 (tp30) cc_final: 0.7847 (tt0) REVERT: A 791 PHE cc_start: 0.8171 (p90) cc_final: 0.7817 (p90) REVERT: F 36 LEU cc_start: 0.6039 (pt) cc_final: 0.5621 (tm) REVERT: F 109 TRP cc_start: 0.7641 (t60) cc_final: 0.7118 (t60) REVERT: F 223 THR cc_start: 0.6511 (m) cc_final: 0.6270 (m) outliers start: 34 outliers final: 18 residues processed: 169 average time/residue: 0.4369 time to fit residues: 81.3346 Evaluate side-chains 162 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 139 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 58 optimal weight: 8.9990 chunk 86 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 0.0370 chunk 154 optimal weight: 20.0000 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 GLN A 469 ASN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.235090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.150940 restraints weight = 14878.309| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 3.54 r_work: 0.3462 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13067 Z= 0.121 Angle : 0.567 8.563 17735 Z= 0.294 Chirality : 0.045 0.172 1951 Planarity : 0.004 0.047 2331 Dihedral : 4.353 22.640 1809 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.11 % Allowed : 15.29 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.20), residues: 1626 helix: 1.56 (0.32), residues: 280 sheet: 0.37 (0.22), residues: 521 loop : -1.16 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 47 TYR 0.025 0.001 TYR F 204 PHE 0.010 0.001 PHE A 726 TRP 0.013 0.001 TRP A 375 HIS 0.006 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (13066) covalent geometry : angle 0.56652 / 0.29 (17733) SS BOND : bond 0.00230 / 0.12 ( 1) SS BOND : angle 1.92137 / 1.02 ( 2) hydrogen bonds : bond 0.03752 / 2.50 ( 508) hydrogen bonds : angle 4.82471 / 3.44 ( 1425) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 117 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6970 (m-30) REVERT: D 140 ARG cc_start: 0.7100 (tpt90) cc_final: 0.5983 (mtt90) REVERT: D 141 ASP cc_start: 0.8339 (t0) cc_final: 0.8119 (t0) REVERT: D 145 GLU cc_start: 0.8060 (mp0) cc_final: 0.7162 (mp0) REVERT: D 153 PHE cc_start: 0.7385 (m-80) cc_final: 0.7033 (m-80) REVERT: D 157 ARG cc_start: 0.8185 (ptp-110) cc_final: 0.7976 (ptp-170) REVERT: D 206 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7274 (mm-30) REVERT: B 77 ARG cc_start: 0.6375 (ttp80) cc_final: 0.5829 (ttp80) REVERT: B 193 MET cc_start: 0.5178 (tpt) cc_final: 0.4715 (mtm) REVERT: B 217 GLN cc_start: 0.5855 (tm-30) cc_final: 0.5016 (tm-30) REVERT: B 225 ARG cc_start: 0.6222 (mpt180) cc_final: 0.5605 (mmt180) REVERT: A 271 LYS cc_start: 0.8303 (ptpp) cc_final: 0.7887 (ptpt) REVERT: A 285 ARG cc_start: 0.8254 (ttm-80) cc_final: 0.7952 (mtm180) REVERT: A 344 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7355 (mtpt) REVERT: A 694 GLU cc_start: 0.8108 (tp30) cc_final: 0.7710 (tt0) REVERT: A 752 ASN cc_start: 0.8029 (t0) cc_final: 0.7762 (t0) REVERT: A 791 PHE cc_start: 0.8145 (p90) cc_final: 0.7788 (p90) REVERT: F 36 LEU cc_start: 0.6072 (pt) cc_final: 0.5617 (tm) REVERT: F 109 TRP cc_start: 0.7649 (t60) cc_final: 0.7246 (t60) outliers start: 29 outliers final: 14 residues processed: 166 average time/residue: 0.4475 time to fit residues: 81.8731 Evaluate side-chains 157 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 139 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 111 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 106 optimal weight: 0.2980 chunk 157 optimal weight: 30.0000 chunk 98 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 GLN A 469 ASN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.235345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.151323 restraints weight = 14911.590| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.80 r_work: 0.3463 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13067 Z= 0.121 Angle : 0.561 9.063 17735 Z= 0.291 Chirality : 0.045 0.164 1951 Planarity : 0.004 0.046 2331 Dihedral : 4.264 21.102 1809 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.62 % Allowed : 16.17 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.20), residues: 1626 helix: 1.61 (0.32), residues: 280 sheet: 0.37 (0.21), residues: 531 loop : -1.12 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 365 TYR 0.021 0.001 TYR A 228 PHE 0.011 0.001 PHE A 726 TRP 0.012 0.001 TRP B 215 HIS 0.004 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (13066) covalent geometry : angle 0.56098 / 0.29 (17733) SS BOND : bond 0.00248 / 0.13 ( 1) SS BOND : angle 1.78955 / 0.95 ( 2) hydrogen bonds : bond 0.03722 / 2.47 ( 508) hydrogen bonds : angle 4.78132 / 3.41 ( 1425) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 117 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6973 (m-30) REVERT: D 140 ARG cc_start: 0.7043 (tpt90) cc_final: 0.5925 (mtt90) REVERT: D 145 GLU cc_start: 0.8099 (mp0) cc_final: 0.7884 (mp0) REVERT: D 206 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7232 (mm-30) REVERT: B 77 ARG cc_start: 0.6398 (ttp80) cc_final: 0.5851 (ttp80) REVERT: B 217 GLN cc_start: 0.5926 (tm-30) cc_final: 0.5073 (tm-30) REVERT: B 298 ARG cc_start: 0.5954 (tpm170) cc_final: 0.5682 (tpp-160) REVERT: A 271 LYS cc_start: 0.8319 (ptpp) cc_final: 0.7916 (ptpt) REVERT: A 285 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.7953 (mtm180) REVERT: A 344 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7396 (mtpt) REVERT: A 694 GLU cc_start: 0.8144 (tp30) cc_final: 0.7703 (tt0) REVERT: A 752 ASN cc_start: 0.8041 (t0) cc_final: 0.7784 (t0) REVERT: A 791 PHE cc_start: 0.8106 (p90) cc_final: 0.7787 (p90) REVERT: F 36 LEU cc_start: 0.6071 (pt) cc_final: 0.5592 (tm) REVERT: F 109 TRP cc_start: 0.7687 (t60) cc_final: 0.7331 (t60) REVERT: F 157 GLN cc_start: 0.6854 (tm-30) cc_final: 0.6641 (tm-30) outliers start: 36 outliers final: 18 residues processed: 171 average time/residue: 0.4332 time to fit residues: 81.8270 Evaluate side-chains 163 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 139 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 4 optimal weight: 0.0170 chunk 102 optimal weight: 0.9990 chunk 43 optimal weight: 30.0000 chunk 2 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 98 optimal weight: 0.0870 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN A 469 ASN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.237322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141471 restraints weight = 14799.678| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.49 r_work: 0.3547 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13067 Z= 0.099 Angle : 0.565 10.230 17735 Z= 0.288 Chirality : 0.044 0.168 1951 Planarity : 0.004 0.046 2331 Dihedral : 4.121 20.719 1809 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.40 % Allowed : 16.75 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1626 helix: 1.73 (0.33), residues: 278 sheet: 0.39 (0.22), residues: 529 loop : -1.08 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 152 TYR 0.024 0.001 TYR F 204 PHE 0.008 0.001 PHE D 143 TRP 0.013 0.001 TRP A 375 HIS 0.004 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (13066) covalent geometry : angle 0.56444 / 0.29 (17733) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 1.52765 / 0.81 ( 2) hydrogen bonds : bond 0.03180 / 2.11 ( 508) hydrogen bonds : angle 4.61204 / 3.29 ( 1425) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 110 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6997 (mm) REVERT: D 117 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6895 (m-30) REVERT: D 140 ARG cc_start: 0.6949 (tpt90) cc_final: 0.5869 (mtt90) REVERT: D 145 GLU cc_start: 0.8025 (mp0) cc_final: 0.7816 (mp0) REVERT: D 206 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7116 (mm-30) REVERT: B 77 ARG cc_start: 0.6437 (ttp80) cc_final: 0.5856 (ttp80) REVERT: B 217 GLN cc_start: 0.5870 (tm-30) cc_final: 0.5041 (tm-30) REVERT: B 225 ARG cc_start: 0.6287 (mpt180) cc_final: 0.5962 (ptm-80) REVERT: A 271 LYS cc_start: 0.8306 (ptpp) cc_final: 0.7910 (ptpt) REVERT: A 285 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7901 (mtm180) REVERT: A 344 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7306 (mtpt) REVERT: A 443 ILE cc_start: 0.7814 (mp) cc_final: 0.7318 (pt) REVERT: A 694 GLU cc_start: 0.7906 (tp30) cc_final: 0.7479 (tt0) REVERT: A 752 ASN cc_start: 0.7999 (t0) cc_final: 0.7781 (t0) REVERT: A 791 PHE cc_start: 0.8089 (p90) cc_final: 0.7787 (p90) REVERT: F 36 LEU cc_start: 0.6077 (pt) cc_final: 0.5586 (tm) REVERT: F 109 TRP cc_start: 0.7663 (t60) cc_final: 0.7281 (t60) REVERT: F 157 GLN cc_start: 0.6919 (tm-30) cc_final: 0.6713 (tm130) outliers start: 33 outliers final: 19 residues processed: 176 average time/residue: 0.4486 time to fit residues: 87.5564 Evaluate side-chains 166 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 737 CYS Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 139 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 58 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN B 287 GLN A 469 ASN A 648 ASN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.229010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.133107 restraints weight = 14690.926| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.40 r_work: 0.3417 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.089 13067 Z= 0.409 Angle : 0.810 11.987 17735 Z= 0.425 Chirality : 0.055 0.228 1951 Planarity : 0.006 0.071 2331 Dihedral : 5.044 25.803 1809 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.99 % Allowed : 17.55 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.20), residues: 1626 helix: 0.56 (0.31), residues: 285 sheet: 0.14 (0.21), residues: 524 loop : -1.37 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 365 TYR 0.025 0.003 TYR D 176 PHE 0.036 0.003 PHE A 726 TRP 0.012 0.002 TRP A 763 HIS 0.009 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.01004 / 0.41 (13066) covalent geometry : angle 0.80927 / 0.43 (17733) SS BOND : bond 0.00530 / 0.28 ( 1) SS BOND : angle 3.19510 / 1.68 ( 2) hydrogen bonds : bond 0.06531 / 4.31 ( 508) hydrogen bonds : angle 5.30079 / 3.83 ( 1425) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 153 PHE cc_start: 0.7528 (m-80) cc_final: 0.7080 (m-80) REVERT: D 206 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7444 (mm-30) REVERT: B 217 GLN cc_start: 0.5927 (tm-30) cc_final: 0.5157 (tm-30) REVERT: B 225 ARG cc_start: 0.6217 (mpt180) cc_final: 0.5956 (ptm-80) REVERT: B 338 GLN cc_start: 0.5561 (tt0) cc_final: 0.4905 (pm20) REVERT: A 271 LYS cc_start: 0.8217 (ptpp) cc_final: 0.8007 (ptpt) REVERT: A 285 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7827 (ttm170) REVERT: A 344 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7215 (mtpt) REVERT: A 694 GLU cc_start: 0.8314 (tp30) cc_final: 0.7912 (tt0) REVERT: A 791 PHE cc_start: 0.8143 (p90) cc_final: 0.7786 (p90) REVERT: F 36 LEU cc_start: 0.5916 (pt) cc_final: 0.5283 (tm) REVERT: F 109 TRP cc_start: 0.7665 (t60) cc_final: 0.7215 (t60) outliers start: 41 outliers final: 26 residues processed: 172 average time/residue: 0.4196 time to fit residues: 80.2898 Evaluate side-chains 163 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 219 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 101 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 60 optimal weight: 0.1980 chunk 123 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN B 287 GLN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.231604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.139559 restraints weight = 14634.852| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.08 r_work: 0.3442 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13067 Z= 0.200 Angle : 0.655 10.077 17735 Z= 0.341 Chirality : 0.047 0.208 1951 Planarity : 0.005 0.047 2331 Dihedral : 4.738 23.003 1809 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.33 % Allowed : 18.72 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.20), residues: 1626 helix: 0.93 (0.31), residues: 286 sheet: 0.17 (0.21), residues: 511 loop : -1.31 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 365 TYR 0.020 0.002 TYR F 91 PHE 0.021 0.002 PHE A 726 TRP 0.014 0.001 TRP B 215 HIS 0.004 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (13066) covalent geometry : angle 0.65450 / 0.34 (17733) SS BOND : bond 0.00095 / 0.05 ( 1) SS BOND : angle 2.99026 / 1.59 ( 2) hydrogen bonds : bond 0.04694 / 3.11 ( 508) hydrogen bonds : angle 5.03985 / 3.61 ( 1425) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 140 ARG cc_start: 0.7086 (tpt90) cc_final: 0.5956 (ttm-80) REVERT: D 153 PHE cc_start: 0.7452 (m-80) cc_final: 0.7009 (m-80) REVERT: B 217 GLN cc_start: 0.5829 (tm-30) cc_final: 0.4968 (tm-30) REVERT: B 225 ARG cc_start: 0.6239 (mpt180) cc_final: 0.5966 (ptm-80) REVERT: B 338 GLN cc_start: 0.5471 (tt0) cc_final: 0.4887 (pm20) REVERT: A 271 LYS cc_start: 0.8235 (ptpp) cc_final: 0.8034 (ptpt) REVERT: A 285 ARG cc_start: 0.8151 (ttm-80) cc_final: 0.7784 (mtm180) REVERT: A 344 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7214 (mtpt) REVERT: A 694 GLU cc_start: 0.8229 (tp30) cc_final: 0.7707 (tt0) REVERT: A 752 ASN cc_start: 0.7988 (t0) cc_final: 0.7747 (t0) REVERT: A 791 PHE cc_start: 0.8127 (p90) cc_final: 0.7802 (p90) REVERT: F 36 LEU cc_start: 0.5963 (pt) cc_final: 0.5403 (tm) REVERT: F 109 TRP cc_start: 0.7640 (t60) cc_final: 0.7338 (t60) outliers start: 32 outliers final: 24 residues processed: 166 average time/residue: 0.4425 time to fit residues: 81.4164 Evaluate side-chains 164 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 139 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN B 287 GLN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.233817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.137387 restraints weight = 14874.418| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.48 r_work: 0.3480 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13067 Z= 0.155 Angle : 0.633 11.741 17735 Z= 0.326 Chirality : 0.046 0.199 1951 Planarity : 0.004 0.047 2331 Dihedral : 4.580 22.540 1809 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.55 % Allowed : 18.50 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1626 helix: 1.19 (0.32), residues: 286 sheet: 0.17 (0.21), residues: 509 loop : -1.25 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 365 TYR 0.023 0.001 TYR A 228 PHE 0.016 0.001 PHE A 726 TRP 0.014 0.001 TRP B 215 HIS 0.004 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (13066) covalent geometry : angle 0.63199 / 0.33 (17733) SS BOND : bond 0.00296 / 0.16 ( 1) SS BOND : angle 2.66914 / 1.42 ( 2) hydrogen bonds : bond 0.04168 / 2.77 ( 508) hydrogen bonds : angle 4.92656 / 3.53 ( 1425) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 ASN cc_start: 0.7394 (p0) cc_final: 0.6374 (p0) REVERT: D 140 ARG cc_start: 0.7085 (tpt90) cc_final: 0.5945 (ttm-80) REVERT: D 153 PHE cc_start: 0.7361 (m-80) cc_final: 0.6983 (m-80) REVERT: B 77 ARG cc_start: 0.6482 (ttp80) cc_final: 0.6068 (ttp80) REVERT: B 217 GLN cc_start: 0.5835 (tm-30) cc_final: 0.4995 (tm-30) REVERT: B 225 ARG cc_start: 0.6265 (mpt180) cc_final: 0.5975 (ptm-80) REVERT: B 338 GLN cc_start: 0.5452 (tt0) cc_final: 0.4886 (pm20) REVERT: A 285 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7802 (mtm180) REVERT: A 344 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7190 (mtpt) REVERT: A 694 GLU cc_start: 0.8122 (tp30) cc_final: 0.7626 (tt0) REVERT: A 752 ASN cc_start: 0.8034 (t0) cc_final: 0.7805 (t0) REVERT: A 791 PHE cc_start: 0.8120 (p90) cc_final: 0.7757 (p90) REVERT: F 36 LEU cc_start: 0.5952 (pt) cc_final: 0.5424 (tm) REVERT: F 109 TRP cc_start: 0.7657 (t60) cc_final: 0.7352 (t60) outliers start: 35 outliers final: 24 residues processed: 166 average time/residue: 0.4547 time to fit residues: 83.2314 Evaluate side-chains 160 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 219 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 33 optimal weight: 0.0040 chunk 58 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN B 287 GLN E 71 ASN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.235537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138342 restraints weight = 14879.031| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.51 r_work: 0.3517 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13067 Z= 0.112 Angle : 0.617 11.931 17735 Z= 0.313 Chirality : 0.045 0.216 1951 Planarity : 0.004 0.049 2331 Dihedral : 4.346 21.593 1809 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.97 % Allowed : 19.16 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.20), residues: 1626 helix: 1.44 (0.32), residues: 286 sheet: 0.35 (0.22), residues: 492 loop : -1.15 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.023 0.001 TYR A 228 PHE 0.009 0.001 PHE D 143 TRP 0.015 0.001 TRP A 375 HIS 0.004 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (13066) covalent geometry : angle 0.61645 / 0.31 (17733) SS BOND : bond 0.00212 / 0.11 ( 1) SS BOND : angle 2.08084 / 1.11 ( 2) hydrogen bonds : bond 0.03373 / 2.25 ( 508) hydrogen bonds : angle 4.76850 / 3.40 ( 1425) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 ASN cc_start: 0.7297 (p0) cc_final: 0.6319 (p0) REVERT: D 140 ARG cc_start: 0.6966 (tpt90) cc_final: 0.5700 (mtt90) REVERT: D 206 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7205 (mm-30) REVERT: B 77 ARG cc_start: 0.6410 (ttp80) cc_final: 0.6011 (ttp80) REVERT: B 217 GLN cc_start: 0.5852 (tm-30) cc_final: 0.5048 (tm-30) REVERT: B 225 ARG cc_start: 0.6307 (mpt180) cc_final: 0.5980 (ptm-80) REVERT: B 338 GLN cc_start: 0.5442 (tt0) cc_final: 0.4873 (pm20) REVERT: A 285 ARG cc_start: 0.8161 (ttm-80) cc_final: 0.7772 (mtm180) REVERT: A 344 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7395 (mtpt) REVERT: A 408 ASP cc_start: 0.8061 (p0) cc_final: 0.7717 (p0) REVERT: A 694 GLU cc_start: 0.8057 (tp30) cc_final: 0.7566 (tt0) REVERT: A 791 PHE cc_start: 0.8112 (p90) cc_final: 0.7800 (p90) REVERT: F 36 LEU cc_start: 0.5926 (pt) cc_final: 0.5726 (mm) REVERT: F 109 TRP cc_start: 0.7698 (t60) cc_final: 0.7333 (t60) outliers start: 27 outliers final: 18 residues processed: 159 average time/residue: 0.4509 time to fit residues: 79.3572 Evaluate side-chains 151 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 139 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 76 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 9 optimal weight: 0.0570 chunk 95 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 3 optimal weight: 0.3980 chunk 36 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 GLN A 752 ASN E 71 ASN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.235835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.142269 restraints weight = 14664.092| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.40 r_work: 0.3527 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13067 Z= 0.106 Angle : 0.608 11.975 17735 Z= 0.309 Chirality : 0.045 0.188 1951 Planarity : 0.004 0.050 2331 Dihedral : 4.207 21.804 1809 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.75 % Allowed : 19.66 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.20), residues: 1626 helix: 1.67 (0.33), residues: 280 sheet: 0.43 (0.22), residues: 490 loop : -1.03 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 120 TYR 0.024 0.001 TYR A 228 PHE 0.009 0.001 PHE D 143 TRP 0.015 0.001 TRP A 375 HIS 0.005 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (13066) covalent geometry : angle 0.60792 / 0.31 (17733) SS BOND : bond 0.00152 / 0.08 ( 1) SS BOND : angle 1.76625 / 0.94 ( 2) hydrogen bonds : bond 0.03157 / 2.11 ( 508) hydrogen bonds : angle 4.65223 / 3.32 ( 1425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5634.27 seconds wall clock time: 96 minutes 13.54 seconds (5773.54 seconds total)