Starting phenix.real_space_refine on Sun Oct 25 11:23:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xfo_66834/10_2026/9xfo_66834.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xfo_66834/10_2026/9xfo_66834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xfo_66834/10_2026/9xfo_66834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xfo_66834/10_2026/9xfo_66834.map" model { file = "/net/cci-nas-00/data/ceres_data/9xfo_66834/10_2026/9xfo_66834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xfo_66834/10_2026/9xfo_66834.cif" } resolution = 3.04 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= 0.010 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 52 5.16 5 C 10174 2.51 5 N 2809 2.21 5 O 3198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16233 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6233 Classifications: {'peptide': 788} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 758} Chain: "B" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2795 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain: "C" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2307 Classifications: {'peptide': 304} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 287} Chain breaks: 1 Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1761 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 706 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain: "F" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2431 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 9, 'TRANS': 300} Chain breaks: 1 Time building chain proxies: 3.29, per 1000 atoms: 0.20 Number of scatterers: 16233 At special positions: 0 Unit cell: (132.24, 125.4, 158.08, 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 52 16.00 O 3198 8.00 N 2809 7.00 C 10174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS F 336 " distance=2.23 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 818.9 milliseconds 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3834 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 22 sheets defined 31.7% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 117 Processing helix chain 'A' and resid 126 through 144 removed outlier: 3.529A pdb=" N VAL A 144 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.725A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.695A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.898A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'C' and resid 29 through 33 removed outlier: 3.836A pdb=" N LYS C 32 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.533A pdb=" N ALA C 79 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 76 through 80' Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 190 through 214 removed outlier: 3.569A pdb=" N TYR C 197 " --> pdb=" O SER C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 262 Proline residue: C 256 - end of helix Processing helix chain 'C' and resid 284 through 292 Processing helix chain 'C' and resid 327 through 344 removed outlier: 3.856A pdb=" N LYS C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 68 through 83 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 120 removed outlier: 3.659A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.644A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.509A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 215 " --> pdb=" O THR D 211 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 229 through 243 removed outlier: 3.618A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 removed outlier: 3.622A pdb=" N LYS E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 57 Processing helix chain 'F' and resid 62 through 88 Processing helix chain 'F' and resid 92 through 107 Processing helix chain 'F' and resid 110 through 121 Processing helix chain 'F' and resid 124 through 150 Processing helix chain 'F' and resid 153 through 167 removed outlier: 3.964A pdb=" N VAL F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN F 167 " --> pdb=" O GLN F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 316 Processing helix chain 'F' and resid 320 through 329 Processing helix chain 'F' and resid 331 through 336 Processing helix chain 'F' and resid 345 through 349 Processing helix chain 'F' and resid 350 through 360 Processing helix chain 'F' and resid 388 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.549A pdb=" N LEU A 85 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A 77 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN A 87 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL A 75 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS A 89 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 77 " --> pdb=" O ASP F 26 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP F 26 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.462A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N PHE A 169 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 5.857A pdb=" N ILE A 254 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 193 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276 removed outlier: 7.274A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL A 273 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL A 341 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY A 275 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 4.359A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 424 through 429 removed outlier: 5.884A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.656A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.107A pdb=" N THR B 46 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR B 391 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.604A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.274A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.732A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 206 through 210 removed outlier: 6.304A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.804A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292 Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.659A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 96 through 100 removed outlier: 6.731A pdb=" N ARG C 160 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU C 181 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG C 158 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 131 through 135 removed outlier: 4.190A pdb=" N TYR C 161 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG C 158 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU C 181 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG C 160 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 230 through 234 removed outlier: 5.720A pdb=" N PHE C 318 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR C 279 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL C 266 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.082A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 32 through 35 Processing sheet with id=AC3, first strand: chain 'F' and resid 35 through 38 removed outlier: 6.876A pdb=" N GLY F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL F 31 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL F 37 " --> pdb=" O ALA F 29 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 340 through 344 removed outlier: 5.924A pdb=" N ASP F 340 " --> pdb=" O HIS F 289 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N HIS F 289 " --> pdb=" O ASP F 340 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY F 342 " --> pdb=" O ALA F 287 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA F 287 " --> pdb=" O GLY F 342 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG F 288 " --> pdb=" O LEU F 380 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU F 380 " --> pdb=" O ARG F 288 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 290 " --> pdb=" O ILE F 378 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ILE F 378 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU F 292 " --> pdb=" O HIS F 376 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N HIS F 376 " --> pdb=" O LEU F 292 " (cutoff:3.500A) 811 hydrogen bonds defined for protein. 2274 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: 2.88 Time building geometry restraints manager: 1.75 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: 5467 1.34 - 1.47: 3740 1.47 - 1.59: 7245 1.59 - 1.72: 0 1.72 - 1.84: 102 Bond restraints: 16554 Sorted by residual: bond pdb=" N GLN F 337 " pdb=" CA GLN F 337 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.15e-02 7.56e+03 1.22e+01 bond pdb=" N ILE F 280 " pdb=" CA ILE F 280 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.11e-02 8.12e+03 1.22e+01 bond pdb=" C PHE A 586 " pdb=" O PHE A 586 " ideal model delta sigma weight residual 1.235 1.220 0.015 4.70e-03 4.53e+04 1.07e+01 bond pdb=" N VAL B 30 " pdb=" CA VAL B 30 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" N VAL B 29 " pdb=" CA VAL B 29 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.22e-02 6.72e+03 9.63e+00 ... (remaining 16549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 22166 3.86 - 7.71: 287 7.71 - 11.57: 21 11.57 - 15.42: 2 15.42 - 19.28: 1 Bond angle restraints: 22477 Sorted by residual: angle pdb=" C GLU A 90 " pdb=" N ARG A 91 " pdb=" CA ARG A 91 " ideal model delta sigma weight residual 120.39 132.94 -12.55 1.39e+00 5.18e-01 8.15e+01 angle pdb=" N GLY A 424 " pdb=" CA GLY A 424 " pdb=" C GLY A 424 " ideal model delta sigma weight residual 111.15 122.70 -11.55 1.76e+00 3.23e-01 4.31e+01 angle pdb=" CB MET F 114 " pdb=" CG MET F 114 " pdb=" SD MET F 114 " ideal model delta sigma weight residual 112.70 93.42 19.28 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C THR A 423 " pdb=" N GLY A 424 " pdb=" CA GLY A 424 " ideal model delta sigma weight residual 120.92 127.68 -6.76 1.15e+00 7.56e-01 3.46e+01 angle pdb=" N SER F 334 " pdb=" CA SER F 334 " pdb=" C SER F 334 " ideal model delta sigma weight residual 112.89 105.90 6.99 1.24e+00 6.50e-01 3.17e+01 ... (remaining 22472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9034 17.98 - 35.97: 643 35.97 - 53.95: 164 53.95 - 71.94: 37 71.94 - 89.92: 16 Dihedral angle restraints: 9894 sinusoidal: 3897 harmonic: 5997 Sorted by residual: dihedral pdb=" CA ASN B 266 " pdb=" C ASN B 266 " pdb=" N LEU B 267 " pdb=" CA LEU B 267 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA SER F 366 " pdb=" C SER F 366 " pdb=" N ALA F 367 " pdb=" CA ALA F 367 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA MET C 276 " pdb=" C MET C 276 " pdb=" N ALA C 277 " pdb=" CA ALA C 277 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 9891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1668 0.049 - 0.097: 550 0.097 - 0.146: 214 0.146 - 0.194: 38 0.194 - 0.243: 8 Chirality restraints: 2478 Sorted by residual: chirality pdb=" CA MET F 114 " pdb=" N MET F 114 " pdb=" C MET F 114 " pdb=" CB MET F 114 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA PRO A 723 " pdb=" N PRO A 723 " pdb=" C PRO A 723 " pdb=" CB PRO A 723 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB VAL F 24 " pdb=" CA VAL F 24 " pdb=" CG1 VAL F 24 " pdb=" CG2 VAL F 24 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2475 not shown) Planarity restraints: 2968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 64 " -0.035 2.00e-02 2.50e+03 2.78e-02 1.36e+01 pdb=" CG PHE D 64 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE D 64 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE D 64 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 64 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 64 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE D 64 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 413 " -0.022 2.00e-02 2.50e+03 1.98e-02 9.77e+00 pdb=" CG TRP F 413 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP F 413 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP F 413 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 413 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP F 413 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 413 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 413 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 413 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP F 413 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 169 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" C PHE A 169 " 0.051 2.00e-02 2.50e+03 pdb=" O PHE A 169 " -0.019 2.00e-02 2.50e+03 pdb=" N GLN A 170 " -0.017 2.00e-02 2.50e+03 ... (remaining 2965 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 24 2.55 - 3.14: 12541 3.14 - 3.73: 23779 3.73 - 4.31: 33118 4.31 - 4.90: 55584 Nonbonded interactions: 125046 Sorted by model distance: nonbonded pdb=" ND2 ASN A 340 " pdb=" SG CYS F 336 " model vdw 1.963 3.480 nonbonded pdb=" O THR B 239 " pdb=" OD1 ASP B 242 " model vdw 2.374 3.040 nonbonded pdb=" O SER B 112 " pdb=" OG SER B 112 " model vdw 2.397 3.040 nonbonded pdb=" O ASN B 62 " pdb=" OD1 ASN B 62 " model vdw 2.411 3.040 nonbonded pdb=" OG1 THR B 309 " pdb=" O GLY B 312 " model vdw 2.435 3.040 ... (remaining 125041 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: 5.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.940 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 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 : 0.006 0.195 16555 Z= 0.360 Angle : 1.159 43.618 22479 Z= 0.714 Chirality : 0.057 0.243 2478 Planarity : 0.007 0.089 2968 Dihedral : 14.245 89.922 6057 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 1.49 % Allowed : 13.35 % Favored : 85.16 % 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: 0.64 (0.18), residues: 2065 helix: 1.30 (0.19), residues: 618 sheet: 0.81 (0.21), residues: 558 loop : -0.38 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG F 404 TYR 0.029 0.003 TYR A 585 PHE 0.062 0.002 PHE D 64 TRP 0.054 0.003 TRP F 413 HIS 0.008 0.002 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.35 (16554) covalent geometry : angle 1.12061 / 0.70 (22477) SS BOND : bond 0.19511 / 12.19 ( 1) SS BOND : angle 31.44335 / 11.03 ( 2) hydrogen bonds : bond 0.12071 / 8.09 ( 800) hydrogen bonds : angle 5.98631 / 4.25 ( 2274) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8192 (mmm160) REVERT: A 123 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8088 (mm-30) REVERT: A 321 ARG cc_start: 0.8069 (ptm-80) cc_final: 0.7843 (ptt90) REVERT: A 674 TYR cc_start: 0.8063 (m-80) cc_final: 0.7818 (m-80) REVERT: A 703 ASP cc_start: 0.7904 (p0) cc_final: 0.7449 (m-30) REVERT: A 725 ILE cc_start: 0.7718 (mm) cc_final: 0.7203 (tp) REVERT: B 82 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8308 (mtpp) REVERT: C 182 GLU cc_start: 0.7930 (pt0) cc_final: 0.7346 (pm20) REVERT: C 190 ASP cc_start: 0.8281 (t0) cc_final: 0.7902 (t70) REVERT: C 325 THR cc_start: 0.8885 (t) cc_final: 0.8637 (m) REVERT: C 327 THR cc_start: 0.7483 (p) cc_final: 0.6912 (t) REVERT: D 41 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8280 (tm-30) REVERT: E 107 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8543 (mtpp) REVERT: F 36 VAL cc_start: 0.8075 (m) cc_final: 0.7820 (t) REVERT: F 156 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7866 (mt-10) REVERT: F 360 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7926 (mm) REVERT: F 400 MET cc_start: 0.8869 (mtm) cc_final: 0.8306 (tmm) outliers start: 26 outliers final: 9 residues processed: 175 average time/residue: 0.1340 time to fit residues: 34.4120 Evaluate side-chains 126 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain F residue 360 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 523 ASN B 144 GLN B 347 HIS B 360 GLN C 110 ASN C 273 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.108037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.062883 restraints weight = 36652.124| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.34 r_work: 0.2751 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 16555 Z= 0.348 Angle : 0.755 9.405 22479 Z= 0.417 Chirality : 0.050 0.223 2478 Planarity : 0.005 0.062 2968 Dihedral : 5.707 55.011 2297 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.00 % Rotamer: Outliers : 2.29 % Allowed : 12.09 % Favored : 85.62 % 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: 0.72 (0.18), residues: 2065 helix: 1.88 (0.20), residues: 612 sheet: 0.77 (0.20), residues: 589 loop : -0.74 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 399 TYR 0.021 0.002 TYR D 77 PHE 0.026 0.003 PHE A 72 TRP 0.022 0.003 TRP F 413 HIS 0.008 0.002 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00846 / 0.35 (16554) covalent geometry : angle 0.75461 / 0.42 (22477) SS BOND : bond 0.02197 / 1.37 ( 1) SS BOND : angle 2.81321 / 1.33 ( 2) hydrogen bonds : bond 0.08195 / 5.63 ( 800) hydrogen bonds : angle 5.23404 / 3.71 ( 2274) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8165 (mm-30) REVERT: A 206 TRP cc_start: 0.8209 (p90) cc_final: 0.7971 (p-90) REVERT: A 222 ASP cc_start: 0.8617 (m-30) cc_final: 0.8244 (m-30) REVERT: B 58 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8482 (p0) REVERT: C 145 TRP cc_start: 0.8374 (m100) cc_final: 0.7757 (m100) REVERT: C 182 GLU cc_start: 0.7918 (pt0) cc_final: 0.7394 (pm20) REVERT: C 190 ASP cc_start: 0.8021 (t0) cc_final: 0.7543 (t70) REVERT: C 194 MET cc_start: 0.8453 (mmt) cc_final: 0.8191 (mmt) REVERT: C 232 SER cc_start: 0.7202 (OUTLIER) cc_final: 0.6778 (m) REVERT: C 241 MET cc_start: 0.8230 (ptp) cc_final: 0.7977 (pmm) REVERT: D 41 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8289 (tm-30) REVERT: E 107 LYS cc_start: 0.8977 (mtmt) cc_final: 0.8625 (mtpt) REVERT: F 83 MET cc_start: 0.8981 (tpt) cc_final: 0.8440 (tpt) REVERT: F 87 MET cc_start: 0.9062 (mpt) cc_final: 0.8712 (mpt) REVERT: F 114 MET cc_start: 0.8635 (mmt) cc_final: 0.8025 (mmm) REVERT: F 400 MET cc_start: 0.8953 (mtm) cc_final: 0.8376 (tmm) REVERT: F 414 MET cc_start: 0.8175 (mmp) cc_final: 0.7828 (mmm) outliers start: 40 outliers final: 20 residues processed: 146 average time/residue: 0.1254 time to fit residues: 28.1009 Evaluate side-chains 126 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 365 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [10, 3, 118, 19, 204, 14, 89, 163, 139, 9, 203] chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN F 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.110521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.064727 restraints weight = 36452.850| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.58 r_work: 0.2816 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16555 Z= 0.136 Angle : 0.545 7.261 22479 Z= 0.298 Chirality : 0.043 0.176 2478 Planarity : 0.004 0.047 2968 Dihedral : 4.800 59.712 2283 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 1.60 % Allowed : 13.12 % Favored : 85.27 % 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: 0.96 (0.18), residues: 2065 helix: 2.39 (0.20), residues: 605 sheet: 0.71 (0.21), residues: 588 loop : -0.67 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 313 TYR 0.014 0.001 TYR D 184 PHE 0.020 0.001 PHE C 99 TRP 0.016 0.001 TRP B 143 HIS 0.004 0.001 HIS F 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (16554) covalent geometry : angle 0.54422 / 0.30 (22477) SS BOND : bond 0.00025 / 0.02 ( 1) SS BOND : angle 2.51872 / 1.19 ( 2) hydrogen bonds : bond 0.05402 / 3.67 ( 800) hydrogen bonds : angle 4.67293 / 3.32 ( 2274) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.9342 (mmm) cc_final: 0.9125 (mmm) REVERT: A 123 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8132 (mm-30) REVERT: A 206 TRP cc_start: 0.8156 (p90) cc_final: 0.7932 (p-90) REVERT: A 222 ASP cc_start: 0.8536 (m-30) cc_final: 0.8115 (m-30) REVERT: A 725 ILE cc_start: 0.8164 (mm) cc_final: 0.7623 (tp) REVERT: B 58 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8461 (p0) REVERT: C 182 GLU cc_start: 0.7740 (pt0) cc_final: 0.7256 (pm20) REVERT: C 186 LYS cc_start: 0.8081 (mmtm) cc_final: 0.7782 (mppt) REVERT: C 190 ASP cc_start: 0.7972 (t0) cc_final: 0.7401 (t70) REVERT: C 194 MET cc_start: 0.8500 (mmt) cc_final: 0.8287 (mmt) REVERT: C 232 SER cc_start: 0.6801 (OUTLIER) cc_final: 0.6478 (t) REVERT: D 41 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8243 (tm-30) REVERT: E 107 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8374 (mtpt) REVERT: F 83 MET cc_start: 0.8993 (tpt) cc_final: 0.8333 (tpt) REVERT: F 87 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8725 (mpt) REVERT: F 114 MET cc_start: 0.8612 (mmt) cc_final: 0.8202 (mmm) REVERT: F 156 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8549 (pm20) REVERT: F 400 MET cc_start: 0.8928 (mtm) cc_final: 0.8340 (tmm) REVERT: F 402 MET cc_start: 0.8676 (mmm) cc_final: 0.8414 (mmm) REVERT: F 414 MET cc_start: 0.8038 (mmp) cc_final: 0.7744 (mmm) outliers start: 28 outliers final: 12 residues processed: 132 average time/residue: 0.1323 time to fit residues: 26.3116 Evaluate side-chains 120 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 156 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [63, 45, 30, 104, 110, 7, 21, 147, 173, 204, 171] chunk 63 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS A 323 GLN C 330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.108117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.063034 restraints weight = 35948.603| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.37 r_work: 0.2756 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16555 Z= 0.191 Angle : 0.563 6.852 22479 Z= 0.308 Chirality : 0.044 0.155 2478 Planarity : 0.004 0.048 2968 Dihedral : 4.719 56.064 2279 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.58 % Favored : 96.37 % Rotamer: Outliers : 1.89 % Allowed : 13.75 % Favored : 84.36 % 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: 0.85 (0.18), residues: 2065 helix: 2.36 (0.20), residues: 606 sheet: 0.77 (0.21), residues: 574 loop : -0.88 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 273 TYR 0.015 0.001 TYR C 197 PHE 0.021 0.002 PHE A 24 TRP 0.016 0.002 TRP B 143 HIS 0.004 0.001 HIS F 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (16554) covalent geometry : angle 0.56239 / 0.31 (22477) SS BOND : bond 0.01962 / 1.23 ( 1) SS BOND : angle 2.19447 / 1.04 ( 2) hydrogen bonds : bond 0.06174 / 4.21 ( 800) hydrogen bonds : angle 4.62959 / 3.29 ( 2274) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8185 (mm-30) REVERT: A 206 TRP cc_start: 0.8138 (p90) cc_final: 0.7910 (p-90) REVERT: A 222 ASP cc_start: 0.8548 (m-30) cc_final: 0.8100 (m-30) REVERT: A 725 ILE cc_start: 0.8314 (mm) cc_final: 0.7759 (tp) REVERT: B 58 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8413 (p0) REVERT: B 294 ASN cc_start: 0.9230 (m110) cc_final: 0.8936 (t0) REVERT: C 145 TRP cc_start: 0.8316 (m100) cc_final: 0.7754 (m100) REVERT: C 182 GLU cc_start: 0.7707 (pt0) cc_final: 0.7278 (pm20) REVERT: C 186 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7784 (mppt) REVERT: C 190 ASP cc_start: 0.7903 (t0) cc_final: 0.7353 (t70) REVERT: C 232 SER cc_start: 0.6903 (OUTLIER) cc_final: 0.6624 (t) REVERT: D 41 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8256 (tm-30) REVERT: E 107 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8537 (mtpp) REVERT: F 83 MET cc_start: 0.9005 (tpt) cc_final: 0.8383 (tpt) REVERT: F 87 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8736 (mpt) REVERT: F 114 MET cc_start: 0.8627 (mmt) cc_final: 0.8167 (mmm) REVERT: F 156 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8450 (pm20) REVERT: F 400 MET cc_start: 0.8903 (mtm) cc_final: 0.8350 (tmm) REVERT: F 402 MET cc_start: 0.8641 (mmm) cc_final: 0.8413 (mmm) REVERT: F 414 MET cc_start: 0.8048 (mmp) cc_final: 0.7723 (mmm) outliers start: 33 outliers final: 18 residues processed: 135 average time/residue: 0.1187 time to fit residues: 24.5594 Evaluate side-chains 132 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 365 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [78, 174, 144, 183, 132, 137, 91, 152, 182, 35, 200] chunk 78 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 678 GLN C 168 GLN C 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.106553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.060486 restraints weight = 36430.308| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.52 r_work: 0.2700 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16555 Z= 0.266 Angle : 0.611 6.443 22479 Z= 0.335 Chirality : 0.046 0.154 2478 Planarity : 0.005 0.061 2968 Dihedral : 4.795 52.460 2277 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.87 % Favored : 96.08 % Rotamer: Outliers : 2.12 % Allowed : 14.38 % Favored : 83.50 % 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: 0.54 (0.18), residues: 2065 helix: 2.21 (0.20), residues: 606 sheet: 0.49 (0.21), residues: 573 loop : -1.07 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 223 TYR 0.017 0.002 TYR D 77 PHE 0.017 0.002 PHE A 24 TRP 0.019 0.002 TRP A 776 HIS 0.005 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.27 (16554) covalent geometry : angle 0.61063 / 0.34 (22477) SS BOND : bond 0.00275 / 0.17 ( 1) SS BOND : angle 1.99640 / 0.95 ( 2) hydrogen bonds : bond 0.06985 / 4.78 ( 800) hydrogen bonds : angle 4.70335 / 3.35 ( 2274) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8374 (mm-30) REVERT: A 206 TRP cc_start: 0.8203 (p90) cc_final: 0.8002 (p-90) REVERT: A 222 ASP cc_start: 0.8590 (m-30) cc_final: 0.8175 (m-30) REVERT: A 552 MET cc_start: 0.8835 (tpp) cc_final: 0.8515 (tpp) REVERT: B 58 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8382 (p0) REVERT: B 294 ASN cc_start: 0.9256 (m110) cc_final: 0.8951 (t0) REVERT: C 145 TRP cc_start: 0.8317 (m100) cc_final: 0.7818 (m100) REVERT: C 182 GLU cc_start: 0.7800 (pt0) cc_final: 0.7361 (pm20) REVERT: C 186 LYS cc_start: 0.8168 (mmtm) cc_final: 0.7877 (mppt) REVERT: C 190 ASP cc_start: 0.7877 (t0) cc_final: 0.7395 (t70) REVERT: C 232 SER cc_start: 0.7036 (OUTLIER) cc_final: 0.6751 (t) REVERT: D 41 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8237 (tm-30) REVERT: E 107 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8490 (mtpt) REVERT: F 83 MET cc_start: 0.9034 (tpt) cc_final: 0.8575 (tpt) REVERT: F 87 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8771 (mpt) REVERT: F 114 MET cc_start: 0.8700 (mmt) cc_final: 0.8160 (mmm) REVERT: F 156 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8557 (pm20) REVERT: F 158 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8713 (pp20) REVERT: F 400 MET cc_start: 0.8934 (mtm) cc_final: 0.8389 (tmm) REVERT: F 402 MET cc_start: 0.8688 (mmm) cc_final: 0.8431 (mmm) REVERT: F 414 MET cc_start: 0.8100 (mmp) cc_final: 0.7790 (mmm) outliers start: 37 outliers final: 22 residues processed: 134 average time/residue: 0.1240 time to fit residues: 25.3434 Evaluate side-chains 132 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 365 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [202, 30, 22, 49, 157, 44, 123, 107, 78, 15, 138] chunk 202 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 138 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.108473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.062866 restraints weight = 36196.996| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.49 r_work: 0.2773 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16555 Z= 0.151 Angle : 0.531 6.888 22479 Z= 0.289 Chirality : 0.043 0.149 2478 Planarity : 0.004 0.047 2968 Dihedral : 4.560 49.715 2277 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.95 % Rotamer: Outliers : 1.95 % Allowed : 14.90 % Favored : 83.15 % 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: 0.67 (0.18), residues: 2065 helix: 2.44 (0.20), residues: 606 sheet: 0.49 (0.21), residues: 567 loop : -1.02 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 223 TYR 0.015 0.001 TYR D 67 PHE 0.016 0.001 PHE A 24 TRP 0.015 0.001 TRP B 143 HIS 0.003 0.001 HIS F 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (16554) covalent geometry : angle 0.53051 / 0.29 (22477) SS BOND : bond 0.00058 / 0.04 ( 1) SS BOND : angle 1.80455 / 0.86 ( 2) hydrogen bonds : bond 0.05462 / 3.72 ( 800) hydrogen bonds : angle 4.45526 / 3.17 ( 2274) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8566 (m-30) cc_final: 0.8156 (m-30) REVERT: B 26 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: B 43 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8329 (t) REVERT: B 58 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8379 (p0) REVERT: B 294 ASN cc_start: 0.9187 (m110) cc_final: 0.8915 (t0) REVERT: C 96 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7506 (ttp80) REVERT: C 145 TRP cc_start: 0.8314 (m100) cc_final: 0.7830 (m100) REVERT: C 182 GLU cc_start: 0.7834 (pt0) cc_final: 0.7420 (pm20) REVERT: C 186 LYS cc_start: 0.8270 (mmtm) cc_final: 0.7963 (mppt) REVERT: C 190 ASP cc_start: 0.7812 (t0) cc_final: 0.7247 (t70) REVERT: C 194 MET cc_start: 0.8452 (mmt) cc_final: 0.8223 (mmt) REVERT: C 232 SER cc_start: 0.7162 (OUTLIER) cc_final: 0.6850 (t) REVERT: D 41 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8346 (tm-30) REVERT: E 107 LYS cc_start: 0.8886 (mtmt) cc_final: 0.8492 (mtpt) REVERT: F 83 MET cc_start: 0.9047 (tpt) cc_final: 0.8810 (tpt) REVERT: F 114 MET cc_start: 0.8730 (mmt) cc_final: 0.8215 (mmm) REVERT: F 156 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8572 (pm20) REVERT: F 158 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8724 (pp20) REVERT: F 400 MET cc_start: 0.8919 (mtm) cc_final: 0.8405 (tmm) REVERT: F 402 MET cc_start: 0.8725 (mmm) cc_final: 0.8453 (mmm) REVERT: F 414 MET cc_start: 0.8131 (mmp) cc_final: 0.7887 (ttm) outliers start: 34 outliers final: 19 residues processed: 132 average time/residue: 0.1243 time to fit residues: 25.1078 Evaluate side-chains 134 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 156 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [157, 147, 191, 163, 23, 126, 105, 117, 182, 203, 103] chunk 157 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 191 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 126 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 182 optimal weight: 0.6980 chunk 203 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.109023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.063503 restraints weight = 36000.702| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.47 r_work: 0.2806 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16555 Z= 0.129 Angle : 0.508 7.102 22479 Z= 0.275 Chirality : 0.042 0.150 2478 Planarity : 0.004 0.045 2968 Dihedral : 4.399 50.455 2277 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.39 % Favored : 96.56 % Rotamer: Outliers : 1.72 % Allowed : 15.24 % Favored : 83.04 % 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: 0.78 (0.18), residues: 2065 helix: 2.56 (0.20), residues: 606 sheet: 0.49 (0.21), residues: 582 loop : -0.96 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 223 TYR 0.014 0.001 TYR D 184 PHE 0.014 0.001 PHE A 24 TRP 0.014 0.001 TRP B 143 HIS 0.003 0.001 HIS F 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (16554) covalent geometry : angle 0.50741 / 0.27 (22477) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 1.76047 / 0.84 ( 2) hydrogen bonds : bond 0.05032 / 3.42 ( 800) hydrogen bonds : angle 4.31694 / 3.07 ( 2274) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8561 (m-30) cc_final: 0.8119 (m-30) REVERT: B 26 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: B 43 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8324 (t) REVERT: B 58 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8398 (p0) REVERT: B 294 ASN cc_start: 0.9164 (m110) cc_final: 0.8900 (t0) REVERT: C 145 TRP cc_start: 0.8308 (m100) cc_final: 0.7807 (m100) REVERT: C 182 GLU cc_start: 0.7779 (pt0) cc_final: 0.7378 (pm20) REVERT: C 186 LYS cc_start: 0.8326 (mmtm) cc_final: 0.8061 (mppt) REVERT: C 190 ASP cc_start: 0.7649 (t0) cc_final: 0.7032 (t70) REVERT: C 194 MET cc_start: 0.8400 (mmt) cc_final: 0.8142 (mmt) REVERT: C 232 SER cc_start: 0.7072 (OUTLIER) cc_final: 0.6748 (t) REVERT: D 41 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8321 (tm-30) REVERT: E 107 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8400 (mtpt) REVERT: F 83 MET cc_start: 0.9098 (tpt) cc_final: 0.8355 (tpt) REVERT: F 87 MET cc_start: 0.9009 (mpt) cc_final: 0.8543 (mpt) REVERT: F 114 MET cc_start: 0.8745 (mmt) cc_final: 0.8260 (mmm) REVERT: F 156 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8585 (pm20) REVERT: F 158 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8720 (pp20) REVERT: F 400 MET cc_start: 0.8913 (mtm) cc_final: 0.8405 (tmm) REVERT: F 402 MET cc_start: 0.8693 (mmm) cc_final: 0.8417 (mmm) REVERT: F 414 MET cc_start: 0.8125 (mmp) cc_final: 0.7913 (ttm) outliers start: 30 outliers final: 19 residues processed: 135 average time/residue: 0.1150 time to fit residues: 23.7798 Evaluate side-chains 133 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 360 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [74, 170, 163, 76, 104, 62, 111, 101, 110, 59, 38] chunk 74 optimal weight: 5.9990 chunk 170 optimal weight: 0.0040 chunk 163 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.0020 overall best weight: 1.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.109575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.064136 restraints weight = 36233.106| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.49 r_work: 0.2847 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16555 Z= 0.117 Angle : 0.501 7.186 22479 Z= 0.269 Chirality : 0.042 0.149 2478 Planarity : 0.004 0.044 2968 Dihedral : 4.273 50.990 2277 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.05 % Favored : 96.90 % Rotamer: Outliers : 1.78 % Allowed : 15.36 % Favored : 82.87 % 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: 0.89 (0.19), residues: 2065 helix: 2.72 (0.21), residues: 605 sheet: 0.49 (0.22), residues: 584 loop : -0.89 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 223 TYR 0.014 0.001 TYR D 184 PHE 0.013 0.001 PHE A 24 TRP 0.014 0.001 TRP B 317 HIS 0.003 0.001 HIS F 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (16554) covalent geometry : angle 0.50047 / 0.27 (22477) SS BOND : bond 0.00049 / 0.03 ( 1) SS BOND : angle 1.70410 / 0.81 ( 2) hydrogen bonds : bond 0.04632 / 3.14 ( 800) hydrogen bonds : angle 4.21538 / 3.00 ( 2274) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 725 ILE cc_start: 0.8481 (mm) cc_final: 0.7998 (tp) REVERT: B 26 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: B 43 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8408 (t) REVERT: B 58 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8426 (p0) REVERT: C 96 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7533 (ttp80) REVERT: C 145 TRP cc_start: 0.8346 (m100) cc_final: 0.7837 (m100) REVERT: C 177 LYS cc_start: 0.9353 (tmtt) cc_final: 0.9089 (tptp) REVERT: C 182 GLU cc_start: 0.7793 (pt0) cc_final: 0.7389 (pm20) REVERT: C 186 LYS cc_start: 0.8419 (mmtm) cc_final: 0.8169 (mppt) REVERT: C 190 ASP cc_start: 0.7497 (t0) cc_final: 0.6879 (t70) REVERT: C 232 SER cc_start: 0.7058 (OUTLIER) cc_final: 0.6723 (t) REVERT: D 41 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8339 (tm-30) REVERT: E 107 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8442 (mtpt) REVERT: F 83 MET cc_start: 0.9078 (tpt) cc_final: 0.8471 (tpt) REVERT: F 87 MET cc_start: 0.9059 (mpt) cc_final: 0.8624 (mpt) REVERT: F 94 GLU cc_start: 0.9284 (tm-30) cc_final: 0.8997 (pm20) REVERT: F 114 MET cc_start: 0.8731 (mmt) cc_final: 0.8243 (mmm) REVERT: F 156 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8565 (mp0) REVERT: F 158 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8712 (pp20) REVERT: F 400 MET cc_start: 0.8900 (mtm) cc_final: 0.8396 (tmm) REVERT: F 402 MET cc_start: 0.8704 (mmm) cc_final: 0.8371 (mmm) outliers start: 31 outliers final: 19 residues processed: 135 average time/residue: 0.1251 time to fit residues: 25.7294 Evaluate side-chains 134 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 360 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [193, 113, 21, 27, 102, 78, 91, 30, 108, 12, 56] chunk 193 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 108 optimal weight: 0.0670 chunk 12 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.107145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.061357 restraints weight = 36288.172| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.52 r_work: 0.2736 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16555 Z= 0.219 Angle : 0.567 7.203 22479 Z= 0.308 Chirality : 0.044 0.150 2478 Planarity : 0.004 0.046 2968 Dihedral : 4.395 48.123 2275 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.31 % Favored : 95.64 % Rotamer: Outliers : 1.55 % Allowed : 15.70 % Favored : 82.75 % 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: 0.69 (0.18), residues: 2065 helix: 2.53 (0.20), residues: 605 sheet: 0.45 (0.22), residues: 573 loop : -1.03 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 197 TYR 0.015 0.001 TYR D 77 PHE 0.013 0.002 PHE A 31 TRP 0.014 0.002 TRP A 776 HIS 0.004 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 (16554) covalent geometry : angle 0.56714 / 0.31 (22477) SS BOND : bond 0.00134 / 0.08 ( 1) SS BOND : angle 1.80259 / 0.86 ( 2) hydrogen bonds : bond 0.06222 / 4.25 ( 800) hydrogen bonds : angle 4.46285 / 3.18 ( 2274) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8579 (m-30) cc_final: 0.8158 (m-30) REVERT: B 43 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8410 (t) REVERT: B 58 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8380 (p0) REVERT: C 96 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7491 (ttp80) REVERT: C 145 TRP cc_start: 0.8346 (m100) cc_final: 0.7900 (m100) REVERT: C 177 LYS cc_start: 0.9338 (tmtt) cc_final: 0.9081 (tptp) REVERT: C 182 GLU cc_start: 0.7884 (pt0) cc_final: 0.7444 (pm20) REVERT: C 190 ASP cc_start: 0.7487 (t0) cc_final: 0.6952 (t70) REVERT: C 232 SER cc_start: 0.7045 (OUTLIER) cc_final: 0.6729 (t) REVERT: D 41 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8327 (tm-30) REVERT: E 107 LYS cc_start: 0.8908 (mtmt) cc_final: 0.8510 (mtpt) REVERT: F 83 MET cc_start: 0.9112 (tpt) cc_final: 0.8530 (tpt) REVERT: F 87 MET cc_start: 0.9119 (mpt) cc_final: 0.8657 (mpt) REVERT: F 109 MET cc_start: 0.4401 (ttt) cc_final: 0.4051 (ttp) REVERT: F 114 MET cc_start: 0.8729 (mmt) cc_final: 0.8172 (mmm) REVERT: F 156 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8528 (pm20) REVERT: F 400 MET cc_start: 0.8942 (mtm) cc_final: 0.8427 (tmm) REVERT: F 402 MET cc_start: 0.8736 (mmm) cc_final: 0.8448 (mmm) outliers start: 27 outliers final: 21 residues processed: 127 average time/residue: 0.1261 time to fit residues: 24.4776 Evaluate side-chains 132 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 360 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [60, 112, 52, 145, 0, 137, 92, 15, 46, 34, 192] chunk 60 optimal weight: 0.0010 chunk 112 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 145 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 192 optimal weight: 0.1980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 GLN ** F 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.110043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.064945 restraints weight = 36276.470| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.53 r_work: 0.2824 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16555 Z= 0.101 Angle : 0.508 7.738 22479 Z= 0.272 Chirality : 0.041 0.151 2478 Planarity : 0.004 0.044 2968 Dihedral : 4.130 53.207 2275 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.48 % Rotamer: Outliers : 1.26 % Allowed : 15.99 % Favored : 82.75 % 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: 0.89 (0.19), residues: 2065 helix: 2.73 (0.21), residues: 605 sheet: 0.48 (0.21), residues: 584 loop : -0.90 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.014 0.001 TYR F 125 PHE 0.012 0.001 PHE A 24 TRP 0.016 0.001 TRP B 317 HIS 0.004 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (16554) covalent geometry : angle 0.50746 / 0.27 (22477) SS BOND : bond 0.00037 / 0.02 ( 1) SS BOND : angle 1.65439 / 0.78 ( 2) hydrogen bonds : bond 0.04176 / 2.82 ( 800) hydrogen bonds : angle 4.17337 / 2.97 ( 2274) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 725 ILE cc_start: 0.8556 (mm) cc_final: 0.8093 (tp) REVERT: B 58 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8436 (p0) REVERT: C 96 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7513 (ttp80) REVERT: C 145 TRP cc_start: 0.8303 (m100) cc_final: 0.7792 (m100) REVERT: C 177 LYS cc_start: 0.9389 (tmtt) cc_final: 0.9151 (tptp) REVERT: C 182 GLU cc_start: 0.7764 (pt0) cc_final: 0.7350 (pm20) REVERT: C 190 ASP cc_start: 0.7397 (t0) cc_final: 0.6865 (t70) REVERT: C 232 SER cc_start: 0.7041 (p) cc_final: 0.6732 (t) REVERT: C 276 MET cc_start: 0.7478 (mmm) cc_final: 0.7159 (mtt) REVERT: D 41 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8338 (tm-30) REVERT: E 107 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8408 (mtpt) REVERT: F 83 MET cc_start: 0.9084 (tpt) cc_final: 0.8489 (tpt) REVERT: F 87 MET cc_start: 0.9149 (mpt) cc_final: 0.8697 (mpt) REVERT: F 94 GLU cc_start: 0.9290 (tm-30) cc_final: 0.9017 (pm20) REVERT: F 109 MET cc_start: 0.4401 (ttt) cc_final: 0.3736 (ttp) REVERT: F 114 MET cc_start: 0.8714 (mmt) cc_final: 0.8267 (mmt) REVERT: F 400 MET cc_start: 0.8887 (mtm) cc_final: 0.8408 (tmm) REVERT: F 402 MET cc_start: 0.8721 (mmm) cc_final: 0.8386 (mmm) REVERT: F 414 MET cc_start: 0.8110 (ttm) cc_final: 0.7865 (ttm) outliers start: 22 outliers final: 19 residues processed: 127 average time/residue: 0.1243 time to fit residues: 23.9854 Evaluate side-chains 131 residues out of total 1745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 360 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [155, 146, 121, 80, 91, 96, 127, 1, 63, 118, 133] chunk 155 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 121 optimal weight: 0.0070 chunk 80 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.108735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.064189 restraints weight = 35662.599| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.41 r_work: 0.2800 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16555 Z= 0.127 Angle : 0.512 7.615 22479 Z= 0.274 Chirality : 0.042 0.147 2478 Planarity : 0.004 0.044 2968 Dihedral : 4.086 50.626 2275 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 1.38 % Allowed : 15.82 % Favored : 82.81 % 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: 0.90 (0.19), residues: 2065 helix: 2.76 (0.21), residues: 605 sheet: 0.48 (0.21), residues: 589 loop : -0.91 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 223 TYR 0.014 0.001 TYR D 184 PHE 0.012 0.001 PHE A 24 TRP 0.013 0.001 TRP B 317 HIS 0.003 0.001 HIS F 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (16554) covalent geometry : angle 0.51171 / 0.27 (22477) SS BOND : bond 0.00075 / 0.05 ( 1) SS BOND : angle 1.68958 / 0.80 ( 2) hydrogen bonds : bond 0.04692 / 3.18 ( 800) hydrogen bonds : angle 4.17003 / 2.97 ( 2274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4803.00 seconds wall clock time: 82 minutes 42.66 seconds (4962.66 seconds total)