Starting phenix.real_space_refine on Sun Oct 25 10:21:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24gl_69488/10_2026/24gl_69488.cif Found real_map, /net/cci-nas-00/data/ceres_data/24gl_69488/10_2026/24gl_69488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/24gl_69488/10_2026/24gl_69488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24gl_69488/10_2026/24gl_69488.map" model { file = "/net/cci-nas-00/data/ceres_data/24gl_69488/10_2026/24gl_69488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24gl_69488/10_2026/24gl_69488.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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 49 5.16 5 C 10071 2.51 5 N 2791 2.21 5 O 3158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 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: 16069 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: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1414 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 10, 'TRANS': 175} 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: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3160 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 14, 'TRANS': 393} Time building chain proxies: 3.20, per 1000 atoms: 0.20 Number of scatterers: 16069 At special positions: 0 Unit cell: (132.24, 126.16, 150.48, 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 49 16.00 O 3158 8.00 N 2791 7.00 C 10071 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 696.4 milliseconds 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3790 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 22 sheets defined 32.0% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 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 Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.805A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.623A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.876A 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 34 removed outlier: 4.149A pdb=" N GLN C 34 " --> pdb=" O TYR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.628A pdb=" N ALA C 44 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.737A pdb=" N ALA C 79 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 190 through 214 removed outlier: 3.672A pdb=" N MET C 194 " --> pdb=" O ASP C 190 " (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 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 120 removed outlier: 3.654A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.513A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.633A 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: 3.617A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 removed outlier: 3.528A pdb=" N ILE E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 56 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 122 Processing helix chain 'F' and resid 124 through 150 Processing helix chain 'F' and resid 153 through 167 Processing helix chain 'F' and resid 188 through 208 Processing helix chain 'F' and resid 211 through 219 Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 240 through 248 Processing helix chain 'F' and resid 299 through 316 Processing helix chain 'F' and resid 320 through 329 Processing helix chain 'F' and resid 334 through 338 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: 3.778A pdb=" N LEU A 84 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N VAL A 77 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL F 25 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.229A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.648A 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: 5.816A pdb=" N ILE A 254 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY A 253 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU A 247 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR A 255 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL A 245 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR A 257 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A 243 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN A 259 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.752A 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: 7.313A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 273 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL A 341 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 4.708A 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: 6.378A pdb=" N VAL A 412 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS A 351 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 430 removed outlier: 3.857A pdb=" N SER A 425 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN A 445 " --> pdb=" O SER A 425 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 537 " --> pdb=" O THR A 505 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A 507 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 710 " --> pdb=" O TRP A 745 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 674 removed outlier: 6.029A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 8.163A 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: 7.107A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER B 49 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 387 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 3.650A 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: 6.652A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.720A 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: 6.478A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.638A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.902A 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: 6.314A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.645A 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: 6.862A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.048A 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 removed outlier: 7.249A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.785A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.510A 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: 4.094A pdb=" N TYR C 161 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR C 140 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG C 134 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR C 142 " --> pdb=" O THR C 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.087A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 35 Processing sheet with id=AC2, first strand: chain 'F' and resid 35 through 38 removed outlier: 6.707A pdb=" N GLY F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL F 31 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL F 37 " --> pdb=" O ALA F 29 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 232 through 235 removed outlier: 3.836A pdb=" N ASP F 272 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N SER F 177 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL F 270 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE F 179 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU F 268 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE F 181 " --> pdb=" O HIS F 266 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N HIS F 266 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG F 260 " --> pdb=" O GLY F 264 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N HIS F 266 " --> pdb=" O PRO F 258 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 340 through 344 removed outlier: 6.147A pdb=" N ALA F 287 " --> pdb=" O LEU F 341 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP F 343 " --> pdb=" O VAL F 285 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL F 285 " --> pdb=" O TRP F 343 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG F 288 " --> pdb=" O LEU F 380 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU F 380 " --> pdb=" O ARG F 288 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE F 290 " --> pdb=" O ILE F 378 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE F 378 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU F 292 " --> pdb=" O HIS F 376 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N HIS F 376 " --> pdb=" O LEU F 292 " (cutoff:3.500A) 790 hydrogen bonds defined for protein. 2202 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: 2.76 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4785 1.33 - 1.46: 2709 1.46 - 1.58: 8798 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 16388 Sorted by residual: bond pdb=" N ILE A 430 " pdb=" CA ILE A 430 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.08e-02 8.57e+03 1.13e+01 bond pdb=" N VAL B 30 " pdb=" CA VAL B 30 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" N ASN A 55 " pdb=" CA ASN A 55 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.18e-02 7.18e+03 1.01e+01 bond pdb=" N VAL C 108 " pdb=" CA VAL C 108 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.22e-02 6.72e+03 9.92e+00 bond pdb=" N VAL A 48 " pdb=" CA VAL A 48 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.89e+00 ... (remaining 16383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 21610 2.88 - 5.76: 579 5.76 - 8.64: 50 8.64 - 11.52: 9 11.52 - 14.40: 3 Bond angle restraints: 22251 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 120.39 132.37 -11.98 1.39e+00 5.18e-01 7.42e+01 angle pdb=" CA MET F 414 " pdb=" CB MET F 414 " pdb=" CG MET F 414 " ideal model delta sigma weight residual 114.10 128.50 -14.40 2.00e+00 2.50e-01 5.19e+01 angle pdb=" C TYR A 432 " pdb=" CA TYR A 432 " pdb=" CB TYR A 432 " ideal model delta sigma weight residual 116.63 108.81 7.82 1.16e+00 7.43e-01 4.54e+01 angle pdb=" N VAL A 444 " pdb=" CA VAL A 444 " pdb=" C VAL A 444 " ideal model delta sigma weight residual 108.11 117.46 -9.35 1.40e+00 5.10e-01 4.46e+01 angle pdb=" CA GLN A 112 " pdb=" CB GLN A 112 " pdb=" CG GLN A 112 " ideal model delta sigma weight residual 114.10 125.89 -11.79 2.00e+00 2.50e-01 3.47e+01 ... (remaining 22246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 8959 17.46 - 34.91: 607 34.91 - 52.37: 149 52.37 - 69.82: 68 69.82 - 87.28: 9 Dihedral angle restraints: 9792 sinusoidal: 3859 harmonic: 5933 Sorted by residual: dihedral pdb=" CB CYS A 274 " pdb=" SG CYS A 274 " pdb=" SG CYS F 336 " pdb=" CB CYS F 336 " ideal model delta sinusoidal sigma weight residual -86.00 -133.00 47.00 1 1.00e+01 1.00e-02 3.05e+01 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 180.00 154.56 25.44 0 5.00e+00 4.00e-02 2.59e+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 180.00 156.50 23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 9789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1743 0.052 - 0.103: 510 0.103 - 0.155: 160 0.155 - 0.207: 33 0.207 - 0.259: 3 Chirality restraints: 2449 Sorted by residual: chirality pdb=" CA MET F 414 " pdb=" N MET F 414 " pdb=" C MET F 414 " pdb=" CB MET F 414 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA PHE A 517 " pdb=" N PHE A 517 " pdb=" C PHE A 517 " pdb=" CB PHE A 517 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL A 54 " pdb=" N VAL A 54 " pdb=" C VAL A 54 " pdb=" CB VAL A 54 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2446 not shown) Planarity restraints: 2943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 79 " 0.537 9.50e-02 1.11e+02 2.41e-01 3.55e+01 pdb=" NE ARG A 79 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 79 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 79 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 79 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 25 " 0.413 9.50e-02 1.11e+02 1.85e-01 2.10e+01 pdb=" NE ARG E 25 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG E 25 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG E 25 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 25 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 49 " 0.303 9.50e-02 1.11e+02 1.36e-01 1.13e+01 pdb=" NE ARG A 49 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 49 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 49 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 49 " 0.011 2.00e-02 2.50e+03 ... (remaining 2940 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 5472 2.86 - 3.37: 14962 3.37 - 3.88: 26555 3.88 - 4.39: 28960 4.39 - 4.90: 49769 Nonbonded interactions: 125718 Sorted by model distance: nonbonded pdb=" OD2 ASP F 331 " pdb=" OG SER F 334 " model vdw 2.351 3.040 nonbonded pdb=" O ILE A 519 " pdb=" OD1 ASN A 520 " model vdw 2.455 3.040 nonbonded pdb=" O ASN A 506 " pdb=" OG SER A 508 " model vdw 2.455 3.040 nonbonded pdb=" OH TYR A 674 " pdb=" O TYR A 688 " model vdw 2.460 3.040 nonbonded pdb=" O GLY A 378 " pdb=" OG SER A 379 " model vdw 2.461 3.040 ... (remaining 125713 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: 6.140 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: 0.400 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.470 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: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 0.061 16389 Z= 0.359 Angle : 1.080 14.403 22253 Z= 0.688 Chirality : 0.056 0.259 2449 Planarity : 0.009 0.241 2943 Dihedral : 14.042 87.277 5999 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.78 % Favored : 97.12 % Rotamer: Outliers : 1.86 % Allowed : 11.50 % Favored : 86.64 % 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: 0.75 (0.18), residues: 2049 helix: 1.37 (0.20), residues: 612 sheet: 0.83 (0.20), residues: 550 loop : -0.27 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.003 ARG F 67 TYR 0.031 0.003 TYR F 422 PHE 0.031 0.002 PHE B 356 TRP 0.033 0.003 TRP A 627 HIS 0.009 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.36 (16388) covalent geometry : angle 1.07965 / 0.69 (22251) SS BOND : bond 0.00135 / 0.08 ( 1) SS BOND : angle 0.62358 / 0.22 ( 2) hydrogen bonds : bond 0.12208 / 8.56 ( 786) hydrogen bonds : angle 6.13311 / 4.36 ( 2202) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 TYR cc_start: 0.8667 (t80) cc_final: 0.8383 (t80) REVERT: A 514 THR cc_start: 0.8762 (m) cc_final: 0.8496 (p) REVERT: A 539 MET cc_start: 0.7982 (mtm) cc_final: 0.7689 (mpp) REVERT: B 73 TYR cc_start: 0.8945 (m-80) cc_final: 0.8650 (m-80) REVERT: C 102 ASP cc_start: 0.6111 (p0) cc_final: 0.5798 (p0) REVERT: C 157 TYR cc_start: 0.8634 (m-80) cc_final: 0.8415 (m-80) REVERT: E 23 LEU cc_start: 0.8982 (mp) cc_final: 0.8748 (tt) REVERT: F 87 MET cc_start: 0.9115 (mmm) cc_final: 0.8870 (mtp) REVERT: F 109 MET cc_start: 0.4263 (mtp) cc_final: 0.3955 (mtp) REVERT: F 178 HIS cc_start: 0.4204 (t-170) cc_final: 0.3812 (t-90) REVERT: F 298 MET cc_start: 0.8702 (ttm) cc_final: 0.8408 (ttm) outliers start: 32 outliers final: 22 residues processed: 169 average time/residue: 0.1208 time to fit residues: 30.5235 Evaluate side-chains 137 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 219 HIS Chi-restraints excluded: chain F residue 426 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 GLN A 681 ASN B 230 GLN B 360 GLN E 34 GLN F 85 GLN F 107 ASN ** F 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.098849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.060246 restraints weight = 55291.281| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.78 r_work: 0.2906 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16389 Z= 0.226 Angle : 0.648 9.799 22253 Z= 0.347 Chirality : 0.044 0.147 2449 Planarity : 0.004 0.048 2943 Dihedral : 5.774 59.703 2287 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.76 % Favored : 98.19 % Rotamer: Outliers : 3.08 % Allowed : 9.87 % Favored : 87.05 % 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: 1.15 (0.18), residues: 2049 helix: 2.11 (0.20), residues: 610 sheet: 0.78 (0.21), residues: 585 loop : -0.19 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 76 TYR 0.018 0.002 TYR A 504 PHE 0.016 0.002 PHE E 74 TRP 0.019 0.002 TRP A 745 HIS 0.006 0.002 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (16388) covalent geometry : angle 0.64777 / 0.35 (22251) SS BOND : bond 0.01744 / 1.09 ( 1) SS BOND : angle 2.22370 / 1.01 ( 2) hydrogen bonds : bond 0.06041 / 4.00 ( 786) hydrogen bonds : angle 5.15869 / 3.64 ( 2202) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 114 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7603 (t80) REVERT: B 73 TYR cc_start: 0.9031 (m-80) cc_final: 0.8778 (m-80) REVERT: B 106 LYS cc_start: 0.6994 (mmtt) cc_final: 0.5845 (tttp) REVERT: B 221 MET cc_start: 0.9026 (tmm) cc_final: 0.8705 (ppp) REVERT: E 50 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8510 (mtp) REVERT: F 87 MET cc_start: 0.9145 (mmm) cc_final: 0.8917 (mtp) REVERT: F 109 MET cc_start: 0.4179 (mtp) cc_final: 0.3649 (mtp) REVERT: F 219 HIS cc_start: 0.5417 (OUTLIER) cc_final: 0.4415 (p-80) REVERT: F 298 MET cc_start: 0.8677 (ttm) cc_final: 0.8437 (ttm) outliers start: 53 outliers final: 30 residues processed: 156 average time/residue: 0.1378 time to fit residues: 31.6822 Evaluate side-chains 140 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 219 HIS Chi-restraints excluded: chain F residue 266 HIS Chi-restraints excluded: chain F residue 398 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [135, 79, 168, 129, 127, 4, 134, 99, 143, 75, 107] chunk 135 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 99 optimal weight: 0.0770 chunk 143 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 overall best weight: 1.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 542 GLN ** F 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.099018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.060534 restraints weight = 55550.558| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.76 r_work: 0.2924 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16389 Z= 0.129 Angle : 0.548 13.289 22253 Z= 0.285 Chirality : 0.042 0.188 2449 Planarity : 0.004 0.062 2943 Dihedral : 5.319 59.911 2279 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.81 % Favored : 98.15 % Rotamer: Outliers : 2.50 % Allowed : 10.45 % Favored : 87.05 % 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: 1.28 (0.19), residues: 2049 helix: 2.40 (0.20), residues: 610 sheet: 0.89 (0.21), residues: 566 loop : -0.27 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 79 TYR 0.021 0.001 TYR A 504 PHE 0.012 0.001 PHE A 675 TRP 0.023 0.002 TRP B 317 HIS 0.005 0.001 HIS F 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (16388) covalent geometry : angle 0.54764 / 0.29 (22251) SS BOND : bond 0.00126 / 0.08 ( 1) SS BOND : angle 1.55630 / 0.74 ( 2) hydrogen bonds : bond 0.04749 / 3.13 ( 786) hydrogen bonds : angle 4.64722 / 3.28 ( 2202) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 113 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.7727 (ptp-170) cc_final: 0.7520 (ptp90) REVERT: A 479 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8607 (p) REVERT: A 768 MET cc_start: 0.9220 (mtp) cc_final: 0.8891 (ttm) REVERT: A 804 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7979 (t80) REVERT: B 93 TRP cc_start: 0.8808 (p-90) cc_final: 0.8290 (p-90) REVERT: B 126 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8708 (p) REVERT: B 221 MET cc_start: 0.9030 (tmm) cc_final: 0.8785 (tmm) REVERT: C 200 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8783 (mt-10) REVERT: F 109 MET cc_start: 0.4148 (mtp) cc_final: 0.3548 (mtp) REVERT: F 219 HIS cc_start: 0.5634 (OUTLIER) cc_final: 0.4788 (p-80) REVERT: F 298 MET cc_start: 0.8665 (ttm) cc_final: 0.8455 (ttm) outliers start: 43 outliers final: 30 residues processed: 147 average time/residue: 0.1235 time to fit residues: 27.6256 Evaluate side-chains 137 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 228 TRP Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 219 HIS Chi-restraints excluded: chain F residue 266 HIS Chi-restraints excluded: chain F residue 426 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [33, 7, 37, 88, 47, 120, 190, 77, 3, 150, 73] chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 77 optimal weight: 0.0010 chunk 3 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 GLN F 289 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.097300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.059344 restraints weight = 56250.998| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 4.20 r_work: 0.2854 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16389 Z= 0.164 Angle : 0.558 9.941 22253 Z= 0.293 Chirality : 0.042 0.173 2449 Planarity : 0.004 0.045 2943 Dihedral : 5.249 58.501 2277 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.20 % Favored : 97.76 % Rotamer: Outliers : 2.32 % Allowed : 11.50 % Favored : 86.18 % 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: 1.20 (0.19), residues: 2049 helix: 2.40 (0.20), residues: 610 sheet: 0.75 (0.21), residues: 580 loop : -0.32 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 134 TYR 0.014 0.001 TYR A 618 PHE 0.011 0.001 PHE E 74 TRP 0.036 0.002 TRP B 317 HIS 0.006 0.001 HIS F 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (16388) covalent geometry : angle 0.55835 / 0.29 (22251) SS BOND : bond 0.00112 / 0.07 ( 1) SS BOND : angle 1.39689 / 0.66 ( 2) hydrogen bonds : bond 0.05194 / 3.43 ( 786) hydrogen bonds : angle 4.60818 / 3.26 ( 2202) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8728 (p) REVERT: A 561 GLN cc_start: 0.4104 (tt0) cc_final: 0.3853 (tt0) REVERT: A 804 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8163 (t80) REVERT: B 126 SER cc_start: 0.9076 (OUTLIER) cc_final: 0.8782 (p) REVERT: B 221 MET cc_start: 0.9079 (tmm) cc_final: 0.8861 (tmm) REVERT: C 157 TYR cc_start: 0.8572 (m-80) cc_final: 0.8349 (m-80) REVERT: C 200 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8716 (mt-10) REVERT: E 50 MET cc_start: 0.8780 (mtp) cc_final: 0.8464 (mtp) REVERT: F 109 MET cc_start: 0.4216 (mtp) cc_final: 0.3603 (mtp) REVERT: F 219 HIS cc_start: 0.5858 (OUTLIER) cc_final: 0.5124 (p-80) REVERT: F 298 MET cc_start: 0.8593 (ttm) cc_final: 0.8389 (ttm) outliers start: 40 outliers final: 28 residues processed: 144 average time/residue: 0.1116 time to fit residues: 25.0267 Evaluate side-chains 132 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 219 HIS Chi-restraints excluded: chain F residue 266 HIS Chi-restraints excluded: chain F residue 426 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [96, 180, 49, 91, 44, 56, 104, 16, 160, 52, 191] chunk 96 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 104 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 HIS ** 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 = 0.3905 r_free = 0.3905 target = 0.097357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059790 restraints weight = 56468.576| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 4.17 r_work: 0.2857 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16389 Z= 0.132 Angle : 0.521 9.603 22253 Z= 0.272 Chirality : 0.041 0.144 2449 Planarity : 0.004 0.047 2943 Dihedral : 5.127 58.676 2277 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.95 % Rotamer: Outliers : 2.61 % Allowed : 12.02 % Favored : 85.37 % 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: 1.24 (0.19), residues: 2049 helix: 2.52 (0.20), residues: 610 sheet: 0.77 (0.21), residues: 579 loop : -0.36 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 399 TYR 0.013 0.001 TYR A 618 PHE 0.012 0.001 PHE A 67 TRP 0.038 0.001 TRP B 317 HIS 0.005 0.001 HIS F 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (16388) covalent geometry : angle 0.52074 / 0.27 (22251) SS BOND : bond 0.00114 / 0.07 ( 1) SS BOND : angle 1.23635 / 0.58 ( 2) hydrogen bonds : bond 0.04663 / 3.07 ( 786) hydrogen bonds : angle 4.44468 / 3.15 ( 2202) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 111 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8684 (p) REVERT: A 561 GLN cc_start: 0.4100 (tt0) cc_final: 0.3503 (tt0) REVERT: A 566 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8267 (mtpt) REVERT: A 804 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8324 (t80) REVERT: B 126 SER cc_start: 0.9006 (OUTLIER) cc_final: 0.8665 (p) REVERT: B 183 TRP cc_start: 0.7985 (p90) cc_final: 0.7426 (p90) REVERT: B 221 MET cc_start: 0.9119 (tmm) cc_final: 0.8632 (tmm) REVERT: B 226 MET cc_start: 0.7808 (mmm) cc_final: 0.7437 (mmm) REVERT: B 276 GLN cc_start: 0.9383 (mm-40) cc_final: 0.9031 (pt0) REVERT: C 43 GLU cc_start: 0.7996 (mp0) cc_final: 0.7647 (mp0) REVERT: C 200 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8616 (mt-10) REVERT: F 109 MET cc_start: 0.4273 (mtp) cc_final: 0.3805 (mtp) REVERT: F 219 HIS cc_start: 0.5978 (OUTLIER) cc_final: 0.5274 (p-80) outliers start: 45 outliers final: 32 residues processed: 148 average time/residue: 0.1164 time to fit residues: 26.8151 Evaluate side-chains 139 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 219 HIS Chi-restraints excluded: chain F residue 266 HIS Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 426 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [180, 154, 167, 22, 17, 81, 88, 29, 8, 106, 115] chunk 180 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 22 optimal weight: 0.0670 chunk 17 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 overall best weight: 3.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 523 ASN C 147 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.094911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.057021 restraints weight = 55583.487| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 4.03 r_work: 0.2781 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 16389 Z= 0.254 Angle : 0.628 9.573 22253 Z= 0.332 Chirality : 0.044 0.182 2449 Planarity : 0.005 0.058 2943 Dihedral : 5.365 56.013 2276 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 2.96 % Allowed : 12.66 % Favored : 84.38 % 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: 0.83 (0.19), residues: 2049 helix: 2.27 (0.20), residues: 609 sheet: 0.47 (0.22), residues: 561 loop : -0.62 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 223 TYR 0.015 0.002 TYR D 77 PHE 0.016 0.002 PHE A 675 TRP 0.020 0.002 TRP B 317 HIS 0.005 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.25 (16388) covalent geometry : angle 0.62806 / 0.33 (22251) SS BOND : bond 0.00077 / 0.05 ( 1) SS BOND : angle 1.24531 / 0.59 ( 2) hydrogen bonds : bond 0.06200 / 4.12 ( 786) hydrogen bonds : angle 4.80730 / 3.40 ( 2202) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 104 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8807 (p) REVERT: A 561 GLN cc_start: 0.4476 (tt0) cc_final: 0.3800 (tt0) REVERT: A 566 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8385 (mtpt) REVERT: A 804 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8417 (t80) REVERT: B 126 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8761 (p) REVERT: B 183 TRP cc_start: 0.7984 (p90) cc_final: 0.7414 (p90) REVERT: B 221 MET cc_start: 0.9121 (tmm) cc_final: 0.8630 (tmm) REVERT: B 226 MET cc_start: 0.7840 (mmm) cc_final: 0.7465 (mmm) REVERT: C 43 GLU cc_start: 0.8013 (mp0) cc_final: 0.7601 (mp0) REVERT: C 200 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8602 (mt-10) REVERT: F 109 MET cc_start: 0.4647 (mtp) cc_final: 0.4020 (mtp) REVERT: F 219 HIS cc_start: 0.6143 (OUTLIER) cc_final: 0.5566 (p-80) outliers start: 51 outliers final: 36 residues processed: 148 average time/residue: 0.1196 time to fit residues: 27.3192 Evaluate side-chains 141 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 219 HIS Chi-restraints excluded: chain F residue 266 HIS Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 426 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [20, 165, 65, 67, 48, 89, 55, 76, 164, 116, 62] chunk 20 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.095876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.058367 restraints weight = 55353.577| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 4.01 r_work: 0.2820 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16389 Z= 0.156 Angle : 0.553 9.778 22253 Z= 0.289 Chirality : 0.043 0.246 2449 Planarity : 0.004 0.056 2943 Dihedral : 5.025 56.121 2273 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.34 % Favored : 97.61 % Rotamer: Outliers : 2.38 % Allowed : 13.82 % Favored : 83.80 % 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: 0.92 (0.19), residues: 2049 helix: 2.38 (0.20), residues: 610 sheet: 0.48 (0.22), residues: 564 loop : -0.56 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 304 TYR 0.023 0.001 TYR C 129 PHE 0.011 0.001 PHE C 99 TRP 0.017 0.002 TRP B 48 HIS 0.005 0.001 HIS F 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (16388) covalent geometry : angle 0.55274 / 0.29 (22251) SS BOND : bond 0.00121 / 0.08 ( 1) SS BOND : angle 1.14116 / 0.54 ( 2) hydrogen bonds : bond 0.05116 / 3.39 ( 786) hydrogen bonds : angle 4.59360 / 3.25 ( 2202) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8852 (mm) REVERT: A 479 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8768 (p) REVERT: A 539 MET cc_start: 0.7310 (tpp) cc_final: 0.6782 (mmm) REVERT: A 561 GLN cc_start: 0.4262 (tt0) cc_final: 0.3495 (tt0) REVERT: A 566 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8292 (mtpt) REVERT: A 804 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8401 (t80) REVERT: B 126 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8546 (p) REVERT: B 183 TRP cc_start: 0.8004 (p90) cc_final: 0.7482 (p90) REVERT: B 221 MET cc_start: 0.9114 (tmm) cc_final: 0.8589 (tmm) REVERT: B 226 MET cc_start: 0.7881 (mmm) cc_final: 0.7615 (mmm) REVERT: C 43 GLU cc_start: 0.8050 (mp0) cc_final: 0.7645 (mp0) REVERT: C 200 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8580 (mt-10) REVERT: D 56 GLU cc_start: 0.9331 (tm-30) cc_final: 0.9071 (tm-30) REVERT: F 109 MET cc_start: 0.4250 (mtp) cc_final: 0.3885 (mtp) REVERT: F 219 HIS cc_start: 0.6234 (OUTLIER) cc_final: 0.5650 (p-80) REVERT: F 245 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8564 (mm-40) outliers start: 41 outliers final: 27 residues processed: 144 average time/residue: 0.1094 time to fit residues: 24.3788 Evaluate side-chains 134 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 219 HIS Chi-restraints excluded: chain F residue 266 HIS Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 426 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [29, 13, 69, 130, 11, 200, 63, 92, 94, 142, 80] chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 142 optimal weight: 0.3980 chunk 80 optimal weight: 10.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 520 ASN B 360 GLN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.095763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.058260 restraints weight = 55511.407| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 4.04 r_work: 0.2817 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16389 Z= 0.163 Angle : 0.553 9.734 22253 Z= 0.288 Chirality : 0.042 0.182 2449 Planarity : 0.004 0.055 2943 Dihedral : 4.968 55.923 2273 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.12 % Rotamer: Outliers : 2.50 % Allowed : 14.11 % Favored : 83.39 % 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: 0.97 (0.19), residues: 2049 helix: 2.44 (0.20), residues: 610 sheet: 0.56 (0.22), residues: 555 loop : -0.57 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 304 TYR 0.014 0.001 TYR A 618 PHE 0.018 0.001 PHE F 265 TRP 0.020 0.001 TRP B 48 HIS 0.005 0.001 HIS F 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (16388) covalent geometry : angle 0.55311 / 0.29 (22251) SS BOND : bond 0.00113 / 0.07 ( 1) SS BOND : angle 1.08520 / 0.51 ( 2) hydrogen bonds : bond 0.05084 / 3.38 ( 786) hydrogen bonds : angle 4.54224 / 3.21 ( 2202) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8814 (mm) REVERT: A 441 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6977 (pp30) REVERT: A 479 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8772 (p) REVERT: A 539 MET cc_start: 0.7353 (tpp) cc_final: 0.6781 (mmm) REVERT: A 561 GLN cc_start: 0.4323 (tt0) cc_final: 0.3548 (tt0) REVERT: A 566 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8307 (mtpt) REVERT: A 804 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8390 (t80) REVERT: B 126 SER cc_start: 0.9085 (OUTLIER) cc_final: 0.8572 (p) REVERT: B 183 TRP cc_start: 0.8012 (p90) cc_final: 0.7502 (p90) REVERT: B 221 MET cc_start: 0.9119 (tmm) cc_final: 0.8589 (tmm) REVERT: B 226 MET cc_start: 0.7949 (mmm) cc_final: 0.7635 (mmm) REVERT: C 43 GLU cc_start: 0.8057 (mp0) cc_final: 0.7646 (mp0) REVERT: C 200 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8600 (mt-10) REVERT: D 56 GLU cc_start: 0.9316 (tm-30) cc_final: 0.9056 (tm-30) REVERT: F 109 MET cc_start: 0.4401 (mtp) cc_final: 0.4119 (mtp) REVERT: F 219 HIS cc_start: 0.6291 (OUTLIER) cc_final: 0.5748 (p-80) REVERT: F 245 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8570 (mm-40) outliers start: 43 outliers final: 30 residues processed: 141 average time/residue: 0.1213 time to fit residues: 26.2944 Evaluate side-chains 135 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 219 HIS Chi-restraints excluded: chain F residue 266 HIS Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 426 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [22, 77, 172, 37, 114, 21, 12, 9, 30, 177, 170] chunk 22 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.095349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.057789 restraints weight = 55312.932| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 4.03 r_work: 0.2801 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16389 Z= 0.188 Angle : 0.576 10.465 22253 Z= 0.300 Chirality : 0.043 0.160 2449 Planarity : 0.004 0.055 2943 Dihedral : 4.985 55.337 2273 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 2.26 % Allowed : 14.69 % 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: 0.89 (0.19), residues: 2049 helix: 2.42 (0.20), residues: 610 sheet: 0.51 (0.22), residues: 542 loop : -0.65 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 304 TYR 0.014 0.001 TYR A 618 PHE 0.043 0.001 PHE F 265 TRP 0.020 0.002 TRP B 48 HIS 0.008 0.001 HIS F 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (16388) covalent geometry : angle 0.57571 / 0.30 (22251) SS BOND : bond 0.00098 / 0.06 ( 1) SS BOND : angle 1.01900 / 0.48 ( 2) hydrogen bonds : bond 0.05309 / 3.53 ( 786) hydrogen bonds : angle 4.59483 / 3.25 ( 2202) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.9336 (mtt180) cc_final: 0.9059 (mtt-85) REVERT: A 110 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8826 (mm) REVERT: A 441 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6850 (pp30) REVERT: A 479 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8790 (p) REVERT: A 539 MET cc_start: 0.7414 (tpp) cc_final: 0.6838 (mmm) REVERT: A 566 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8289 (mtpt) REVERT: A 768 MET cc_start: 0.9349 (mtp) cc_final: 0.8801 (mtp) REVERT: A 804 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8419 (t80) REVERT: B 126 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8703 (p) REVERT: B 226 MET cc_start: 0.7969 (mmm) cc_final: 0.7663 (mmm) REVERT: C 43 GLU cc_start: 0.8084 (mp0) cc_final: 0.7664 (mp0) REVERT: C 200 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8614 (mt-10) REVERT: C 202 MET cc_start: 0.8943 (tmm) cc_final: 0.8587 (ttm) REVERT: D 56 GLU cc_start: 0.9315 (tm-30) cc_final: 0.9053 (tm-30) REVERT: F 109 MET cc_start: 0.4652 (mtp) cc_final: 0.4213 (mtp) REVERT: F 219 HIS cc_start: 0.6216 (OUTLIER) cc_final: 0.5693 (p-80) REVERT: F 245 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8575 (mm-40) outliers start: 39 outliers final: 29 residues processed: 138 average time/residue: 0.1223 time to fit residues: 25.6413 Evaluate side-chains 133 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 219 HIS Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 426 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [33, 28, 153, 162, 19, 200, 172, 87, 57, 20, 106] chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 153 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.096649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.059311 restraints weight = 55309.509| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.07 r_work: 0.2843 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16389 Z= 0.110 Angle : 0.542 10.439 22253 Z= 0.278 Chirality : 0.042 0.173 2449 Planarity : 0.004 0.054 2943 Dihedral : 4.811 55.845 2273 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.15 % Favored : 97.80 % Rotamer: Outliers : 1.97 % Allowed : 15.10 % Favored : 82.93 % 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: 1.06 (0.19), residues: 2049 helix: 2.55 (0.20), residues: 610 sheet: 0.60 (0.22), residues: 551 loop : -0.54 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 160 TYR 0.017 0.001 TYR F 422 PHE 0.014 0.001 PHE F 265 TRP 0.022 0.001 TRP B 48 HIS 0.008 0.001 HIS F 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (16388) covalent geometry : angle 0.54157 / 0.28 (22251) SS BOND : bond 0.00124 / 0.08 ( 1) SS BOND : angle 1.01316 / 0.47 ( 2) hydrogen bonds : bond 0.04400 / 2.92 ( 786) hydrogen bonds : angle 4.36604 / 3.10 ( 2202) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.9308 (mtt180) cc_final: 0.9028 (mtt-85) REVERT: A 441 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.7006 (pp30) REVERT: A 479 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8723 (p) REVERT: A 539 MET cc_start: 0.7242 (tpp) cc_final: 0.6786 (mmm) REVERT: A 566 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8306 (mtpt) REVERT: A 768 MET cc_start: 0.9329 (mtp) cc_final: 0.8780 (mtp) REVERT: A 804 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8366 (t80) REVERT: B 126 SER cc_start: 0.9023 (OUTLIER) cc_final: 0.8491 (p) REVERT: B 226 MET cc_start: 0.7982 (mmm) cc_final: 0.7696 (mmm) REVERT: B 276 GLN cc_start: 0.9428 (mm-40) cc_final: 0.8964 (pm20) REVERT: C 43 GLU cc_start: 0.8083 (mp0) cc_final: 0.7665 (mp0) REVERT: C 114 ASN cc_start: 0.9228 (p0) cc_final: 0.8982 (m-40) REVERT: C 200 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8435 (mp0) REVERT: C 202 MET cc_start: 0.8938 (tmm) cc_final: 0.8556 (ttm) REVERT: D 56 GLU cc_start: 0.9296 (tm-30) cc_final: 0.9029 (tm-30) REVERT: F 109 MET cc_start: 0.4500 (mtp) cc_final: 0.4122 (mtp) REVERT: F 219 HIS cc_start: 0.6206 (OUTLIER) cc_final: 0.5696 (p-80) REVERT: F 265 PHE cc_start: 0.7926 (m-80) cc_final: 0.7541 (t80) outliers start: 34 outliers final: 26 residues processed: 136 average time/residue: 0.1196 time to fit residues: 24.7840 Evaluate side-chains 134 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 219 HIS Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 426 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: [116, 3, 145, 32, 6, 25, 33, 102, 141, 140, 2] chunk 116 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 141 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 GLN ** F 113 GLN ** 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 = 0.3883 r_free = 0.3883 target = 0.095917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.058330 restraints weight = 55363.921| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.94 r_work: 0.2826 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16389 Z= 0.158 Angle : 0.575 10.289 22253 Z= 0.298 Chirality : 0.042 0.158 2449 Planarity : 0.004 0.053 2943 Dihedral : 4.799 55.511 2271 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.22 % Rotamer: Outliers : 2.09 % Allowed : 15.39 % Favored : 82.52 % 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: 0.93 (0.19), residues: 2049 helix: 2.35 (0.20), residues: 612 sheet: 0.59 (0.22), residues: 551 loop : -0.59 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 158 TYR 0.026 0.001 TYR D 107 PHE 0.016 0.001 PHE F 265 TRP 0.017 0.001 TRP B 48 HIS 0.006 0.001 HIS F 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (16388) covalent geometry : angle 0.57532 / 0.30 (22251) SS BOND : bond 0.00091 / 0.06 ( 1) SS BOND : angle 0.92315 / 0.44 ( 2) hydrogen bonds : bond 0.04933 / 3.27 ( 786) hydrogen bonds : angle 4.46311 / 3.16 ( 2202) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5036.54 seconds wall clock time: 86 minutes 30.51 seconds (5190.51 seconds total)