Starting phenix.real_space_refine on Sat Aug 23 23:09:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1o_41819/08_2025/8u1o_41819.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1o_41819/08_2025/8u1o_41819.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/8u1o_41819/08_2025/8u1o_41819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1o_41819/08_2025/8u1o_41819.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1o_41819/08_2025/8u1o_41819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1o_41819/08_2025/8u1o_41819.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= 0.005 sd= 0.044 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 48 5.16 5 C 9519 2.51 5 N 2568 2.21 5 O 2961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15096 Number of models: 1 Model: "" Number of chains: 3 Chain: "o" Number of atoms: 5032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5032 Classifications: {'peptide': 663} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 634} Chain: "p" Number of atoms: 5032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5032 Classifications: {'peptide': 663} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 634} Chain: "q" Number of atoms: 5032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5032 Classifications: {'peptide': 663} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 634} Time building chain proxies: 3.15, per 1000 atoms: 0.21 Number of scatterers: 15096 At special positions: 0 Unit cell: (103.758, 95.5971, 184.199, 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 48 16.00 O 2961 8.00 N 2568 7.00 C 9519 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 699.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 35 sheets defined 7.0% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'o' and resid 110 through 122 removed outlier: 4.033A pdb=" N ILE o 116 " --> pdb=" O ASP o 112 " (cutoff:3.500A) Processing helix chain 'o' and resid 134 through 141 Processing helix chain 'o' and resid 217 through 223 Processing helix chain 'o' and resid 237 through 243 removed outlier: 4.052A pdb=" N VAL o 241 " --> pdb=" O VAL o 237 " (cutoff:3.500A) Processing helix chain 'o' and resid 245 through 250 removed outlier: 3.954A pdb=" N LEU o 249 " --> pdb=" O GLY o 245 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU o 250 " --> pdb=" O ILE o 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 245 through 250' Processing helix chain 'o' and resid 610 through 614 Processing helix chain 'p' and resid 42 through 46 removed outlier: 3.507A pdb=" N GLN p 46 " --> pdb=" O PRO p 43 " (cutoff:3.500A) Processing helix chain 'p' and resid 105 through 110 removed outlier: 3.673A pdb=" N ASP p 110 " --> pdb=" O LEU p 107 " (cutoff:3.500A) Processing helix chain 'p' and resid 113 through 120 removed outlier: 4.758A pdb=" N GLU p 117 " --> pdb=" O GLN p 113 " (cutoff:3.500A) Processing helix chain 'p' and resid 129 through 131 No H-bonds generated for 'chain 'p' and resid 129 through 131' Processing helix chain 'p' and resid 133 through 141 Processing helix chain 'p' and resid 217 through 224 Processing helix chain 'p' and resid 236 through 243 removed outlier: 3.646A pdb=" N VAL p 241 " --> pdb=" O VAL p 237 " (cutoff:3.500A) Processing helix chain 'p' and resid 245 through 250 Processing helix chain 'p' and resid 251 through 255 Processing helix chain 'p' and resid 532 through 534 No H-bonds generated for 'chain 'p' and resid 532 through 534' Processing helix chain 'q' and resid 113 through 122 removed outlier: 3.854A pdb=" N GLU q 117 " --> pdb=" O GLN q 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 129 through 131 No H-bonds generated for 'chain 'q' and resid 129 through 131' Processing helix chain 'q' and resid 133 through 141 removed outlier: 3.586A pdb=" N ALA q 137 " --> pdb=" O THR q 133 " (cutoff:3.500A) Processing helix chain 'q' and resid 218 through 224 Processing helix chain 'q' and resid 611 through 614 Processing sheet with id=AA1, first strand: chain 'o' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'o' and resid 73 through 74 removed outlier: 4.227A pdb=" N ILE o 66 " --> pdb=" O VAL o 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'o' and resid 58 through 61 removed outlier: 4.519A pdb=" N VAL o 49 " --> pdb=" O ILE o 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'o' and resid 126 through 127 removed outlier: 6.557A pdb=" N VAL o 126 " --> pdb=" O LEU o 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'o' and resid 151 through 154 removed outlier: 3.812A pdb=" N ASP o 177 " --> pdb=" O PHE o 153 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU o 197 " --> pdb=" O PHE o 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'o' and resid 158 through 159 removed outlier: 5.640A pdb=" N THR o 262 " --> pdb=" O GLY o 176 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY o 178 " --> pdb=" O THR o 262 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU o 264 " --> pdb=" O GLY o 178 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU o 180 " --> pdb=" O GLU o 264 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARG o 266 " --> pdb=" O LEU o 180 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE o 182 " --> pdb=" O ARG o 266 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU o 284 " --> pdb=" O SER o 261 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU o 263 " --> pdb=" O LEU o 284 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ARG o 286 " --> pdb=" O LEU o 263 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE o 265 " --> pdb=" O ARG o 286 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N PHE o 285 " --> pdb=" O GLU o 310 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE o 307 " --> pdb=" O GLN o 336 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU o 338 " --> pdb=" O ILE o 307 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE o 309 " --> pdb=" O LEU o 338 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ALA o 335 " --> pdb=" O LYS o 364 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL o 363 " --> pdb=" O ASP o 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'o' and resid 167 through 169 removed outlier: 6.256A pdb=" N ILE o 191 " --> pdb=" O HIS o 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'o' and resid 203 through 205 Processing sheet with id=AA9, first strand: chain 'o' and resid 322 through 323 removed outlier: 6.279A pdb=" N VAL o 322 " --> pdb=" O ILE o 351 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL o 350 " --> pdb=" O ARG o 383 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE o 429 " --> pdb=" O SER o 452 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE o 473 " --> pdb=" O ASN o 500 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU o 502 " --> pdb=" O PHE o 473 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE o 527 " --> pdb=" O GLY o 501 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ARG o 503 " --> pdb=" O ILE o 527 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE o 491 " --> pdb=" O ASP o 518 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'o' and resid 322 through 323 removed outlier: 6.279A pdb=" N VAL o 322 " --> pdb=" O ILE o 351 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL o 350 " --> pdb=" O ARG o 383 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE o 429 " --> pdb=" O SER o 452 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE o 473 " --> pdb=" O ASN o 500 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU o 502 " --> pdb=" O PHE o 473 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE o 527 " --> pdb=" O GLY o 501 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ARG o 503 " --> pdb=" O ILE o 527 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL o 538 " --> pdb=" O PRO o 520 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N SER o 522 " --> pdb=" O VAL o 538 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN o 540 " --> pdb=" O SER o 522 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA o 542 " --> pdb=" O VAL o 524 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY o 526 " --> pdb=" O ALA o 542 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN p 548 " --> pdb=" O LEU o 541 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU o 543 " --> pdb=" O ASN p 548 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG p 550 " --> pdb=" O GLU o 543 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE p 549 " --> pdb=" O ALA q 560 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL q 605 " --> pdb=" O ALA q 596 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N SER q 606 " --> pdb=" O PRO q 620 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA q 617 " --> pdb=" O PRO o 639 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE q 619 " --> pdb=" O PHE o 637 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE o 637 " --> pdb=" O ILE q 619 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU o 648 " --> pdb=" O LEU o 664 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'o' and resid 354 through 356 removed outlier: 3.714A pdb=" N ARG o 435 " --> pdb=" O VAL o 387 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL o 434 " --> pdb=" O GLU o 457 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'o' and resid 369 through 370 removed outlier: 4.212A pdb=" N THR o 373 " --> pdb=" O VAL o 370 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'o' and resid 550 through 553 removed outlier: 3.719A pdb=" N VAL p 605 " --> pdb=" O ALA p 596 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'o' and resid 605 through 609 removed outlier: 3.770A pdb=" N VAL o 605 " --> pdb=" O ALA o 596 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'o' and resid 619 through 620 removed outlier: 3.911A pdb=" N ILE o 619 " --> pdb=" O PHE p 637 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU p 642 " --> pdb=" O SER p 647 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER p 647 " --> pdb=" O GLU p 642 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'q' and resid 59 through 61 removed outlier: 4.640A pdb=" N VAL q 49 " --> pdb=" O ILE q 61 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS q 108 " --> pdb=" O VAL p 9 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'p' and resid 73 through 74 removed outlier: 4.204A pdb=" N ILE p 66 " --> pdb=" O VAL p 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'p' and resid 126 through 127 removed outlier: 6.528A pdb=" N VAL p 126 " --> pdb=" O LEU p 146 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LEU p 145 " --> pdb=" O GLU p 169 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER p 189 " --> pdb=" O GLU p 272 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N HIS p 274 " --> pdb=" O SER p 189 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE p 191 " --> pdb=" O HIS p 274 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL p 271 " --> pdb=" O LYS p 292 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL p 294 " --> pdb=" O VAL p 271 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL p 273 " --> pdb=" O VAL p 294 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N MET p 293 " --> pdb=" O ILE p 323 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL p 322 " --> pdb=" O ILE p 351 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG p 383 " --> pdb=" O VAL p 350 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE p 429 " --> pdb=" O SER p 452 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR p 474 " --> pdb=" O VAL p 451 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER p 471 " --> pdb=" O ARG p 498 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASN p 500 " --> pdb=" O SER p 471 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE p 473 " --> pdb=" O ASN p 500 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N CYS p 497 " --> pdb=" O THR p 523 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER p 525 " --> pdb=" O CYS p 497 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL p 499 " --> pdb=" O SER p 525 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN p 537 " --> pdb=" O ASP p 518 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N SER p 522 " --> pdb=" O ALA p 539 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'p' and resid 151 through 152 removed outlier: 5.962A pdb=" N TYR p 151 " --> pdb=" O ILE p 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'p' and resid 158 through 160 removed outlier: 6.431A pdb=" N VAL p 159 " --> pdb=" O THR p 183 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER p 261 " --> pdb=" O GLY p 282 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU p 284 " --> pdb=" O SER p 261 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU p 263 " --> pdb=" O LEU p 284 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ARG p 286 " --> pdb=" O LEU p 263 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE p 265 " --> pdb=" O ARG p 286 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N THR p 308 " --> pdb=" O ALA p 281 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE p 283 " --> pdb=" O THR p 308 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLU p 310 " --> pdb=" O PHE p 283 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE p 285 " --> pdb=" O GLU p 310 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE p 307 " --> pdb=" O GLN p 336 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU p 338 " --> pdb=" O ILE p 307 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE p 309 " --> pdb=" O LEU p 338 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA p 335 " --> pdb=" O LYS p 364 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL p 363 " --> pdb=" O ASP p 396 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHE p 442 " --> pdb=" O TYR p 465 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA p 464 " --> pdb=" O TYR p 492 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'p' and resid 203 through 204 Processing sheet with id=AC4, first strand: chain 'p' and resid 297 through 301 removed outlier: 4.330A pdb=" N ASN p 297 " --> pdb=" O ARG p 326 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N SER p 328 " --> pdb=" O ASN p 297 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N SER p 355 " --> pdb=" O ILE p 388 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL p 434 " --> pdb=" O GLU p 457 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'p' and resid 340 through 341 removed outlier: 6.650A pdb=" N ASN p 340 " --> pdb=" O TYR p 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'p' and resid 369 through 370 removed outlier: 3.855A pdb=" N THR p 373 " --> pdb=" O VAL p 370 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'p' and resid 619 through 620 removed outlier: 3.717A pdb=" N ILE p 619 " --> pdb=" O PHE q 637 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU q 648 " --> pdb=" O LEU q 664 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'q' and resid 78 through 79 removed outlier: 4.537A pdb=" N ILE q 66 " --> pdb=" O VAL q 74 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N HIS q 88 " --> pdb=" O ASN q 105 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN q 105 " --> pdb=" O HIS q 88 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'q' and resid 126 through 127 removed outlier: 6.491A pdb=" N VAL q 126 " --> pdb=" O LEU q 146 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU q 145 " --> pdb=" O THR q 167 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE q 191 " --> pdb=" O HIS q 274 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA q 276 " --> pdb=" O ILE q 191 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N MET q 196 " --> pdb=" O LEU q 279 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE q 174 " --> pdb=" O GLU q 197 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR q 151 " --> pdb=" O ILE q 175 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'q' and resid 126 through 127 removed outlier: 6.491A pdb=" N VAL q 126 " --> pdb=" O LEU q 146 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU q 145 " --> pdb=" O THR q 167 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE q 191 " --> pdb=" O HIS q 274 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA q 276 " --> pdb=" O ILE q 191 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ALA q 296 " --> pdb=" O ARG q 275 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER q 277 " --> pdb=" O ALA q 296 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'q' and resid 157 through 160 removed outlier: 6.269A pdb=" N GLU q 157 " --> pdb=" O ILE q 181 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR q 183 " --> pdb=" O GLU q 157 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL q 159 " --> pdb=" O THR q 183 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY q 178 " --> pdb=" O THR q 262 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU q 264 " --> pdb=" O GLY q 178 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU q 180 " --> pdb=" O GLU q 264 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ARG q 266 " --> pdb=" O LEU q 180 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE q 182 " --> pdb=" O ARG q 266 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER q 261 " --> pdb=" O GLY q 282 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU q 284 " --> pdb=" O SER q 261 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU q 263 " --> pdb=" O LEU q 284 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG q 286 " --> pdb=" O LEU q 263 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE q 265 " --> pdb=" O ARG q 286 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N THR q 308 " --> pdb=" O ALA q 281 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE q 283 " --> pdb=" O THR q 308 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLU q 310 " --> pdb=" O PHE q 283 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE q 285 " --> pdb=" O GLU q 310 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA q 335 " --> pdb=" O LYS q 364 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL q 363 " --> pdb=" O ASP q 396 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'q' and resid 203 through 204 Processing sheet with id=AD4, first strand: chain 'q' and resid 320 through 323 removed outlier: 6.620A pdb=" N ASN q 320 " --> pdb=" O GLY q 349 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE q 351 " --> pdb=" O ASN q 320 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL q 322 " --> pdb=" O ILE q 351 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE q 353 " --> pdb=" O VAL q 322 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'q' and resid 320 through 323 removed outlier: 6.620A pdb=" N ASN q 320 " --> pdb=" O GLY q 349 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE q 351 " --> pdb=" O ASN q 320 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL q 322 " --> pdb=" O ILE q 351 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE q 353 " --> pdb=" O VAL q 322 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N SER q 385 " --> pdb=" O GLY q 352 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR q 354 " --> pdb=" O SER q 385 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL q 387 " --> pdb=" O THR q 354 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR q 356 " --> pdb=" O VAL q 387 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU q 432 " --> pdb=" O ASP q 384 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL q 386 " --> pdb=" O LEU q 432 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL q 434 " --> pdb=" O VAL q 386 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE q 388 " --> pdb=" O VAL q 434 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLU q 457 " --> pdb=" O LEU q 432 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL q 434 " --> pdb=" O GLU q 457 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL q 456 " --> pdb=" O ILE q 479 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN q 475 " --> pdb=" O ASN q 500 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU q 502 " --> pdb=" O ASN q 475 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA q 477 " --> pdb=" O LEU q 502 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'q' and resid 369 through 370 Processing sheet with id=AD7, first strand: chain 'q' and resid 443 through 444 removed outlier: 3.604A pdb=" N MET q 444 " --> pdb=" O TYR q 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'q' and resid 517 through 519 305 hydrogen bonds defined for protein. 810 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: 2.73 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2789 1.32 - 1.45: 3926 1.45 - 1.57: 8617 1.57 - 1.69: 1 1.69 - 1.82: 72 Bond restraints: 15405 Sorted by residual: bond pdb=" CA ASN o 258 " pdb=" CB ASN o 258 " ideal model delta sigma weight residual 1.526 1.593 -0.067 1.70e-02 3.46e+03 1.54e+01 bond pdb=" C ARG o 409 " pdb=" N PRO o 410 " ideal model delta sigma weight residual 1.335 1.367 -0.032 8.70e-03 1.32e+04 1.39e+01 bond pdb=" N LEU o 180 " pdb=" CA LEU o 180 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.22e+00 bond pdb=" C PRO o 410 " pdb=" O PRO o 410 " ideal model delta sigma weight residual 1.233 1.208 0.025 9.60e-03 1.09e+04 6.81e+00 bond pdb=" C PRO o 419 " pdb=" O PRO o 419 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.30e-02 5.92e+03 6.74e+00 ... (remaining 15400 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 20458 2.90 - 5.79: 406 5.79 - 8.69: 52 8.69 - 11.59: 15 11.59 - 14.48: 3 Bond angle restraints: 20934 Sorted by residual: angle pdb=" C PRO o 410 " pdb=" CA PRO o 410 " pdb=" CB PRO o 410 " ideal model delta sigma weight residual 111.40 104.49 6.91 9.10e-01 1.21e+00 5.77e+01 angle pdb=" C PRO p 419 " pdb=" CA PRO p 419 " pdb=" CB PRO p 419 " ideal model delta sigma weight residual 111.22 102.56 8.66 1.51e+00 4.39e-01 3.29e+01 angle pdb=" CA LYS o 206 " pdb=" CB LYS o 206 " pdb=" CG LYS o 206 " ideal model delta sigma weight residual 114.10 124.25 -10.15 2.00e+00 2.50e-01 2.58e+01 angle pdb=" C ASP o 143 " pdb=" N GLY o 144 " pdb=" CA GLY o 144 " ideal model delta sigma weight residual 121.58 117.30 4.28 8.60e-01 1.35e+00 2.48e+01 angle pdb=" CA TYR q 389 " pdb=" C TYR q 389 " pdb=" N PRO q 390 " ideal model delta sigma weight residual 118.16 121.61 -3.45 7.00e-01 2.04e+00 2.42e+01 ... (remaining 20929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7843 17.98 - 35.96: 981 35.96 - 53.94: 199 53.94 - 71.93: 46 71.93 - 89.91: 15 Dihedral angle restraints: 9084 sinusoidal: 3465 harmonic: 5619 Sorted by residual: dihedral pdb=" CA ASP q 511 " pdb=" C ASP q 511 " pdb=" N GLY q 512 " pdb=" CA GLY q 512 " ideal model delta harmonic sigma weight residual -180.00 -141.89 -38.11 0 5.00e+00 4.00e-02 5.81e+01 dihedral pdb=" CA GLN q 513 " pdb=" C GLN q 513 " pdb=" N GLY q 514 " pdb=" CA GLY q 514 " ideal model delta harmonic sigma weight residual -180.00 -143.52 -36.48 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" CA CYS o 170 " pdb=" C CYS o 170 " pdb=" N LYS o 171 " pdb=" CA LYS o 171 " ideal model delta harmonic sigma weight residual -180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 9081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1729 0.058 - 0.116: 510 0.116 - 0.174: 97 0.174 - 0.232: 13 0.232 - 0.289: 3 Chirality restraints: 2352 Sorted by residual: chirality pdb=" CG LEU p 284 " pdb=" CB LEU p 284 " pdb=" CD1 LEU p 284 " pdb=" CD2 LEU p 284 " both_signs ideal model delta sigma weight residual False -2.59 -2.88 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB ILE q 175 " pdb=" CA ILE q 175 " pdb=" CG1 ILE q 175 " pdb=" CG2 ILE q 175 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CG LEU o 263 " pdb=" CB LEU o 263 " pdb=" CD1 LEU o 263 " pdb=" CD2 LEU o 263 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2349 not shown) Planarity restraints: 2745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR p 418 " -0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C TYR p 418 " 0.066 2.00e-02 2.50e+03 pdb=" O TYR p 418 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO p 419 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR q 114 " 0.010 2.00e-02 2.50e+03 1.98e-02 7.81e+00 pdb=" CG TYR q 114 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR q 114 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR q 114 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR q 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR q 114 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR q 114 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR q 114 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR p 329 " 0.019 2.00e-02 2.50e+03 1.75e-02 6.15e+00 pdb=" CG TYR p 329 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR p 329 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR p 329 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR p 329 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR p 329 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR p 329 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR p 329 " 0.002 2.00e-02 2.50e+03 ... (remaining 2742 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2395 2.76 - 3.30: 15198 3.30 - 3.83: 27222 3.83 - 4.37: 31816 4.37 - 4.90: 53969 Nonbonded interactions: 130600 Sorted by model distance: nonbonded pdb=" OH TYR p 378 " pdb=" OD1 ASP p 412 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR p 209 " pdb=" OE1 GLN p 213 " model vdw 2.226 3.040 nonbonded pdb=" O GLN o 513 " pdb=" NH2 ARG o 535 " model vdw 2.229 3.120 nonbonded pdb=" O GLY o 495 " pdb=" OG SER o 522 " model vdw 2.239 3.040 nonbonded pdb=" O GLY p 495 " pdb=" OG SER p 522 " model vdw 2.251 3.040 ... (remaining 130595 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: 0.02 Found NCS groups: ncs_group { reference = chain 'o' selection = chain 'p' selection = chain 'q' } 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: 8.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.830 Find NCS groups from input model: 0.480 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 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 : 0.005 0.070 15405 Z= 0.232 Angle : 0.999 14.484 20934 Z= 0.547 Chirality : 0.057 0.289 2352 Planarity : 0.006 0.075 2745 Dihedral : 16.712 89.907 5532 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.67 % Favored : 91.98 % Rotamer: Outliers : 0.92 % Allowed : 30.82 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -2.51 (0.17), residues: 1983 helix: -2.01 (0.50), residues: 89 sheet: -1.40 (0.22), residues: 490 loop : -1.84 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG q 266 TYR 0.047 0.002 TYR q 114 PHE 0.031 0.002 PHE o 182 TRP 0.034 0.003 TRP p 392 HIS 0.013 0.002 HIS o 421 Details of bonding type rmsd covalent geometry : bond 0.00468 (15405) covalent geometry : angle 0.99883 (20934) hydrogen bonds : bond 0.18285 ( 293) hydrogen bonds : angle 8.85878 ( 810) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 352 time to evaluate : 0.461 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: o 336 GLN cc_start: 0.7019 (mp10) cc_final: 0.6769 (mp10) REVERT: p 19 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7979 (mm-30) REVERT: p 54 GLU cc_start: 0.6879 (tm-30) cc_final: 0.6409 (tm-30) REVERT: p 206 LYS cc_start: 0.8294 (tptp) cc_final: 0.7959 (tppt) REVERT: p 386 VAL cc_start: 0.7323 (t) cc_final: 0.6826 (m) REVERT: p 467 LEU cc_start: 0.7693 (tp) cc_final: 0.7368 (tt) REVERT: p 530 MET cc_start: 0.5603 (ptp) cc_final: 0.5252 (ptp) REVERT: q 177 ASP cc_start: 0.7150 (m-30) cc_final: 0.6914 (m-30) REVERT: q 320 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8075 (t0) outliers start: 15 outliers final: 8 residues processed: 360 average time/residue: 0.1230 time to fit residues: 62.8911 Evaluate side-chains 342 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 333 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 284 LEU Chi-restraints excluded: chain o residue 333 SER Chi-restraints excluded: chain o residue 420 LEU Chi-restraints excluded: chain p residue 42 ASN Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain q residue 130 ASP Chi-restraints excluded: chain q residue 209 THR Chi-restraints excluded: chain q residue 320 ASN Chi-restraints excluded: chain q residue 509 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.0370 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 overall best weight: 3.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 7 ASN ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 320 ASN q 537 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.178027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.135542 restraints weight = 26342.285| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 3.71 r_work: 0.3681 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15405 Z= 0.242 Angle : 0.721 9.484 20934 Z= 0.381 Chirality : 0.050 0.181 2352 Planarity : 0.005 0.063 2745 Dihedral : 6.545 57.306 2155 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.37 % Favored : 91.38 % Rotamer: Outliers : 5.27 % Allowed : 26.78 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -2.43 (0.17), residues: 1983 helix: -1.19 (0.53), residues: 86 sheet: -1.23 (0.23), residues: 468 loop : -1.90 (0.15), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG q 266 TYR 0.022 0.002 TYR o 378 PHE 0.016 0.002 PHE o 182 TRP 0.022 0.002 TRP p 392 HIS 0.005 0.001 HIS o 421 Details of bonding type rmsd covalent geometry : bond 0.00512 (15405) covalent geometry : angle 0.72104 (20934) hydrogen bonds : bond 0.04334 ( 293) hydrogen bonds : angle 6.91204 ( 810) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 345 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 151 TYR cc_start: 0.8026 (t80) cc_final: 0.7772 (t80) REVERT: o 258 ASN cc_start: 0.8389 (p0) cc_final: 0.8033 (p0) REVERT: o 280 MET cc_start: 0.7923 (tmm) cc_final: 0.7571 (tmm) REVERT: o 318 LYS cc_start: 0.7606 (tptt) cc_final: 0.7368 (tptt) REVERT: o 336 GLN cc_start: 0.7358 (mp10) cc_final: 0.6867 (mp10) REVERT: o 535 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6228 (mmm160) REVERT: o 608 LYS cc_start: 0.5380 (OUTLIER) cc_final: 0.5081 (ttmm) REVERT: p 54 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6832 (tm-30) REVERT: p 187 LYS cc_start: 0.8471 (tptt) cc_final: 0.8270 (tptt) REVERT: p 196 MET cc_start: 0.7785 (mmm) cc_final: 0.7515 (mmm) REVERT: p 213 GLN cc_start: 0.7708 (pm20) cc_final: 0.7263 (pm20) REVERT: p 230 THR cc_start: 0.6679 (OUTLIER) cc_final: 0.6297 (t) REVERT: p 280 MET cc_start: 0.6572 (ppp) cc_final: 0.6010 (ppp) REVERT: p 315 ASP cc_start: 0.8139 (t0) cc_final: 0.7767 (t0) REVERT: p 329 TYR cc_start: 0.6876 (m-80) cc_final: 0.5694 (m-80) REVERT: p 378 TYR cc_start: 0.7069 (m-80) cc_final: 0.6839 (m-80) REVERT: p 402 ASP cc_start: 0.2895 (OUTLIER) cc_final: 0.2369 (p0) REVERT: p 467 LEU cc_start: 0.7540 (tp) cc_final: 0.7083 (tt) REVERT: p 484 LYS cc_start: 0.7388 (tmtt) cc_final: 0.7115 (tmtt) REVERT: q 150 ASP cc_start: 0.7708 (m-30) cc_final: 0.7316 (m-30) REVERT: q 169 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: q 226 LYS cc_start: 0.7949 (tptp) cc_final: 0.7691 (tptp) REVERT: q 266 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.8235 (ttm-80) REVERT: q 345 GLU cc_start: 0.8181 (mp0) cc_final: 0.7651 (mp0) REVERT: q 346 ARG cc_start: 0.7210 (mmt90) cc_final: 0.6892 (mmt90) REVERT: q 378 TYR cc_start: 0.7745 (m-80) cc_final: 0.7452 (m-80) REVERT: q 381 GLN cc_start: 0.7848 (pm20) cc_final: 0.7307 (pm20) REVERT: q 444 MET cc_start: 0.6613 (ppp) cc_final: 0.6360 (ppp) outliers start: 86 outliers final: 41 residues processed: 398 average time/residue: 0.1232 time to fit residues: 70.3335 Evaluate side-chains 383 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 337 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 98 SER Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 165 VAL Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 300 SER Chi-restraints excluded: chain o residue 421 HIS Chi-restraints excluded: chain o residue 497 CYS Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 537 ASN Chi-restraints excluded: chain o residue 540 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 383 ARG Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 480 ASP Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 169 GLU Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 289 HIS Chi-restraints excluded: chain q residue 308 THR Chi-restraints excluded: chain q residue 385 SER Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 571 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 120 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 62 optimal weight: 30.0000 chunk 73 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 7 ASN p 234 GLN ** p 566 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 = 0.4371 r_free = 0.4371 target = 0.176748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.134321 restraints weight = 26680.256| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.72 r_work: 0.3668 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 15405 Z= 0.232 Angle : 0.709 14.477 20934 Z= 0.372 Chirality : 0.050 0.263 2352 Planarity : 0.005 0.054 2745 Dihedral : 6.040 35.753 2139 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.37 % Favored : 91.38 % Rotamer: Outliers : 6.00 % Allowed : 26.72 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -2.47 (0.17), residues: 1983 helix: -1.41 (0.52), residues: 88 sheet: -1.19 (0.24), residues: 455 loop : -1.93 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG q 266 TYR 0.021 0.002 TYR q 233 PHE 0.018 0.002 PHE o 382 TRP 0.012 0.002 TRP p 392 HIS 0.005 0.001 HIS o 421 Details of bonding type rmsd covalent geometry : bond 0.00495 (15405) covalent geometry : angle 0.70873 (20934) hydrogen bonds : bond 0.04286 ( 293) hydrogen bonds : angle 6.67618 ( 810) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 356 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 135 GLN cc_start: 0.8325 (tp40) cc_final: 0.8098 (tp-100) REVERT: o 151 TYR cc_start: 0.8062 (t80) cc_final: 0.7759 (t80) REVERT: o 226 LYS cc_start: 0.7572 (mmtt) cc_final: 0.7085 (mmtt) REVERT: o 234 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7091 (tt0) REVERT: o 258 ASN cc_start: 0.8477 (p0) cc_final: 0.8127 (p0) REVERT: o 266 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.8311 (ttm-80) REVERT: o 279 LEU cc_start: 0.8530 (mm) cc_final: 0.8282 (mm) REVERT: o 280 MET cc_start: 0.7981 (tmm) cc_final: 0.7620 (tmm) REVERT: o 336 GLN cc_start: 0.7513 (mp10) cc_final: 0.6780 (mp10) REVERT: o 339 ARG cc_start: 0.5872 (ttt180) cc_final: 0.5534 (ttt-90) REVERT: o 346 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6544 (mtt-85) REVERT: o 367 GLN cc_start: 0.5148 (OUTLIER) cc_final: 0.3380 (pm20) REVERT: o 381 GLN cc_start: 0.7425 (mt0) cc_final: 0.7137 (mt0) REVERT: o 535 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6475 (mmm160) REVERT: o 608 LYS cc_start: 0.5615 (OUTLIER) cc_final: 0.5273 (ttmm) REVERT: p 54 GLU cc_start: 0.6422 (tm-30) cc_final: 0.5915 (tm-30) REVERT: p 134 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8717 (tt) REVERT: p 169 GLU cc_start: 0.7497 (tm-30) cc_final: 0.6731 (tm-30) REVERT: p 196 MET cc_start: 0.7645 (mmm) cc_final: 0.7333 (mmm) REVERT: p 213 GLN cc_start: 0.7730 (pm20) cc_final: 0.7345 (pm20) REVERT: p 230 THR cc_start: 0.6675 (OUTLIER) cc_final: 0.6328 (t) REVERT: p 264 GLU cc_start: 0.7026 (pm20) cc_final: 0.6809 (pm20) REVERT: p 280 MET cc_start: 0.6638 (ppp) cc_final: 0.6285 (ppp) REVERT: p 315 ASP cc_start: 0.8221 (t0) cc_final: 0.7895 (t70) REVERT: p 386 VAL cc_start: 0.7637 (t) cc_final: 0.7014 (m) REVERT: p 402 ASP cc_start: 0.2969 (OUTLIER) cc_final: 0.2443 (p0) REVERT: p 467 LEU cc_start: 0.7577 (tp) cc_final: 0.7053 (tt) REVERT: p 481 THR cc_start: 0.6332 (p) cc_final: 0.6095 (p) REVERT: p 484 LYS cc_start: 0.7427 (tmtt) cc_final: 0.7127 (tmtt) REVERT: p 530 MET cc_start: 0.6046 (ptp) cc_final: 0.5502 (ptp) REVERT: p 538 VAL cc_start: 0.5006 (OUTLIER) cc_final: 0.4553 (t) REVERT: q 37 ASP cc_start: 0.7671 (t0) cc_final: 0.7448 (t0) REVERT: q 49 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8495 (m) REVERT: q 174 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7736 (m-10) REVERT: q 217 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7160 (p0) REVERT: q 226 LYS cc_start: 0.7977 (tptp) cc_final: 0.7704 (tptp) REVERT: q 266 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.8310 (ttm-80) REVERT: q 345 GLU cc_start: 0.8175 (mp0) cc_final: 0.7492 (mp0) REVERT: q 378 TYR cc_start: 0.7803 (m-80) cc_final: 0.7486 (m-80) REVERT: q 381 GLN cc_start: 0.7822 (pm20) cc_final: 0.7176 (pm20) REVERT: q 444 MET cc_start: 0.6587 (ppp) cc_final: 0.6169 (ppp) outliers start: 98 outliers final: 61 residues processed: 422 average time/residue: 0.1285 time to fit residues: 76.9621 Evaluate side-chains 407 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 334 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 165 VAL Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 234 GLN Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 265 ILE Chi-restraints excluded: chain o residue 333 SER Chi-restraints excluded: chain o residue 346 ARG Chi-restraints excluded: chain o residue 367 GLN Chi-restraints excluded: chain o residue 421 HIS Chi-restraints excluded: chain o residue 493 ILE Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 537 ASN Chi-restraints excluded: chain o residue 540 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 42 ASN Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 134 LEU Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 263 LEU Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain p residue 383 ARG Chi-restraints excluded: chain p residue 388 ILE Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 413 TYR Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 471 SER Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain p residue 538 VAL Chi-restraints excluded: chain q residue 7 ASN Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 165 VAL Chi-restraints excluded: chain q residue 174 PHE Chi-restraints excluded: chain q residue 183 THR Chi-restraints excluded: chain q residue 199 THR Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 217 ASP Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 237 VAL Chi-restraints excluded: chain q residue 240 TYR Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 283 PHE Chi-restraints excluded: chain q residue 289 HIS Chi-restraints excluded: chain q residue 308 THR Chi-restraints excluded: chain q residue 326 ARG Chi-restraints excluded: chain q residue 379 ASN Chi-restraints excluded: chain q residue 385 SER Chi-restraints excluded: chain q residue 425 LEU Chi-restraints excluded: chain q residue 428 LEU Chi-restraints excluded: chain q residue 449 MET Chi-restraints excluded: chain q residue 451 VAL Chi-restraints excluded: chain q residue 459 CYS Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 509 SER Chi-restraints excluded: chain q residue 521 ASN Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 571 THR Chi-restraints excluded: chain q residue 631 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 105 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 170 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 178 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.176800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.134569 restraints weight = 26599.032| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 3.69 r_work: 0.3671 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15405 Z= 0.193 Angle : 0.670 12.962 20934 Z= 0.351 Chirality : 0.049 0.179 2352 Planarity : 0.004 0.041 2745 Dihedral : 5.794 35.150 2139 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.07 % Favored : 91.68 % Rotamer: Outliers : 6.43 % Allowed : 26.78 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -2.46 (0.17), residues: 1983 helix: -1.31 (0.54), residues: 82 sheet: -1.23 (0.24), residues: 461 loop : -1.92 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG p 14 TYR 0.026 0.002 TYR o 356 PHE 0.014 0.002 PHE o 353 TRP 0.015 0.002 TRP o 316 HIS 0.006 0.001 HIS o 421 Details of bonding type rmsd covalent geometry : bond 0.00414 (15405) covalent geometry : angle 0.67022 (20934) hydrogen bonds : bond 0.03793 ( 293) hydrogen bonds : angle 6.39417 ( 810) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 362 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 135 GLN cc_start: 0.8365 (tp40) cc_final: 0.8032 (tp-100) REVERT: o 151 TYR cc_start: 0.8049 (t80) cc_final: 0.7774 (t80) REVERT: o 195 PHE cc_start: 0.8567 (t80) cc_final: 0.7941 (t80) REVERT: o 197 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.5610 (pm20) REVERT: o 234 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.6992 (tt0) REVERT: o 258 ASN cc_start: 0.8496 (p0) cc_final: 0.8170 (p0) REVERT: o 280 MET cc_start: 0.7978 (tmm) cc_final: 0.7459 (tmm) REVERT: o 336 GLN cc_start: 0.7688 (mp10) cc_final: 0.6929 (mp10) REVERT: o 339 ARG cc_start: 0.6007 (ttt180) cc_final: 0.5722 (ttt-90) REVERT: o 502 LEU cc_start: 0.5954 (OUTLIER) cc_final: 0.5654 (mt) REVERT: o 535 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6479 (mmm160) REVERT: o 608 LYS cc_start: 0.5727 (OUTLIER) cc_final: 0.5380 (ttmt) REVERT: p 54 GLU cc_start: 0.6452 (tm-30) cc_final: 0.5895 (tm-30) REVERT: p 112 ASP cc_start: 0.8198 (t0) cc_final: 0.7815 (t0) REVERT: p 134 LEU cc_start: 0.8922 (tt) cc_final: 0.8706 (tt) REVERT: p 169 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6686 (tm-30) REVERT: p 196 MET cc_start: 0.7510 (mmm) cc_final: 0.7139 (mmm) REVERT: p 213 GLN cc_start: 0.7729 (pm20) cc_final: 0.7391 (pm20) REVERT: p 230 THR cc_start: 0.6725 (OUTLIER) cc_final: 0.6360 (t) REVERT: p 264 GLU cc_start: 0.7091 (pm20) cc_final: 0.6840 (pm20) REVERT: p 266 ARG cc_start: 0.8015 (ttm170) cc_final: 0.7769 (ttm170) REVERT: p 280 MET cc_start: 0.6618 (ppp) cc_final: 0.6357 (ppp) REVERT: p 315 ASP cc_start: 0.8221 (t0) cc_final: 0.7905 (t70) REVERT: p 386 VAL cc_start: 0.7548 (t) cc_final: 0.6941 (m) REVERT: p 402 ASP cc_start: 0.2838 (OUTLIER) cc_final: 0.2106 (p0) REVERT: p 415 ILE cc_start: 0.6179 (OUTLIER) cc_final: 0.5866 (mt) REVERT: p 445 ASP cc_start: 0.5065 (OUTLIER) cc_final: 0.4222 (p0) REVERT: p 449 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.5988 (pmm) REVERT: p 467 LEU cc_start: 0.7580 (tp) cc_final: 0.6922 (tt) REVERT: p 484 LYS cc_start: 0.7348 (tmtt) cc_final: 0.7074 (tmtt) REVERT: p 530 MET cc_start: 0.5755 (ptp) cc_final: 0.5164 (ptp) REVERT: p 538 VAL cc_start: 0.5048 (OUTLIER) cc_final: 0.4570 (t) REVERT: q 37 ASP cc_start: 0.7658 (t0) cc_final: 0.7399 (t0) REVERT: q 49 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8499 (m) REVERT: q 174 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7521 (m-10) REVERT: q 226 LYS cc_start: 0.7979 (tptp) cc_final: 0.7700 (tptp) REVERT: q 238 SER cc_start: 0.8835 (m) cc_final: 0.8235 (p) REVERT: q 266 ARG cc_start: 0.8465 (ttm-80) cc_final: 0.8213 (ttm-80) REVERT: q 269 ILE cc_start: 0.9139 (mp) cc_final: 0.8843 (mt) REVERT: q 320 ASN cc_start: 0.7886 (m110) cc_final: 0.7432 (m-40) REVERT: q 345 GLU cc_start: 0.8186 (mp0) cc_final: 0.7633 (mp0) REVERT: q 346 ARG cc_start: 0.7443 (mmt90) cc_final: 0.7157 (mmt90) REVERT: q 378 TYR cc_start: 0.7791 (m-80) cc_final: 0.7429 (m-80) REVERT: q 381 GLN cc_start: 0.7808 (pm20) cc_final: 0.7089 (pm20) REVERT: q 392 TRP cc_start: 0.7800 (m100) cc_final: 0.7481 (m100) REVERT: q 444 MET cc_start: 0.6646 (ppp) cc_final: 0.6091 (ppp) outliers start: 105 outliers final: 68 residues processed: 431 average time/residue: 0.1139 time to fit residues: 70.2071 Evaluate side-chains 433 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 352 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 41 VAL Chi-restraints excluded: chain o residue 83 VAL Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 149 ARG Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 165 VAL Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 197 GLU Chi-restraints excluded: chain o residue 234 GLN Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 333 SER Chi-restraints excluded: chain o residue 341 ASN Chi-restraints excluded: chain o residue 345 GLU Chi-restraints excluded: chain o residue 403 MET Chi-restraints excluded: chain o residue 421 HIS Chi-restraints excluded: chain o residue 493 ILE Chi-restraints excluded: chain o residue 502 LEU Chi-restraints excluded: chain o residue 507 ILE Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 537 ASN Chi-restraints excluded: chain o residue 540 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 19 GLU Chi-restraints excluded: chain p residue 42 ASN Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 203 TRP Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 413 TYR Chi-restraints excluded: chain p residue 415 ILE Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 445 ASP Chi-restraints excluded: chain p residue 449 MET Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 471 SER Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain p residue 517 ILE Chi-restraints excluded: chain p residue 538 VAL Chi-restraints excluded: chain p residue 660 VAL Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 128 LEU Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 165 VAL Chi-restraints excluded: chain q residue 174 PHE Chi-restraints excluded: chain q residue 183 THR Chi-restraints excluded: chain q residue 199 THR Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 237 VAL Chi-restraints excluded: chain q residue 240 TYR Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 283 PHE Chi-restraints excluded: chain q residue 304 ASP Chi-restraints excluded: chain q residue 308 THR Chi-restraints excluded: chain q residue 326 ARG Chi-restraints excluded: chain q residue 379 ASN Chi-restraints excluded: chain q residue 385 SER Chi-restraints excluded: chain q residue 425 LEU Chi-restraints excluded: chain q residue 449 MET Chi-restraints excluded: chain q residue 459 CYS Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 509 SER Chi-restraints excluded: chain q residue 521 ASN Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 571 THR Chi-restraints excluded: chain q residue 631 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 189 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 184 optimal weight: 0.0770 chunk 130 optimal weight: 20.0000 chunk 95 optimal weight: 0.0040 chunk 131 optimal weight: 20.0000 chunk 196 optimal weight: 40.0000 chunk 25 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 overall best weight: 3.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 421 HIS ** o 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 257 GLN q 404 ASN ** q 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.174118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.132671 restraints weight = 26569.283| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 3.62 r_work: 0.3637 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 15405 Z= 0.279 Angle : 0.723 12.212 20934 Z= 0.382 Chirality : 0.050 0.174 2352 Planarity : 0.005 0.042 2745 Dihedral : 6.036 34.099 2139 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.58 % Favored : 90.17 % Rotamer: Outliers : 7.35 % Allowed : 27.27 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -2.57 (0.18), residues: 1983 helix: -1.54 (0.53), residues: 82 sheet: -1.43 (0.23), residues: 496 loop : -1.94 (0.15), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG o 14 TYR 0.022 0.002 TYR q 233 PHE 0.016 0.002 PHE o 174 TRP 0.024 0.002 TRP p 214 HIS 0.007 0.001 HIS p 566 Details of bonding type rmsd covalent geometry : bond 0.00592 (15405) covalent geometry : angle 0.72341 (20934) hydrogen bonds : bond 0.04177 ( 293) hydrogen bonds : angle 6.51010 ( 810) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 364 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 101 ASP cc_start: 0.7788 (t0) cc_final: 0.7581 (t0) REVERT: o 151 TYR cc_start: 0.8057 (t80) cc_final: 0.7799 (t80) REVERT: o 213 GLN cc_start: 0.7652 (pp30) cc_final: 0.7433 (pp30) REVERT: o 234 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.6828 (tt0) REVERT: o 257 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.5019 (pm20) REVERT: o 258 ASN cc_start: 0.8554 (p0) cc_final: 0.8267 (p0) REVERT: o 266 ARG cc_start: 0.8644 (ttm-80) cc_final: 0.8352 (ttm-80) REVERT: o 280 MET cc_start: 0.8005 (tmm) cc_final: 0.7725 (tmm) REVERT: o 336 GLN cc_start: 0.7764 (mp10) cc_final: 0.7169 (mp10) REVERT: o 502 LEU cc_start: 0.5983 (OUTLIER) cc_final: 0.5656 (mt) REVERT: o 535 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6499 (mmm160) REVERT: o 607 LEU cc_start: 0.4585 (OUTLIER) cc_final: 0.4238 (pp) REVERT: o 608 LYS cc_start: 0.5909 (OUTLIER) cc_final: 0.5432 (ttmt) REVERT: p 54 GLU cc_start: 0.6711 (tm-30) cc_final: 0.6002 (tm-30) REVERT: p 112 ASP cc_start: 0.8200 (t0) cc_final: 0.7858 (t0) REVERT: p 134 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8741 (tt) REVERT: p 169 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6936 (tm-30) REVERT: p 230 THR cc_start: 0.6628 (OUTLIER) cc_final: 0.6293 (t) REVERT: p 264 GLU cc_start: 0.7171 (pm20) cc_final: 0.6896 (pm20) REVERT: p 280 MET cc_start: 0.6768 (ppp) cc_final: 0.6456 (ppp) REVERT: p 293 MET cc_start: 0.8393 (mtm) cc_final: 0.8186 (mtm) REVERT: p 315 ASP cc_start: 0.8248 (t0) cc_final: 0.7976 (t70) REVERT: p 321 TYR cc_start: 0.6800 (m-80) cc_final: 0.6517 (m-10) REVERT: p 337 PHE cc_start: 0.7602 (m-80) cc_final: 0.7085 (m-10) REVERT: p 383 ARG cc_start: 0.7116 (ptm160) cc_final: 0.6821 (ptm160) REVERT: p 402 ASP cc_start: 0.3085 (OUTLIER) cc_final: 0.2573 (p0) REVERT: p 415 ILE cc_start: 0.6269 (OUTLIER) cc_final: 0.6024 (tt) REVERT: p 445 ASP cc_start: 0.4765 (OUTLIER) cc_final: 0.3865 (p0) REVERT: p 467 LEU cc_start: 0.7847 (tp) cc_final: 0.7214 (tt) REVERT: p 484 LYS cc_start: 0.7520 (tmtt) cc_final: 0.7050 (tmtt) REVERT: p 530 MET cc_start: 0.6007 (ptp) cc_final: 0.5302 (ptp) REVERT: p 550 ARG cc_start: 0.7016 (ptm-80) cc_final: 0.6473 (ptm-80) REVERT: p 664 LEU cc_start: 0.5970 (mt) cc_final: 0.5726 (mt) REVERT: q 37 ASP cc_start: 0.7710 (t0) cc_final: 0.7436 (t0) REVERT: q 174 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7391 (m-10) REVERT: q 217 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7254 (p0) REVERT: q 226 LYS cc_start: 0.7980 (tptp) cc_final: 0.7702 (tptp) REVERT: q 238 SER cc_start: 0.8854 (m) cc_final: 0.8322 (p) REVERT: q 249 LEU cc_start: 0.3509 (OUTLIER) cc_final: 0.2221 (mt) REVERT: q 266 ARG cc_start: 0.8521 (ttm-80) cc_final: 0.8237 (ttm-80) REVERT: q 312 LEU cc_start: 0.8482 (pp) cc_final: 0.8281 (pt) REVERT: q 320 ASN cc_start: 0.7936 (m110) cc_final: 0.7498 (m-40) REVERT: q 341 ASN cc_start: 0.8082 (m-40) cc_final: 0.7599 (m-40) REVERT: q 345 GLU cc_start: 0.8198 (mp0) cc_final: 0.7724 (mp0) REVERT: q 346 ARG cc_start: 0.7536 (mmt90) cc_final: 0.7253 (mmt90) REVERT: q 378 TYR cc_start: 0.7795 (m-80) cc_final: 0.7572 (m-80) REVERT: q 381 GLN cc_start: 0.7814 (pm20) cc_final: 0.7095 (pm20) REVERT: q 392 TRP cc_start: 0.7810 (m100) cc_final: 0.7537 (m-10) REVERT: q 418 TYR cc_start: 0.7664 (m-80) cc_final: 0.7265 (m-80) REVERT: q 444 MET cc_start: 0.6644 (ppp) cc_final: 0.6400 (ppp) outliers start: 120 outliers final: 84 residues processed: 448 average time/residue: 0.1160 time to fit residues: 75.5993 Evaluate side-chains 453 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 355 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 41 VAL Chi-restraints excluded: chain o residue 149 ARG Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 165 VAL Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 234 GLN Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 257 GLN Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 265 ILE Chi-restraints excluded: chain o residue 269 ILE Chi-restraints excluded: chain o residue 333 SER Chi-restraints excluded: chain o residue 341 ASN Chi-restraints excluded: chain o residue 345 GLU Chi-restraints excluded: chain o residue 363 VAL Chi-restraints excluded: chain o residue 403 MET Chi-restraints excluded: chain o residue 421 HIS Chi-restraints excluded: chain o residue 422 GLN Chi-restraints excluded: chain o residue 431 ASN Chi-restraints excluded: chain o residue 451 VAL Chi-restraints excluded: chain o residue 481 THR Chi-restraints excluded: chain o residue 493 ILE Chi-restraints excluded: chain o residue 502 LEU Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 537 ASN Chi-restraints excluded: chain o residue 540 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 607 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 19 GLU Chi-restraints excluded: chain p residue 42 ASN Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 134 LEU Chi-restraints excluded: chain p residue 146 LEU Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 203 TRP Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 286 ARG Chi-restraints excluded: chain p residue 307 ILE Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain p residue 363 VAL Chi-restraints excluded: chain p residue 388 ILE Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 413 TYR Chi-restraints excluded: chain p residue 415 ILE Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 445 ASP Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 471 SER Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain p residue 517 ILE Chi-restraints excluded: chain p residue 538 VAL Chi-restraints excluded: chain q residue 7 ASN Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 128 LEU Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 165 VAL Chi-restraints excluded: chain q residue 174 PHE Chi-restraints excluded: chain q residue 183 THR Chi-restraints excluded: chain q residue 199 THR Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 217 ASP Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 237 VAL Chi-restraints excluded: chain q residue 240 TYR Chi-restraints excluded: chain q residue 249 LEU Chi-restraints excluded: chain q residue 257 GLN Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 283 PHE Chi-restraints excluded: chain q residue 289 HIS Chi-restraints excluded: chain q residue 304 ASP Chi-restraints excluded: chain q residue 308 THR Chi-restraints excluded: chain q residue 326 ARG Chi-restraints excluded: chain q residue 379 ASN Chi-restraints excluded: chain q residue 385 SER Chi-restraints excluded: chain q residue 425 LEU Chi-restraints excluded: chain q residue 449 MET Chi-restraints excluded: chain q residue 459 CYS Chi-restraints excluded: chain q residue 483 THR Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 509 SER Chi-restraints excluded: chain q residue 521 ASN Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 571 THR Chi-restraints excluded: chain q residue 631 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 165 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 59 optimal weight: 0.0070 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 50 optimal weight: 0.0170 chunk 61 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 421 HIS ** o 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 610 ASN ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 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 = 0.4384 r_free = 0.4384 target = 0.179047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.137434 restraints weight = 26298.207| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.69 r_work: 0.3707 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15405 Z= 0.129 Angle : 0.680 12.265 20934 Z= 0.352 Chirality : 0.049 0.180 2352 Planarity : 0.004 0.054 2745 Dihedral : 5.516 35.115 2139 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.56 % Favored : 93.19 % Rotamer: Outliers : 5.21 % Allowed : 29.17 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.37 (0.18), residues: 1983 helix: -1.09 (0.55), residues: 83 sheet: -1.24 (0.23), residues: 498 loop : -1.84 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG q 190 TYR 0.023 0.002 TYR q 465 PHE 0.029 0.001 PHE q 153 TRP 0.020 0.002 TRP o 316 HIS 0.009 0.001 HIS o 421 Details of bonding type rmsd covalent geometry : bond 0.00275 (15405) covalent geometry : angle 0.67970 (20934) hydrogen bonds : bond 0.03310 ( 293) hydrogen bonds : angle 6.16597 ( 810) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 360 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 135 GLN cc_start: 0.8245 (tp40) cc_final: 0.8008 (tp-100) REVERT: o 151 TYR cc_start: 0.8032 (t80) cc_final: 0.7787 (t80) REVERT: o 197 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.5655 (pm20) REVERT: o 234 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7274 (tp40) REVERT: o 258 ASN cc_start: 0.8531 (p0) cc_final: 0.8219 (p0) REVERT: o 266 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.8162 (ttm-80) REVERT: o 280 MET cc_start: 0.7906 (tmm) cc_final: 0.7635 (tmm) REVERT: o 322 VAL cc_start: 0.8725 (t) cc_final: 0.8369 (m) REVERT: o 329 TYR cc_start: 0.8378 (m-80) cc_final: 0.7765 (m-80) REVERT: o 333 SER cc_start: 0.7958 (p) cc_final: 0.7105 (m) REVERT: o 357 ARG cc_start: 0.7745 (mtp85) cc_final: 0.7467 (mtt-85) REVERT: o 535 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6497 (mmm160) REVERT: o 607 LEU cc_start: 0.4566 (OUTLIER) cc_final: 0.4207 (pp) REVERT: o 608 LYS cc_start: 0.5718 (OUTLIER) cc_final: 0.5262 (ttmt) REVERT: p 46 GLN cc_start: 0.8553 (mt0) cc_final: 0.8265 (mt0) REVERT: p 54 GLU cc_start: 0.6487 (tm-30) cc_final: 0.5715 (tm-30) REVERT: p 112 ASP cc_start: 0.8090 (t0) cc_final: 0.7553 (t0) REVERT: p 134 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8647 (tt) REVERT: p 169 GLU cc_start: 0.7484 (tm-30) cc_final: 0.6913 (tm-30) REVERT: p 187 LYS cc_start: 0.8415 (tptt) cc_final: 0.8111 (tptt) REVERT: p 195 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.6567 (t80) REVERT: p 213 GLN cc_start: 0.7300 (pm20) cc_final: 0.7061 (mp-120) REVERT: p 230 THR cc_start: 0.6825 (OUTLIER) cc_final: 0.6332 (t) REVERT: p 264 GLU cc_start: 0.7085 (pm20) cc_final: 0.6690 (pm20) REVERT: p 266 ARG cc_start: 0.7936 (ttm170) cc_final: 0.7339 (ttm110) REVERT: p 315 ASP cc_start: 0.8195 (t0) cc_final: 0.7955 (t70) REVERT: p 329 TYR cc_start: 0.7050 (m-10) cc_final: 0.6421 (m-80) REVERT: p 337 PHE cc_start: 0.7489 (m-80) cc_final: 0.6961 (m-10) REVERT: p 356 TYR cc_start: 0.7379 (t80) cc_final: 0.7043 (t80) REVERT: p 383 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.6471 (ptm160) REVERT: p 386 VAL cc_start: 0.7376 (t) cc_final: 0.6751 (m) REVERT: p 392 TRP cc_start: 0.7254 (m100) cc_final: 0.7007 (m100) REVERT: p 402 ASP cc_start: 0.2866 (OUTLIER) cc_final: 0.2143 (p0) REVERT: p 445 ASP cc_start: 0.4910 (OUTLIER) cc_final: 0.4162 (p0) REVERT: p 449 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5907 (pmm) REVERT: p 467 LEU cc_start: 0.7629 (tp) cc_final: 0.6825 (tt) REVERT: p 475 ASN cc_start: 0.8020 (m-40) cc_final: 0.7679 (m110) REVERT: p 484 LYS cc_start: 0.7337 (tmtt) cc_final: 0.7060 (tmtt) REVERT: p 530 MET cc_start: 0.5629 (ptp) cc_final: 0.5006 (ptp) REVERT: p 550 ARG cc_start: 0.7122 (ptm-80) cc_final: 0.6591 (ptm-80) REVERT: q 37 ASP cc_start: 0.7615 (t0) cc_final: 0.7259 (t0) REVERT: q 49 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8326 (m) REVERT: q 238 SER cc_start: 0.8837 (m) cc_final: 0.8257 (p) REVERT: q 266 ARG cc_start: 0.8488 (ttm-80) cc_final: 0.8178 (ttm-80) REVERT: q 274 HIS cc_start: 0.8394 (m-70) cc_final: 0.8164 (m-70) REVERT: q 312 LEU cc_start: 0.8413 (pp) cc_final: 0.8192 (pt) REVERT: q 320 ASN cc_start: 0.7870 (m110) cc_final: 0.7572 (m-40) REVERT: q 341 ASN cc_start: 0.7794 (m-40) cc_final: 0.7359 (m-40) REVERT: q 345 GLU cc_start: 0.8063 (mp0) cc_final: 0.7593 (mp0) REVERT: q 381 GLN cc_start: 0.7764 (pm20) cc_final: 0.7009 (pm20) REVERT: q 392 TRP cc_start: 0.7744 (m100) cc_final: 0.7403 (m-10) REVERT: q 418 TYR cc_start: 0.7605 (m-80) cc_final: 0.7206 (m-80) REVERT: q 444 MET cc_start: 0.6630 (ppp) cc_final: 0.6245 (ppp) REVERT: q 467 LEU cc_start: 0.8058 (mt) cc_final: 0.7483 (tp) outliers start: 85 outliers final: 55 residues processed: 416 average time/residue: 0.1216 time to fit residues: 72.4075 Evaluate side-chains 421 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 353 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 83 VAL Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 103 ILE Chi-restraints excluded: chain o residue 149 ARG Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 197 GLU Chi-restraints excluded: chain o residue 234 GLN Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 345 GLU Chi-restraints excluded: chain o residue 363 VAL Chi-restraints excluded: chain o residue 395 PHE Chi-restraints excluded: chain o residue 403 MET Chi-restraints excluded: chain o residue 497 CYS Chi-restraints excluded: chain o residue 511 ASP Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 537 ASN Chi-restraints excluded: chain o residue 540 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 607 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 19 GLU Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 134 LEU Chi-restraints excluded: chain p residue 146 LEU Chi-restraints excluded: chain p residue 195 PHE Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain p residue 383 ARG Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 413 TYR Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 445 ASP Chi-restraints excluded: chain p residue 449 MET Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 480 ASP Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain p residue 517 ILE Chi-restraints excluded: chain p residue 660 VAL Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 165 VAL Chi-restraints excluded: chain q residue 183 THR Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 240 TYR Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 283 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 308 THR Chi-restraints excluded: chain q residue 449 MET Chi-restraints excluded: chain q residue 459 CYS Chi-restraints excluded: chain q residue 483 THR Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 571 THR Chi-restraints excluded: chain q residue 631 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 32 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 537 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.175466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.134065 restraints weight = 26366.342| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.63 r_work: 0.3665 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15405 Z= 0.204 Angle : 0.695 10.725 20934 Z= 0.362 Chirality : 0.049 0.181 2352 Planarity : 0.004 0.042 2745 Dihedral : 5.645 35.725 2139 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.37 % Favored : 91.38 % Rotamer: Outliers : 5.70 % Allowed : 29.53 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.44 (0.18), residues: 1983 helix: -1.18 (0.55), residues: 82 sheet: -1.41 (0.23), residues: 516 loop : -1.83 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG o 383 TYR 0.032 0.002 TYR o 356 PHE 0.018 0.002 PHE q 153 TRP 0.017 0.002 TRP o 316 HIS 0.005 0.001 HIS o 427 Details of bonding type rmsd covalent geometry : bond 0.00440 (15405) covalent geometry : angle 0.69550 (20934) hydrogen bonds : bond 0.03726 ( 293) hydrogen bonds : angle 6.13129 ( 810) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 357 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 135 GLN cc_start: 0.8283 (tp40) cc_final: 0.7998 (tp-100) REVERT: o 151 TYR cc_start: 0.8082 (t80) cc_final: 0.7836 (t80) REVERT: o 227 GLN cc_start: 0.7791 (mm110) cc_final: 0.7558 (mm-40) REVERT: o 234 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7084 (tt0) REVERT: o 258 ASN cc_start: 0.8548 (p0) cc_final: 0.8179 (p0) REVERT: o 266 ARG cc_start: 0.8621 (ttm-80) cc_final: 0.8180 (ttm-80) REVERT: o 280 MET cc_start: 0.8029 (tmm) cc_final: 0.7738 (tmm) REVERT: o 333 SER cc_start: 0.7992 (p) cc_final: 0.7256 (m) REVERT: o 357 ARG cc_start: 0.7827 (mtp85) cc_final: 0.7575 (mtt-85) REVERT: o 502 LEU cc_start: 0.5903 (OUTLIER) cc_final: 0.5611 (mt) REVERT: o 535 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6450 (mmm160) REVERT: o 607 LEU cc_start: 0.4638 (OUTLIER) cc_final: 0.4284 (pp) REVERT: o 608 LYS cc_start: 0.5836 (OUTLIER) cc_final: 0.5356 (ttmt) REVERT: p 54 GLU cc_start: 0.6656 (tm-30) cc_final: 0.5864 (tm-30) REVERT: p 112 ASP cc_start: 0.8205 (t0) cc_final: 0.7833 (t0) REVERT: p 134 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8713 (tt) REVERT: p 187 LYS cc_start: 0.8495 (tptt) cc_final: 0.8169 (tptt) REVERT: p 195 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.6401 (t80) REVERT: p 213 GLN cc_start: 0.7543 (pm20) cc_final: 0.7296 (mp-120) REVERT: p 230 THR cc_start: 0.6639 (OUTLIER) cc_final: 0.6158 (t) REVERT: p 264 GLU cc_start: 0.7090 (pm20) cc_final: 0.6853 (pm20) REVERT: p 315 ASP cc_start: 0.8267 (t0) cc_final: 0.7983 (t70) REVERT: p 321 TYR cc_start: 0.6759 (m-80) cc_final: 0.6509 (m-10) REVERT: p 329 TYR cc_start: 0.7267 (m-10) cc_final: 0.6616 (m-80) REVERT: p 337 PHE cc_start: 0.7563 (m-80) cc_final: 0.7123 (m-10) REVERT: p 356 TYR cc_start: 0.7478 (t80) cc_final: 0.7065 (t80) REVERT: p 383 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6640 (ptp-170) REVERT: p 386 VAL cc_start: 0.7569 (t) cc_final: 0.6941 (m) REVERT: p 392 TRP cc_start: 0.7268 (m100) cc_final: 0.7000 (m100) REVERT: p 402 ASP cc_start: 0.2966 (OUTLIER) cc_final: 0.2239 (p0) REVERT: p 415 ILE cc_start: 0.6209 (OUTLIER) cc_final: 0.6006 (tt) REVERT: p 445 ASP cc_start: 0.5162 (OUTLIER) cc_final: 0.4290 (p0) REVERT: p 449 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.5982 (pmm) REVERT: p 467 LEU cc_start: 0.7767 (tp) cc_final: 0.6973 (tt) REVERT: p 475 ASN cc_start: 0.8056 (m-40) cc_final: 0.7751 (m110) REVERT: p 530 MET cc_start: 0.5846 (ptp) cc_final: 0.5246 (ptp) REVERT: p 538 VAL cc_start: 0.5232 (OUTLIER) cc_final: 0.4769 (t) REVERT: p 550 ARG cc_start: 0.7191 (ptm-80) cc_final: 0.6712 (ptm-80) REVERT: q 37 ASP cc_start: 0.7689 (t0) cc_final: 0.7322 (t0) REVERT: q 49 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8364 (m) REVERT: q 238 SER cc_start: 0.8842 (m) cc_final: 0.8305 (p) REVERT: q 266 ARG cc_start: 0.8478 (ttm-80) cc_final: 0.8143 (ttm-80) REVERT: q 297 ASN cc_start: 0.7694 (t0) cc_final: 0.7473 (t0) REVERT: q 312 LEU cc_start: 0.8426 (pp) cc_final: 0.8221 (pt) REVERT: q 320 ASN cc_start: 0.7960 (m110) cc_final: 0.7576 (m-40) REVERT: q 345 GLU cc_start: 0.8146 (mp0) cc_final: 0.7610 (mp0) REVERT: q 346 ARG cc_start: 0.7485 (mmt90) cc_final: 0.7245 (mpt-90) REVERT: q 366 TRP cc_start: 0.6412 (m-10) cc_final: 0.6207 (m-10) REVERT: q 381 GLN cc_start: 0.7838 (pm20) cc_final: 0.7075 (pm20) REVERT: q 418 TYR cc_start: 0.7566 (m-80) cc_final: 0.7236 (m-80) REVERT: q 444 MET cc_start: 0.6738 (ppp) cc_final: 0.6449 (ppp) REVERT: q 467 LEU cc_start: 0.8099 (mt) cc_final: 0.7481 (tt) outliers start: 93 outliers final: 68 residues processed: 419 average time/residue: 0.1126 time to fit residues: 68.5186 Evaluate side-chains 438 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 355 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 19 GLU Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 83 VAL Chi-restraints excluded: chain o residue 103 ILE Chi-restraints excluded: chain o residue 149 ARG Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 165 VAL Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 234 GLN Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 341 ASN Chi-restraints excluded: chain o residue 345 GLU Chi-restraints excluded: chain o residue 363 VAL Chi-restraints excluded: chain o residue 403 MET Chi-restraints excluded: chain o residue 421 HIS Chi-restraints excluded: chain o residue 493 ILE Chi-restraints excluded: chain o residue 497 CYS Chi-restraints excluded: chain o residue 502 LEU Chi-restraints excluded: chain o residue 511 ASP Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 537 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 607 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 19 GLU Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 134 LEU Chi-restraints excluded: chain p residue 146 LEU Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 195 PHE Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 307 ILE Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain p residue 363 VAL Chi-restraints excluded: chain p residue 383 ARG Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 413 TYR Chi-restraints excluded: chain p residue 415 ILE Chi-restraints excluded: chain p residue 425 LEU Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 445 ASP Chi-restraints excluded: chain p residue 449 MET Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 480 ASP Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain p residue 517 ILE Chi-restraints excluded: chain p residue 538 VAL Chi-restraints excluded: chain p residue 660 VAL Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 128 LEU Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 165 VAL Chi-restraints excluded: chain q residue 183 THR Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 240 TYR Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 271 VAL Chi-restraints excluded: chain q residue 283 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 304 ASP Chi-restraints excluded: chain q residue 308 THR Chi-restraints excluded: chain q residue 365 THR Chi-restraints excluded: chain q residue 379 ASN Chi-restraints excluded: chain q residue 449 MET Chi-restraints excluded: chain q residue 459 CYS Chi-restraints excluded: chain q residue 483 THR Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 571 THR Chi-restraints excluded: chain q residue 631 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 475 ASN ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 7 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.175857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.134441 restraints weight = 26502.136| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.65 r_work: 0.3653 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15405 Z= 0.181 Angle : 0.692 9.971 20934 Z= 0.359 Chirality : 0.049 0.182 2352 Planarity : 0.004 0.041 2745 Dihedral : 5.626 36.548 2139 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.77 % Favored : 91.98 % Rotamer: Outliers : 6.13 % Allowed : 29.66 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.36 (0.18), residues: 1983 helix: -1.07 (0.57), residues: 82 sheet: -1.28 (0.23), residues: 494 loop : -1.81 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG o 383 TYR 0.028 0.002 TYR o 356 PHE 0.014 0.002 PHE q 153 TRP 0.023 0.002 TRP o 316 HIS 0.004 0.001 HIS o 427 Details of bonding type rmsd covalent geometry : bond 0.00391 (15405) covalent geometry : angle 0.69175 (20934) hydrogen bonds : bond 0.03524 ( 293) hydrogen bonds : angle 6.06907 ( 810) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 365 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 135 GLN cc_start: 0.8276 (tp40) cc_final: 0.8012 (tp-100) REVERT: o 151 TYR cc_start: 0.8047 (t80) cc_final: 0.7813 (t80) REVERT: o 197 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.5644 (pm20) REVERT: o 227 GLN cc_start: 0.7842 (mm110) cc_final: 0.7514 (mm-40) REVERT: o 234 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7055 (tt0) REVERT: o 258 ASN cc_start: 0.8556 (p0) cc_final: 0.8255 (p0) REVERT: o 280 MET cc_start: 0.8003 (tmm) cc_final: 0.7679 (tmm) REVERT: o 329 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7758 (m-80) REVERT: o 333 SER cc_start: 0.7939 (OUTLIER) cc_final: 0.7295 (m) REVERT: o 535 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6456 (mmm160) REVERT: o 607 LEU cc_start: 0.4696 (OUTLIER) cc_final: 0.4328 (pp) REVERT: o 608 LYS cc_start: 0.6012 (OUTLIER) cc_final: 0.5518 (ttmt) REVERT: p 54 GLU cc_start: 0.6688 (tm-30) cc_final: 0.5875 (tm-30) REVERT: p 112 ASP cc_start: 0.8193 (t0) cc_final: 0.7817 (t0) REVERT: p 134 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8697 (tt) REVERT: p 187 LYS cc_start: 0.8496 (tptt) cc_final: 0.8181 (tptt) REVERT: p 195 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.6267 (t80) REVERT: p 230 THR cc_start: 0.6881 (OUTLIER) cc_final: 0.6366 (t) REVERT: p 233 TYR cc_start: 0.6974 (p90) cc_final: 0.6657 (p90) REVERT: p 264 GLU cc_start: 0.7104 (pm20) cc_final: 0.6877 (pm20) REVERT: p 315 ASP cc_start: 0.8275 (t0) cc_final: 0.8050 (t70) REVERT: p 321 TYR cc_start: 0.6770 (m-80) cc_final: 0.6488 (m-10) REVERT: p 329 TYR cc_start: 0.7258 (m-10) cc_final: 0.6720 (m-80) REVERT: p 356 TYR cc_start: 0.7465 (t80) cc_final: 0.7088 (t80) REVERT: p 383 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6686 (ptp-170) REVERT: p 386 VAL cc_start: 0.7536 (t) cc_final: 0.6923 (m) REVERT: p 402 ASP cc_start: 0.2931 (OUTLIER) cc_final: 0.2201 (p0) REVERT: p 442 PHE cc_start: 0.7506 (t80) cc_final: 0.6972 (t80) REVERT: p 445 ASP cc_start: 0.5256 (OUTLIER) cc_final: 0.4238 (p0) REVERT: p 449 MET cc_start: 0.6243 (OUTLIER) cc_final: 0.5976 (pmm) REVERT: p 467 LEU cc_start: 0.7790 (tp) cc_final: 0.6973 (tt) REVERT: p 475 ASN cc_start: 0.8089 (m110) cc_final: 0.7756 (m110) REVERT: p 530 MET cc_start: 0.5813 (ptp) cc_final: 0.5219 (ptp) REVERT: p 538 VAL cc_start: 0.5181 (OUTLIER) cc_final: 0.4692 (t) REVERT: p 550 ARG cc_start: 0.7300 (ptm-80) cc_final: 0.6838 (ptm-80) REVERT: q 37 ASP cc_start: 0.7719 (t0) cc_final: 0.7348 (t0) REVERT: q 49 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8347 (m) REVERT: q 174 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7500 (m-10) REVERT: q 238 SER cc_start: 0.8840 (m) cc_final: 0.8288 (p) REVERT: q 249 LEU cc_start: 0.3670 (OUTLIER) cc_final: 0.2351 (mt) REVERT: q 266 ARG cc_start: 0.8462 (ttm-80) cc_final: 0.8124 (ttm-80) REVERT: q 280 MET cc_start: 0.8038 (mpp) cc_final: 0.7681 (mmt) REVERT: q 297 ASN cc_start: 0.7702 (t0) cc_final: 0.7480 (t0) REVERT: q 320 ASN cc_start: 0.7933 (m110) cc_final: 0.7559 (m-40) REVERT: q 345 GLU cc_start: 0.8073 (mp0) cc_final: 0.7529 (mp0) REVERT: q 346 ARG cc_start: 0.7479 (mmt90) cc_final: 0.7239 (mpt-90) REVERT: q 381 GLN cc_start: 0.7858 (pm20) cc_final: 0.7101 (pm20) REVERT: q 418 TYR cc_start: 0.7562 (m-80) cc_final: 0.7255 (m-80) REVERT: q 444 MET cc_start: 0.6712 (ppp) cc_final: 0.6392 (ppp) REVERT: q 535 ARG cc_start: 0.5168 (mtp-110) cc_final: 0.4953 (mtp-110) outliers start: 100 outliers final: 69 residues processed: 432 average time/residue: 0.1182 time to fit residues: 72.7937 Evaluate side-chains 443 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 356 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 19 GLU Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 83 VAL Chi-restraints excluded: chain o residue 103 ILE Chi-restraints excluded: chain o residue 149 ARG Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 165 VAL Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 197 GLU Chi-restraints excluded: chain o residue 234 GLN Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 329 TYR Chi-restraints excluded: chain o residue 333 SER Chi-restraints excluded: chain o residue 341 ASN Chi-restraints excluded: chain o residue 345 GLU Chi-restraints excluded: chain o residue 363 VAL Chi-restraints excluded: chain o residue 403 MET Chi-restraints excluded: chain o residue 421 HIS Chi-restraints excluded: chain o residue 481 THR Chi-restraints excluded: chain o residue 493 ILE Chi-restraints excluded: chain o residue 497 CYS Chi-restraints excluded: chain o residue 507 ILE Chi-restraints excluded: chain o residue 511 ASP Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 537 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 607 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 19 GLU Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 134 LEU Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 195 PHE Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain p residue 363 VAL Chi-restraints excluded: chain p residue 383 ARG Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 413 TYR Chi-restraints excluded: chain p residue 425 LEU Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 445 ASP Chi-restraints excluded: chain p residue 449 MET Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 480 ASP Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain p residue 517 ILE Chi-restraints excluded: chain p residue 538 VAL Chi-restraints excluded: chain p residue 660 VAL Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 165 VAL Chi-restraints excluded: chain q residue 174 PHE Chi-restraints excluded: chain q residue 183 THR Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 237 VAL Chi-restraints excluded: chain q residue 240 TYR Chi-restraints excluded: chain q residue 249 LEU Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 283 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 304 ASP Chi-restraints excluded: chain q residue 308 THR Chi-restraints excluded: chain q residue 365 THR Chi-restraints excluded: chain q residue 379 ASN Chi-restraints excluded: chain q residue 385 SER Chi-restraints excluded: chain q residue 449 MET Chi-restraints excluded: chain q residue 459 CYS Chi-restraints excluded: chain q residue 483 THR Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 537 ASN Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 571 THR Chi-restraints excluded: chain q residue 631 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 156 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 490 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 = 0.4326 r_free = 0.4326 target = 0.173698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.132665 restraints weight = 26596.967| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.61 r_work: 0.3622 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 15405 Z= 0.263 Angle : 0.751 9.936 20934 Z= 0.393 Chirality : 0.051 0.180 2352 Planarity : 0.005 0.098 2745 Dihedral : 5.889 36.191 2139 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.53 % Favored : 90.22 % Rotamer: Outliers : 6.19 % Allowed : 30.09 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.42 (0.18), residues: 1983 helix: -1.34 (0.55), residues: 82 sheet: -1.36 (0.23), residues: 501 loop : -1.82 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG o 498 TYR 0.047 0.002 TYR o 389 PHE 0.017 0.002 PHE q 161 TRP 0.040 0.002 TRP q 366 HIS 0.009 0.001 HIS o 469 Details of bonding type rmsd covalent geometry : bond 0.00562 (15405) covalent geometry : angle 0.75127 (20934) hydrogen bonds : bond 0.03966 ( 293) hydrogen bonds : angle 6.25671 ( 810) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 370 time to evaluate : 0.422 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: o 151 TYR cc_start: 0.8068 (t80) cc_final: 0.7785 (t80) REVERT: o 171 LYS cc_start: 0.8734 (tptp) cc_final: 0.8528 (tptm) REVERT: o 227 GLN cc_start: 0.7878 (mm110) cc_final: 0.7504 (mm110) REVERT: o 234 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: o 258 ASN cc_start: 0.8553 (p0) cc_final: 0.8249 (p0) REVERT: o 266 ARG cc_start: 0.8678 (ttm-80) cc_final: 0.8320 (ttm-80) REVERT: o 280 MET cc_start: 0.8036 (tmm) cc_final: 0.7700 (tmm) REVERT: o 285 PHE cc_start: 0.8167 (m-10) cc_final: 0.7917 (m-10) REVERT: o 318 LYS cc_start: 0.7898 (tptp) cc_final: 0.7652 (tptt) REVERT: o 329 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: o 333 SER cc_start: 0.7893 (OUTLIER) cc_final: 0.7155 (m) REVERT: o 357 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7587 (mtt-85) REVERT: o 381 GLN cc_start: 0.7095 (mt0) cc_final: 0.6890 (mt0) REVERT: o 535 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6629 (mmm160) REVERT: o 607 LEU cc_start: 0.4817 (OUTLIER) cc_final: 0.4453 (pp) REVERT: o 608 LYS cc_start: 0.6326 (OUTLIER) cc_final: 0.5848 (ttmt) REVERT: p 14 ARG cc_start: 0.8711 (mtt-85) cc_final: 0.8355 (mtm-85) REVERT: p 54 GLU cc_start: 0.6813 (tm-30) cc_final: 0.5973 (tm-30) REVERT: p 112 ASP cc_start: 0.8181 (t0) cc_final: 0.7922 (t0) REVERT: p 134 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8738 (tt) REVERT: p 187 LYS cc_start: 0.8624 (tptt) cc_final: 0.8287 (tptt) REVERT: p 195 PHE cc_start: 0.6709 (OUTLIER) cc_final: 0.5870 (t80) REVERT: p 213 GLN cc_start: 0.7670 (pm20) cc_final: 0.7433 (pm20) REVERT: p 230 THR cc_start: 0.6808 (OUTLIER) cc_final: 0.6366 (t) REVERT: p 233 TYR cc_start: 0.7051 (p90) cc_final: 0.6715 (p90) REVERT: p 321 TYR cc_start: 0.6784 (m-80) cc_final: 0.6546 (m-10) REVERT: p 329 TYR cc_start: 0.7387 (m-10) cc_final: 0.6818 (m-80) REVERT: p 356 TYR cc_start: 0.7602 (t80) cc_final: 0.7211 (t80) REVERT: p 383 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6755 (ptp-170) REVERT: p 402 ASP cc_start: 0.2938 (OUTLIER) cc_final: 0.2203 (p0) REVERT: p 442 PHE cc_start: 0.7570 (t80) cc_final: 0.7035 (t80) REVERT: p 445 ASP cc_start: 0.4852 (OUTLIER) cc_final: 0.3771 (p0) REVERT: p 449 MET cc_start: 0.6334 (OUTLIER) cc_final: 0.6124 (pmm) REVERT: p 467 LEU cc_start: 0.7911 (tp) cc_final: 0.7113 (tt) REVERT: p 475 ASN cc_start: 0.8200 (m110) cc_final: 0.7846 (m110) REVERT: p 550 ARG cc_start: 0.7284 (ptm-80) cc_final: 0.6806 (ptm-80) REVERT: p 664 LEU cc_start: 0.6035 (mt) cc_final: 0.5810 (mt) REVERT: q 37 ASP cc_start: 0.7717 (t0) cc_final: 0.7404 (t0) REVERT: q 49 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8427 (m) REVERT: q 174 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7407 (m-10) REVERT: q 238 SER cc_start: 0.8850 (m) cc_final: 0.8351 (p) REVERT: q 249 LEU cc_start: 0.3396 (OUTLIER) cc_final: 0.1950 (mt) REVERT: q 266 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.8140 (ttm-80) REVERT: q 297 ASN cc_start: 0.7805 (t0) cc_final: 0.7578 (t0) REVERT: q 320 ASN cc_start: 0.7963 (m110) cc_final: 0.7590 (m-40) REVERT: q 345 GLU cc_start: 0.8161 (mp0) cc_final: 0.7629 (mp0) REVERT: q 346 ARG cc_start: 0.7515 (mmt90) cc_final: 0.7264 (mpt-90) REVERT: q 366 TRP cc_start: 0.5916 (m-10) cc_final: 0.5664 (m-90) REVERT: q 381 GLN cc_start: 0.7848 (pm20) cc_final: 0.7090 (pm20) REVERT: q 418 TYR cc_start: 0.7611 (m-80) cc_final: 0.7397 (m-80) REVERT: q 444 MET cc_start: 0.6716 (ppp) cc_final: 0.6337 (ppp) outliers start: 101 outliers final: 73 residues processed: 436 average time/residue: 0.1191 time to fit residues: 74.8665 Evaluate side-chains 457 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 368 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 19 GLU Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 83 VAL Chi-restraints excluded: chain o residue 103 ILE Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 165 VAL Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 234 GLN Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 269 ILE Chi-restraints excluded: chain o residue 329 TYR Chi-restraints excluded: chain o residue 333 SER Chi-restraints excluded: chain o residue 341 ASN Chi-restraints excluded: chain o residue 345 GLU Chi-restraints excluded: chain o residue 363 VAL Chi-restraints excluded: chain o residue 421 HIS Chi-restraints excluded: chain o residue 444 MET Chi-restraints excluded: chain o residue 481 THR Chi-restraints excluded: chain o residue 493 ILE Chi-restraints excluded: chain o residue 497 CYS Chi-restraints excluded: chain o residue 498 ARG Chi-restraints excluded: chain o residue 507 ILE Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 537 ASN Chi-restraints excluded: chain o residue 540 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 607 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 19 GLU Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 134 LEU Chi-restraints excluded: chain p residue 142 VAL Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 195 PHE Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain p residue 363 VAL Chi-restraints excluded: chain p residue 383 ARG Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 425 LEU Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 445 ASP Chi-restraints excluded: chain p residue 449 MET Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 480 ASP Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain p residue 517 ILE Chi-restraints excluded: chain p residue 538 VAL Chi-restraints excluded: chain p residue 556 TYR Chi-restraints excluded: chain p residue 660 VAL Chi-restraints excluded: chain q residue 7 ASN Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 165 VAL Chi-restraints excluded: chain q residue 174 PHE Chi-restraints excluded: chain q residue 183 THR Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 237 VAL Chi-restraints excluded: chain q residue 240 TYR Chi-restraints excluded: chain q residue 249 LEU Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 283 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 304 ASP Chi-restraints excluded: chain q residue 338 LEU Chi-restraints excluded: chain q residue 340 ASN Chi-restraints excluded: chain q residue 365 THR Chi-restraints excluded: chain q residue 379 ASN Chi-restraints excluded: chain q residue 449 MET Chi-restraints excluded: chain q residue 459 CYS Chi-restraints excluded: chain q residue 483 THR Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 521 ASN Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 631 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 25 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 500 ASN ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.174923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.134245 restraints weight = 26834.561| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.60 r_work: 0.3630 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 15405 Z= 0.223 Angle : 0.754 11.160 20934 Z= 0.393 Chirality : 0.051 0.184 2352 Planarity : 0.005 0.082 2745 Dihedral : 5.843 36.622 2139 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.22 % Favored : 91.53 % Rotamer: Outliers : 5.45 % Allowed : 31.31 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.42 (0.18), residues: 1983 helix: -1.37 (0.54), residues: 82 sheet: -1.32 (0.24), residues: 473 loop : -1.83 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG o 498 TYR 0.039 0.002 TYR o 389 PHE 0.022 0.002 PHE q 161 TRP 0.030 0.002 TRP q 366 HIS 0.005 0.001 HIS o 427 Details of bonding type rmsd covalent geometry : bond 0.00481 (15405) covalent geometry : angle 0.75441 (20934) hydrogen bonds : bond 0.03759 ( 293) hydrogen bonds : angle 6.16811 ( 810) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 361 time to evaluate : 0.458 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: o 135 GLN cc_start: 0.8425 (tp40) cc_final: 0.8126 (tp-100) REVERT: o 151 TYR cc_start: 0.8029 (t80) cc_final: 0.7754 (t80) REVERT: o 171 LYS cc_start: 0.8757 (tptp) cc_final: 0.8365 (tttm) REVERT: o 227 GLN cc_start: 0.7748 (mm110) cc_final: 0.7287 (mm-40) REVERT: o 234 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7142 (tt0) REVERT: o 258 ASN cc_start: 0.8521 (p0) cc_final: 0.8139 (p0) REVERT: o 266 ARG cc_start: 0.8700 (ttm-80) cc_final: 0.8344 (ttm-80) REVERT: o 280 MET cc_start: 0.7909 (tmm) cc_final: 0.7600 (tmm) REVERT: o 285 PHE cc_start: 0.8174 (m-10) cc_final: 0.7894 (m-10) REVERT: o 318 LYS cc_start: 0.7893 (tptp) cc_final: 0.7692 (tptt) REVERT: o 329 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.7838 (m-80) REVERT: o 333 SER cc_start: 0.7875 (OUTLIER) cc_final: 0.7329 (m) REVERT: o 535 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6624 (mmm160) REVERT: o 607 LEU cc_start: 0.4753 (OUTLIER) cc_final: 0.4367 (pp) REVERT: o 608 LYS cc_start: 0.6412 (OUTLIER) cc_final: 0.5926 (ttmt) REVERT: p 54 GLU cc_start: 0.6762 (tm-30) cc_final: 0.5898 (tm-30) REVERT: p 112 ASP cc_start: 0.8175 (t0) cc_final: 0.7838 (t0) REVERT: p 134 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8721 (tt) REVERT: p 187 LYS cc_start: 0.8628 (tptt) cc_final: 0.8286 (tptt) REVERT: p 195 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.6363 (t80) REVERT: p 213 GLN cc_start: 0.7633 (pm20) cc_final: 0.7415 (pm20) REVERT: p 230 THR cc_start: 0.6991 (OUTLIER) cc_final: 0.6552 (t) REVERT: p 233 TYR cc_start: 0.7044 (p90) cc_final: 0.6723 (p90) REVERT: p 264 GLU cc_start: 0.7624 (pm20) cc_final: 0.7093 (pm20) REVERT: p 266 ARG cc_start: 0.7818 (ttm170) cc_final: 0.7209 (ttm110) REVERT: p 286 ARG cc_start: 0.8131 (ttm110) cc_final: 0.7893 (ttm110) REVERT: p 321 TYR cc_start: 0.6772 (m-80) cc_final: 0.6549 (m-10) REVERT: p 329 TYR cc_start: 0.7439 (m-10) cc_final: 0.6924 (m-80) REVERT: p 356 TYR cc_start: 0.7599 (t80) cc_final: 0.7154 (t80) REVERT: p 383 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6748 (ptt90) REVERT: p 402 ASP cc_start: 0.2955 (OUTLIER) cc_final: 0.2205 (p0) REVERT: p 445 ASP cc_start: 0.4578 (OUTLIER) cc_final: 0.3498 (p0) REVERT: p 467 LEU cc_start: 0.7852 (tp) cc_final: 0.7154 (tt) REVERT: p 475 ASN cc_start: 0.8207 (m110) cc_final: 0.7839 (m110) REVERT: p 538 VAL cc_start: 0.5600 (OUTLIER) cc_final: 0.5211 (t) REVERT: p 664 LEU cc_start: 0.6143 (mt) cc_final: 0.5943 (mt) REVERT: q 37 ASP cc_start: 0.7720 (t0) cc_final: 0.7419 (t0) REVERT: q 49 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8399 (m) REVERT: q 174 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7387 (m-10) REVERT: q 238 SER cc_start: 0.8925 (m) cc_final: 0.8380 (p) REVERT: q 249 LEU cc_start: 0.3380 (OUTLIER) cc_final: 0.1969 (mt) REVERT: q 266 ARG cc_start: 0.8488 (ttm-80) cc_final: 0.8126 (ttm-80) REVERT: q 280 MET cc_start: 0.8042 (mpp) cc_final: 0.7699 (mmt) REVERT: q 297 ASN cc_start: 0.7779 (t0) cc_final: 0.7561 (t0) REVERT: q 320 ASN cc_start: 0.7978 (m110) cc_final: 0.7550 (m-40) REVERT: q 345 GLU cc_start: 0.8045 (mp0) cc_final: 0.7511 (mp0) REVERT: q 346 ARG cc_start: 0.7452 (mmt90) cc_final: 0.7212 (mpt-90) REVERT: q 381 GLN cc_start: 0.7834 (pm20) cc_final: 0.7076 (pm20) REVERT: q 392 TRP cc_start: 0.7781 (m100) cc_final: 0.7519 (m-10) REVERT: q 444 MET cc_start: 0.6738 (ppp) cc_final: 0.6388 (ppp) outliers start: 89 outliers final: 65 residues processed: 414 average time/residue: 0.1156 time to fit residues: 69.2543 Evaluate side-chains 435 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 354 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 8 VAL Chi-restraints excluded: chain o residue 19 GLU Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 83 VAL Chi-restraints excluded: chain o residue 103 ILE Chi-restraints excluded: chain o residue 158 THR Chi-restraints excluded: chain o residue 165 VAL Chi-restraints excluded: chain o residue 180 LEU Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 234 GLN Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 264 GLU Chi-restraints excluded: chain o residue 329 TYR Chi-restraints excluded: chain o residue 333 SER Chi-restraints excluded: chain o residue 341 ASN Chi-restraints excluded: chain o residue 345 GLU Chi-restraints excluded: chain o residue 363 VAL Chi-restraints excluded: chain o residue 421 HIS Chi-restraints excluded: chain o residue 444 MET Chi-restraints excluded: chain o residue 451 VAL Chi-restraints excluded: chain o residue 491 ILE Chi-restraints excluded: chain o residue 493 ILE Chi-restraints excluded: chain o residue 502 LEU Chi-restraints excluded: chain o residue 507 ILE Chi-restraints excluded: chain o residue 523 THR Chi-restraints excluded: chain o residue 535 ARG Chi-restraints excluded: chain o residue 537 ASN Chi-restraints excluded: chain o residue 540 ASN Chi-restraints excluded: chain o residue 546 LEU Chi-restraints excluded: chain o residue 607 LEU Chi-restraints excluded: chain o residue 608 LYS Chi-restraints excluded: chain p residue 19 GLU Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 133 THR Chi-restraints excluded: chain p residue 134 LEU Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 195 PHE Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 336 GLN Chi-restraints excluded: chain p residue 363 VAL Chi-restraints excluded: chain p residue 383 ARG Chi-restraints excluded: chain p residue 402 ASP Chi-restraints excluded: chain p residue 440 VAL Chi-restraints excluded: chain p residue 445 ASP Chi-restraints excluded: chain p residue 469 HIS Chi-restraints excluded: chain p residue 480 ASP Chi-restraints excluded: chain p residue 491 ILE Chi-restraints excluded: chain p residue 517 ILE Chi-restraints excluded: chain p residue 538 VAL Chi-restraints excluded: chain p residue 556 TYR Chi-restraints excluded: chain p residue 660 VAL Chi-restraints excluded: chain q residue 7 ASN Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 83 VAL Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 165 VAL Chi-restraints excluded: chain q residue 174 PHE Chi-restraints excluded: chain q residue 183 THR Chi-restraints excluded: chain q residue 212 ASN Chi-restraints excluded: chain q residue 230 THR Chi-restraints excluded: chain q residue 237 VAL Chi-restraints excluded: chain q residue 240 TYR Chi-restraints excluded: chain q residue 249 LEU Chi-restraints excluded: chain q residue 265 ILE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 304 ASP Chi-restraints excluded: chain q residue 340 ASN Chi-restraints excluded: chain q residue 379 ASN Chi-restraints excluded: chain q residue 449 MET Chi-restraints excluded: chain q residue 459 CYS Chi-restraints excluded: chain q residue 483 THR Chi-restraints excluded: chain q residue 492 TYR Chi-restraints excluded: chain q residue 566 HIS Chi-restraints excluded: chain q residue 631 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 66 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 153 optimal weight: 0.0770 chunk 162 optimal weight: 9.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 422 GLN ** o 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.175873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.134920 restraints weight = 26361.267| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 3.62 r_work: 0.3664 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15405 Z= 0.149 Angle : 0.721 11.639 20934 Z= 0.374 Chirality : 0.050 0.246 2352 Planarity : 0.005 0.066 2745 Dihedral : 5.564 37.220 2139 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.97 % Favored : 91.78 % Rotamer: Outliers : 5.15 % Allowed : 31.68 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.32 (0.18), residues: 1983 helix: -1.43 (0.52), residues: 88 sheet: -1.46 (0.24), residues: 437 loop : -1.68 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG o 498 TYR 0.032 0.002 TYR o 389 PHE 0.015 0.001 PHE o 382 TRP 0.025 0.002 TRP q 366 HIS 0.004 0.001 HIS o 427 Details of bonding type rmsd covalent geometry : bond 0.00330 (15405) covalent geometry : angle 0.72114 (20934) hydrogen bonds : bond 0.03384 ( 293) hydrogen bonds : angle 5.97658 ( 810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3473.81 seconds wall clock time: 60 minutes 29.03 seconds (3629.03 seconds total)