Starting phenix.real_space_refine on Sat Aug 23 18:32:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l0d_62697/08_2025/9l0d_62697.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l0d_62697/08_2025/9l0d_62697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l0d_62697/08_2025/9l0d_62697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l0d_62697/08_2025/9l0d_62697.map" model { file = "/net/cci-nas-00/data/ceres_data/9l0d_62697/08_2025/9l0d_62697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l0d_62697/08_2025/9l0d_62697.cif" } resolution = 3.41 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= 0.001 sd= 0.071 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 69 5.16 5 C 8900 2.51 5 N 2376 2.21 5 O 2549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 186 residue(s): 0.02s 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: 13894 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3349 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 400} Chain: "B" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3837 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "C" Number of atoms: 5280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5280 Classifications: {'peptide': 657} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 623} Chain: "D" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1428 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Time building chain proxies: 3.29, per 1000 atoms: 0.24 Number of scatterers: 13894 At special positions: 0 Unit cell: (88.62, 117.105, 185.68, 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 69 16.00 O 2549 8.00 N 2376 7.00 C 8900 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: 1.15 Conformation dependent library (CDL) restraints added in 609.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 17 sheets defined 40.6% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 237 through 247 removed outlier: 4.525A pdb=" N GLU A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 276 through 290 removed outlier: 6.245A pdb=" N MET A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 344 Processing helix chain 'A' and resid 345 through 356 removed outlier: 4.002A pdb=" N SER A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.733A pdb=" N ASN A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 398 through 410 removed outlier: 3.993A pdb=" N ALA A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 452 removed outlier: 3.867A pdb=" N SER A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 499 through 517 removed outlier: 4.391A pdb=" N CYS A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG A 513 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 529 removed outlier: 3.641A pdb=" N ALA A 522 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 Processing helix chain 'A' and resid 566 through 584 removed outlier: 3.964A pdb=" N GLU A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 645 removed outlier: 3.827A pdb=" N HIS A 631 " --> pdb=" O VAL A 627 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ASP A 642 " --> pdb=" O ARG A 638 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG A 643 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 644 " --> pdb=" O GLU A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 43 Processing helix chain 'B' and resid 54 through 73 Processing helix chain 'B' and resid 130 through 150 removed outlier: 3.786A pdb=" N TYR B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 176 removed outlier: 3.769A pdb=" N ALA B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N VAL B 161 " --> pdb=" O GLU B 157 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N LYS B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 185 through 191 removed outlier: 3.707A pdb=" N ILE B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 217 Processing helix chain 'B' and resid 238 through 251 removed outlier: 3.645A pdb=" N ARG B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 268 through 272 Processing helix chain 'B' and resid 335 through 368 Proline residue: B 348 - end of helix Processing helix chain 'B' and resid 406 through 421 removed outlier: 3.793A pdb=" N THR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 475 Processing helix chain 'C' and resid 2 through 6 removed outlier: 3.536A pdb=" N TYR C 6 " --> pdb=" O GLU C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 321 through 326 removed outlier: 4.334A pdb=" N VAL C 325 " --> pdb=" O PRO C 322 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR C 326 " --> pdb=" O ALA C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.575A pdb=" N LEU C 370 " --> pdb=" O ILE C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 387 through 397 Processing helix chain 'C' and resid 405 through 436 Processing helix chain 'C' and resid 456 through 463 Processing helix chain 'C' and resid 464 through 471 Processing helix chain 'C' and resid 475 through 493 Processing helix chain 'C' and resid 498 through 512 removed outlier: 3.769A pdb=" N HIS C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 524 Processing helix chain 'C' and resid 530 through 540 Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 544 through 545 No H-bonds generated for 'chain 'C' and resid 544 through 545' Processing helix chain 'C' and resid 546 through 559 removed outlier: 3.676A pdb=" N MET C 554 " --> pdb=" O LEU C 550 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 559 " --> pdb=" O LEU C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 572 Processing helix chain 'C' and resid 574 through 586 removed outlier: 3.709A pdb=" N GLY C 584 " --> pdb=" O ARG C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 590 Processing helix chain 'C' and resid 592 through 599 removed outlier: 4.212A pdb=" N PHE C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU C 597 " --> pdb=" O ALA C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 611 Processing helix chain 'C' and resid 612 through 625 removed outlier: 4.179A pdb=" N ASN C 620 " --> pdb=" O PHE C 616 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ARG C 622 " --> pdb=" O GLN C 618 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU C 623 " --> pdb=" O ARG C 619 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG C 624 " --> pdb=" O ASN C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 removed outlier: 4.208A pdb=" N GLU C 633 " --> pdb=" O THR C 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 removed outlier: 4.012A pdb=" N GLN D 71 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER D 72 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 78 Processing helix chain 'D' and resid 93 through 98 Processing helix chain 'D' and resid 98 through 110 removed outlier: 3.785A pdb=" N ARG D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 118 removed outlier: 3.576A pdb=" N ASN D 117 " --> pdb=" O ASP D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 146 removed outlier: 3.773A pdb=" N ALA D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 184 Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 267 removed outlier: 6.266A pdb=" N SER A 259 " --> pdb=" O PRO A 264 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS A 305 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG A 297 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE B 100 " --> pdb=" O PRO B 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.326A pdb=" N ALA A 390 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 554 " --> pdb=" O SER A 549 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 604 " --> pdb=" O MET A 615 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 605 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 607 " --> pdb=" O LYS A 592 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LYS A 592 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS B 432 " --> pdb=" O LYS A 592 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE A 594 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE B 430 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR A 596 " --> pdb=" O GLU B 428 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU B 428 " --> pdb=" O TYR A 596 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 461 through 464 removed outlier: 4.000A pdb=" N HIS A 478 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 492 " --> pdb=" O HIS A 478 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER A 480 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 490 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 417 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU A 650 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 20 Processing sheet with id=AA5, first strand: chain 'B' and resid 230 through 234 removed outlier: 6.561A pdb=" N PHE B 225 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER B 234 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B 223 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N VAL B 220 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP B 329 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 230 through 234 removed outlier: 6.561A pdb=" N PHE B 225 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER B 234 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B 223 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N VAL B 220 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP B 329 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 393 through 394 Processing sheet with id=AA8, first strand: chain 'C' and resid 8 through 9 Processing sheet with id=AA9, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AB1, first strand: chain 'C' and resid 24 through 29 Processing sheet with id=AB2, first strand: chain 'C' and resid 69 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 113 through 117 removed outlier: 7.193A pdb=" N ILE C 127 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE C 116 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C 125 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE C 132 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER C 149 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE C 134 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 156 through 160 removed outlier: 3.558A pdb=" N TRP C 156 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 156 through 160 removed outlier: 3.558A pdb=" N TRP C 156 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 213 through 218 removed outlier: 6.618A pdb=" N VAL C 241 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE C 257 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU C 243 " --> pdb=" O MET C 255 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 266 through 271 Processing sheet with id=AB8, first strand: chain 'D' and resid 43 through 52 removed outlier: 6.359A pdb=" N LEU D 9 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N TRP D 62 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL D 11 " --> pdb=" O TRP D 62 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N THR D 64 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE D 13 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS D 10 " --> pdb=" O CYS D 83 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL D 85 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE D 12 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL D 87 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU D 14 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N ASP D 89 " --> pdb=" O LEU D 14 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1860 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: 2.55 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3991 1.33 - 1.45: 2300 1.45 - 1.57: 7809 1.57 - 1.69: 0 1.69 - 1.81: 109 Bond restraints: 14209 Sorted by residual: bond pdb=" CA ASN D 22 " pdb=" CB ASN D 22 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.64e-02 3.72e+03 1.21e+01 bond pdb=" C PRO C 545 " pdb=" N PRO C 546 " ideal model delta sigma weight residual 1.336 1.364 -0.028 1.08e-02 8.57e+03 6.64e+00 bond pdb=" CB ASN D 22 " pdb=" CG ASN D 22 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.73e+00 bond pdb=" N LYS D 21 " pdb=" CA LYS D 21 " ideal model delta sigma weight residual 1.458 1.428 0.029 1.29e-02 6.01e+03 5.12e+00 bond pdb=" C SER D 23 " pdb=" O SER D 23 " ideal model delta sigma weight residual 1.235 1.220 0.015 7.50e-03 1.78e+04 4.09e+00 ... (remaining 14204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 18881 2.42 - 4.85: 312 4.85 - 7.27: 28 7.27 - 9.69: 6 9.69 - 12.11: 2 Bond angle restraints: 19229 Sorted by residual: angle pdb=" N ILE A 479 " pdb=" CA ILE A 479 " pdb=" C ILE A 479 " ideal model delta sigma weight residual 106.42 114.06 -7.64 1.51e+00 4.39e-01 2.56e+01 angle pdb=" C THR A 278 " pdb=" N MET A 279 " pdb=" CA MET A 279 " ideal model delta sigma weight residual 121.54 130.34 -8.80 1.91e+00 2.74e-01 2.12e+01 angle pdb=" C SER D 34 " pdb=" N ASN D 35 " pdb=" CA ASN D 35 " ideal model delta sigma weight residual 121.90 116.33 5.57 1.26e+00 6.30e-01 1.96e+01 angle pdb=" N LEU A 364 " pdb=" CA LEU A 364 " pdb=" C LEU A 364 " ideal model delta sigma weight residual 112.72 107.18 5.54 1.28e+00 6.10e-01 1.87e+01 angle pdb=" N ILE A 479 " pdb=" CA ILE A 479 " pdb=" CB ILE A 479 " ideal model delta sigma weight residual 112.65 108.35 4.30 1.00e+00 1.00e+00 1.85e+01 ... (remaining 19224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7282 17.99 - 35.98: 989 35.98 - 53.97: 251 53.97 - 71.96: 67 71.96 - 89.95: 27 Dihedral angle restraints: 8616 sinusoidal: 3537 harmonic: 5079 Sorted by residual: dihedral pdb=" CA THR C 611 " pdb=" C THR C 611 " pdb=" N ILE C 612 " pdb=" CA ILE C 612 " ideal model delta harmonic sigma weight residual 180.00 -144.49 -35.51 0 5.00e+00 4.00e-02 5.04e+01 dihedral pdb=" CA GLN C 649 " pdb=" C GLN C 649 " pdb=" N ALA C 650 " pdb=" CA ALA C 650 " ideal model delta harmonic sigma weight residual 180.00 148.74 31.26 0 5.00e+00 4.00e-02 3.91e+01 dihedral pdb=" CA LEU A 275 " pdb=" C LEU A 275 " pdb=" N SER A 276 " pdb=" CA SER A 276 " ideal model delta harmonic sigma weight residual 180.00 148.94 31.06 0 5.00e+00 4.00e-02 3.86e+01 ... (remaining 8613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1844 0.066 - 0.132: 276 0.132 - 0.198: 11 0.198 - 0.264: 2 0.264 - 0.330: 1 Chirality restraints: 2134 Sorted by residual: chirality pdb=" CA ASN D 22 " pdb=" N ASN D 22 " pdb=" C ASN D 22 " pdb=" CB ASN D 22 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CG LEU D 24 " pdb=" CB LEU D 24 " pdb=" CD1 LEU D 24 " pdb=" CD2 LEU D 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CG LEU A 258 " pdb=" CB LEU A 258 " pdb=" CD1 LEU A 258 " pdb=" CD2 LEU A 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2131 not shown) Planarity restraints: 2478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 279 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C MET A 279 " -0.054 2.00e-02 2.50e+03 pdb=" O MET A 279 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY A 280 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 276 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C SER A 276 " -0.044 2.00e-02 2.50e+03 pdb=" O SER A 276 " 0.017 2.00e-02 2.50e+03 pdb=" N SER A 277 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 20 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C GLY D 20 " 0.042 2.00e-02 2.50e+03 pdb=" O GLY D 20 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS D 21 " -0.014 2.00e-02 2.50e+03 ... (remaining 2475 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 187 2.58 - 3.16: 11886 3.16 - 3.74: 21298 3.74 - 4.32: 29772 4.32 - 4.90: 49068 Nonbonded interactions: 112211 Sorted by model distance: nonbonded pdb=" O MET C 607 " pdb=" OG1 THR C 611 " model vdw 2.002 3.040 nonbonded pdb=" OG1 THR B 202 " pdb=" OE1 GLN B 360 " model vdw 2.087 3.040 nonbonded pdb=" O PHE D 33 " pdb=" OH TYR D 37 " model vdw 2.113 3.040 nonbonded pdb=" O PHE B 196 " pdb=" OH TYR C 524 " model vdw 2.129 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" O ASN B 89 " model vdw 2.140 3.040 ... (remaining 112206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.580 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 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 0.060 14209 Z= 0.247 Angle : 0.794 12.114 19229 Z= 0.462 Chirality : 0.046 0.330 2134 Planarity : 0.004 0.041 2478 Dihedral : 18.358 89.948 5316 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.55 % Favored : 93.33 % Rotamer: Outliers : 8.00 % Allowed : 20.55 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.75 (0.17), residues: 1710 helix: -2.22 (0.17), residues: 600 sheet: -1.94 (0.24), residues: 385 loop : -2.91 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 619 TYR 0.018 0.002 TYR D 37 PHE 0.017 0.002 PHE B 28 TRP 0.015 0.001 TRP A 461 HIS 0.005 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00532 (14209) covalent geometry : angle 0.79436 (19229) hydrogen bonds : bond 0.15991 ( 651) hydrogen bonds : angle 7.22473 ( 1860) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 302 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6868 (mt-10) REVERT: A 362 ARG cc_start: 0.7245 (ptm-80) cc_final: 0.6985 (ttp-110) REVERT: A 466 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7693 (mt) REVERT: A 479 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.6055 (tt) REVERT: A 576 LEU cc_start: 0.8426 (mt) cc_final: 0.7965 (mt) REVERT: A 595 TYR cc_start: 0.8215 (t80) cc_final: 0.7940 (t80) REVERT: A 602 ASN cc_start: 0.8216 (p0) cc_final: 0.7579 (p0) REVERT: B 199 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7833 (p0) REVERT: B 237 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7630 (mm-30) REVERT: B 272 MET cc_start: 0.3994 (mmp) cc_final: 0.3511 (mmm) REVERT: B 376 PHE cc_start: 0.4298 (OUTLIER) cc_final: 0.3910 (p90) REVERT: C 114 LEU cc_start: 0.7356 (mp) cc_final: 0.7109 (mp) REVERT: C 118 TRP cc_start: 0.8287 (m100) cc_final: 0.8083 (m100) REVERT: C 210 GLU cc_start: 0.7999 (mt-10) cc_final: 0.6739 (tm-30) REVERT: C 446 LYS cc_start: 0.7748 (mtpp) cc_final: 0.7531 (mmtm) REVERT: C 619 ARG cc_start: 0.1184 (OUTLIER) cc_final: -0.1495 (mmt180) REVERT: C 622 ARG cc_start: 0.3766 (OUTLIER) cc_final: 0.0646 (mtt90) REVERT: C 628 ASN cc_start: 0.3846 (OUTLIER) cc_final: 0.3258 (t0) outliers start: 123 outliers final: 38 residues processed: 401 average time/residue: 0.1253 time to fit residues: 71.6465 Evaluate side-chains 226 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS A 327 GLN A 339 GLN A 358 ASN A 377 GLN A 424 ASN A 520 HIS A 544 HIS B 108 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 ASN B 417 ASN C 181 HIS ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS C 353 GLN C 476 HIS C 491 ASN C 548 HIS C 562 ASN C 573 HIS C 602 GLN C 620 ASN D 148 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.229169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.191595 restraints weight = 15283.880| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 1.63 r_work: 0.3803 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14209 Z= 0.177 Angle : 0.700 11.936 19229 Z= 0.362 Chirality : 0.047 0.245 2134 Planarity : 0.004 0.061 2478 Dihedral : 8.255 73.219 1959 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.14 % Allowed : 22.43 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.19), residues: 1710 helix: -0.39 (0.21), residues: 581 sheet: -1.45 (0.24), residues: 397 loop : -2.05 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 212 TYR 0.020 0.002 TYR A 617 PHE 0.026 0.002 PHE C 641 TRP 0.020 0.001 TRP D 102 HIS 0.014 0.001 HIS C 304 Details of bonding type rmsd covalent geometry : bond 0.00396 (14209) covalent geometry : angle 0.70000 (19229) hydrogen bonds : bond 0.04806 ( 651) hydrogen bonds : angle 5.47995 ( 1860) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 198 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7670 (mt) REVERT: A 513 ARG cc_start: 0.6189 (ptp-110) cc_final: 0.5878 (ptm160) REVERT: A 566 SER cc_start: 0.6675 (OUTLIER) cc_final: 0.6409 (t) REVERT: A 576 LEU cc_start: 0.8486 (mt) cc_final: 0.8217 (mt) REVERT: B 144 MET cc_start: 0.8269 (tpp) cc_final: 0.8041 (tpp) REVERT: B 272 MET cc_start: 0.4420 (mmp) cc_final: 0.3683 (mmm) REVERT: B 360 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6631 (tm-30) REVERT: B 376 PHE cc_start: 0.4272 (OUTLIER) cc_final: 0.3873 (p90) REVERT: C 210 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7015 (tm-30) REVERT: C 474 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6414 (mmm) REVERT: C 619 ARG cc_start: 0.2792 (OUTLIER) cc_final: -0.0892 (mmp-170) REVERT: C 621 GLN cc_start: 0.2214 (OUTLIER) cc_final: 0.0840 (tm-30) REVERT: C 622 ARG cc_start: 0.2001 (OUTLIER) cc_final: -0.0439 (mtt-85) REVERT: C 628 ASN cc_start: 0.4135 (OUTLIER) cc_final: 0.3695 (t0) REVERT: D 9 LEU cc_start: 0.7168 (mt) cc_final: 0.6796 (mt) outliers start: 79 outliers final: 35 residues processed: 260 average time/residue: 0.1102 time to fit residues: 42.9029 Evaluate side-chains 213 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 621 GLN Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 83 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 41 optimal weight: 0.0170 chunk 9 optimal weight: 0.7980 chunk 110 optimal weight: 0.0060 chunk 17 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 136 optimal weight: 0.0060 overall best weight: 0.3650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 HIS ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN C 34 GLN C 155 ASN ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.232014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.198425 restraints weight = 15260.351| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 1.66 r_work: 0.3873 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14209 Z= 0.123 Angle : 0.624 11.333 19229 Z= 0.319 Chirality : 0.044 0.226 2134 Planarity : 0.004 0.052 2478 Dihedral : 6.890 68.023 1927 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.36 % Allowed : 23.93 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.20), residues: 1710 helix: 0.14 (0.21), residues: 605 sheet: -0.97 (0.24), residues: 387 loop : -1.67 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 362 TYR 0.019 0.001 TYR B 142 PHE 0.022 0.001 PHE D 106 TRP 0.020 0.001 TRP D 102 HIS 0.008 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00270 (14209) covalent geometry : angle 0.62415 (19229) hydrogen bonds : bond 0.04025 ( 651) hydrogen bonds : angle 5.01228 ( 1860) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 185 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7642 (mt) REVERT: A 510 PHE cc_start: 0.4968 (OUTLIER) cc_final: 0.4296 (t80) REVERT: A 514 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7190 (tp) REVERT: B 252 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7690 (tt) REVERT: B 360 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.6600 (tm-30) REVERT: B 376 PHE cc_start: 0.4201 (OUTLIER) cc_final: 0.3876 (p90) REVERT: C 17 PHE cc_start: 0.7449 (p90) cc_final: 0.7236 (p90) REVERT: C 32 ASN cc_start: 0.8036 (m-40) cc_final: 0.7732 (p0) REVERT: C 210 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6826 (tm-30) REVERT: C 597 LEU cc_start: 0.6100 (tt) cc_final: 0.5859 (tt) REVERT: C 621 GLN cc_start: 0.2179 (tp40) cc_final: 0.1121 (tm-30) REVERT: C 622 ARG cc_start: 0.1571 (OUTLIER) cc_final: -0.0741 (mtt-85) outliers start: 67 outliers final: 37 residues processed: 240 average time/residue: 0.1044 time to fit residues: 38.0688 Evaluate side-chains 209 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 572 LYS Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 143 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 120 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN B 19 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 GLN ** C 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.230492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.197573 restraints weight = 15271.451| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 1.58 r_work: 0.3856 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14209 Z= 0.133 Angle : 0.601 10.194 19229 Z= 0.307 Chirality : 0.044 0.221 2134 Planarity : 0.004 0.052 2478 Dihedral : 6.322 60.592 1911 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.55 % Allowed : 23.28 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.20), residues: 1710 helix: 0.34 (0.22), residues: 611 sheet: -0.72 (0.25), residues: 371 loop : -1.51 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 69 TYR 0.017 0.001 TYR B 142 PHE 0.016 0.001 PHE C 193 TRP 0.015 0.001 TRP D 102 HIS 0.007 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00307 (14209) covalent geometry : angle 0.60129 (19229) hydrogen bonds : bond 0.03870 ( 651) hydrogen bonds : angle 4.87757 ( 1860) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 175 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7611 (mt) REVERT: A 514 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7193 (tp) REVERT: B 360 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.6536 (tm-30) REVERT: B 376 PHE cc_start: 0.4314 (OUTLIER) cc_final: 0.3961 (p90) REVERT: C 17 PHE cc_start: 0.7472 (p90) cc_final: 0.7251 (p90) REVERT: C 32 ASN cc_start: 0.8134 (m-40) cc_final: 0.7861 (p0) REVERT: C 135 TYR cc_start: 0.6933 (m-80) cc_final: 0.6706 (m-80) REVERT: C 183 ARG cc_start: 0.6141 (ptp90) cc_final: 0.5620 (mtm110) REVERT: C 597 LEU cc_start: 0.6030 (tt) cc_final: 0.5798 (tt) REVERT: C 621 GLN cc_start: 0.2231 (tp40) cc_final: 0.1123 (tm-30) REVERT: C 622 ARG cc_start: 0.1445 (OUTLIER) cc_final: -0.0808 (mtt-85) REVERT: C 649 GLN cc_start: 0.4110 (pt0) cc_final: 0.3068 (mm-40) outliers start: 70 outliers final: 42 residues processed: 231 average time/residue: 0.0983 time to fit residues: 34.7436 Evaluate side-chains 213 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 572 LYS Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain C residue 638 HIS Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 147 optimal weight: 0.0030 chunk 96 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 152 optimal weight: 0.3980 chunk 114 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 HIS ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.230977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.197068 restraints weight = 15305.349| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 1.59 r_work: 0.3853 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14209 Z= 0.124 Angle : 0.587 9.931 19229 Z= 0.301 Chirality : 0.044 0.225 2134 Planarity : 0.004 0.051 2478 Dihedral : 5.968 59.877 1909 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.75 % Allowed : 23.54 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.20), residues: 1710 helix: 0.44 (0.22), residues: 619 sheet: -0.58 (0.25), residues: 386 loop : -1.38 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 248 TYR 0.017 0.001 TYR B 142 PHE 0.016 0.001 PHE C 193 TRP 0.012 0.001 TRP D 102 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00281 (14209) covalent geometry : angle 0.58703 (19229) hydrogen bonds : bond 0.03714 ( 651) hydrogen bonds : angle 4.76578 ( 1860) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 179 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7541 (mt) REVERT: A 510 PHE cc_start: 0.5228 (OUTLIER) cc_final: 0.4424 (t80) REVERT: A 514 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7042 (tp) REVERT: A 641 GLU cc_start: 0.6940 (tt0) cc_final: 0.6443 (tt0) REVERT: B 360 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6605 (tm-30) REVERT: B 376 PHE cc_start: 0.3957 (OUTLIER) cc_final: 0.3671 (p90) REVERT: B 384 MET cc_start: 0.7612 (mtm) cc_final: 0.7324 (mmp) REVERT: C 32 ASN cc_start: 0.8121 (m-40) cc_final: 0.7885 (p0) REVERT: C 183 ARG cc_start: 0.6169 (ptp90) cc_final: 0.5783 (mtm110) REVERT: C 342 VAL cc_start: 0.7612 (m) cc_final: 0.7401 (p) REVERT: C 597 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5905 (tt) REVERT: C 607 MET cc_start: 0.6040 (tpt) cc_final: 0.5178 (tpt) REVERT: C 621 GLN cc_start: 0.2628 (tp40) cc_final: 0.1843 (tp40) REVERT: C 622 ARG cc_start: 0.1290 (OUTLIER) cc_final: -0.0683 (mtt-85) REVERT: C 649 GLN cc_start: 0.4060 (pt0) cc_final: 0.3200 (mm-40) outliers start: 73 outliers final: 47 residues processed: 237 average time/residue: 0.1009 time to fit residues: 36.2509 Evaluate side-chains 220 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 572 LYS Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 615 PHE Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain C residue 638 HIS Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 131 optimal weight: 0.0170 chunk 91 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 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 = 0.4579 r_free = 0.4579 target = 0.230520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.198991 restraints weight = 15189.460| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 1.47 r_work: 0.3885 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14209 Z= 0.129 Angle : 0.585 10.089 19229 Z= 0.298 Chirality : 0.044 0.217 2134 Planarity : 0.004 0.051 2478 Dihedral : 5.739 53.127 1906 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.68 % Allowed : 23.54 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.20), residues: 1710 helix: 0.54 (0.22), residues: 614 sheet: -0.46 (0.25), residues: 388 loop : -1.26 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 248 TYR 0.023 0.001 TYR B 247 PHE 0.015 0.001 PHE C 116 TRP 0.010 0.001 TRP D 102 HIS 0.007 0.001 HIS C 573 Details of bonding type rmsd covalent geometry : bond 0.00297 (14209) covalent geometry : angle 0.58458 (19229) hydrogen bonds : bond 0.03765 ( 651) hydrogen bonds : angle 4.72976 ( 1860) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 171 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 379 MET cc_start: 0.7862 (mtm) cc_final: 0.7324 (mtm) REVERT: A 466 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7569 (mt) REVERT: A 510 PHE cc_start: 0.4973 (OUTLIER) cc_final: 0.4179 (t80) REVERT: A 514 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7031 (tp) REVERT: A 601 GLU cc_start: 0.8195 (pm20) cc_final: 0.7931 (pm20) REVERT: A 641 GLU cc_start: 0.7311 (tt0) cc_final: 0.6849 (tt0) REVERT: B 169 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8275 (tm-30) REVERT: B 360 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6414 (tm-30) REVERT: B 384 MET cc_start: 0.7938 (mtm) cc_final: 0.7544 (mmp) REVERT: B 411 LYS cc_start: 0.6652 (tmmt) cc_final: 0.6388 (ttpp) REVERT: C 32 ASN cc_start: 0.8351 (m-40) cc_final: 0.8034 (p0) REVERT: C 75 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6876 (mt-10) REVERT: C 183 ARG cc_start: 0.6478 (ptp90) cc_final: 0.6042 (mtm110) REVERT: C 474 MET cc_start: 0.7246 (mmm) cc_final: 0.6928 (mmm) REVERT: C 597 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.6167 (tt) REVERT: C 607 MET cc_start: 0.6131 (tpt) cc_final: 0.5380 (tpt) REVERT: C 622 ARG cc_start: 0.2307 (OUTLIER) cc_final: -0.0239 (mtt-85) REVERT: C 649 GLN cc_start: 0.4399 (pt0) cc_final: 0.3154 (mm-40) REVERT: D 67 GLN cc_start: 0.7941 (mp10) cc_final: 0.7712 (mp10) outliers start: 72 outliers final: 53 residues processed: 230 average time/residue: 0.1021 time to fit residues: 35.6347 Evaluate side-chains 220 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 161 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 615 PHE Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain C residue 638 HIS Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 74 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 HIS ** C 279 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 = 0.4561 r_free = 0.4561 target = 0.228744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.194872 restraints weight = 15175.588| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 1.59 r_work: 0.3840 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14209 Z= 0.147 Angle : 0.601 10.179 19229 Z= 0.308 Chirality : 0.044 0.228 2134 Planarity : 0.004 0.052 2478 Dihedral : 5.663 50.039 1904 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.81 % Allowed : 23.93 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.20), residues: 1710 helix: 0.58 (0.22), residues: 612 sheet: -0.41 (0.25), residues: 393 loop : -1.27 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 248 TYR 0.019 0.001 TYR B 247 PHE 0.016 0.001 PHE B 148 TRP 0.010 0.001 TRP D 102 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00345 (14209) covalent geometry : angle 0.60150 (19229) hydrogen bonds : bond 0.03831 ( 651) hydrogen bonds : angle 4.76053 ( 1860) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 165 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7598 (mt) REVERT: A 510 PHE cc_start: 0.5060 (OUTLIER) cc_final: 0.4278 (t80) REVERT: A 514 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7559 (tp) REVERT: A 601 GLU cc_start: 0.8240 (pm20) cc_final: 0.7984 (pm20) REVERT: A 641 GLU cc_start: 0.7307 (tt0) cc_final: 0.6830 (tt0) REVERT: B 360 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6481 (tm-30) REVERT: B 384 MET cc_start: 0.8026 (mtm) cc_final: 0.7568 (mmp) REVERT: C 75 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6863 (mt-10) REVERT: C 114 LEU cc_start: 0.7675 (mt) cc_final: 0.7403 (mp) REVERT: C 175 ASN cc_start: 0.6641 (OUTLIER) cc_final: 0.6142 (m-40) REVERT: C 183 ARG cc_start: 0.6462 (ptp90) cc_final: 0.6041 (mtm110) REVERT: C 607 MET cc_start: 0.6098 (tpt) cc_final: 0.5473 (tpt) REVERT: C 649 GLN cc_start: 0.4098 (pt0) cc_final: 0.3009 (mm-40) REVERT: D 67 GLN cc_start: 0.8007 (mp10) cc_final: 0.7784 (mp10) outliers start: 74 outliers final: 59 residues processed: 225 average time/residue: 0.0981 time to fit residues: 33.6444 Evaluate side-chains 216 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 152 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 615 PHE Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain C residue 638 HIS Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 37 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 77 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.229392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.197280 restraints weight = 15026.432| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 1.50 r_work: 0.3865 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14209 Z= 0.139 Angle : 0.600 10.219 19229 Z= 0.307 Chirality : 0.044 0.247 2134 Planarity : 0.004 0.052 2478 Dihedral : 5.545 49.426 1902 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.42 % Allowed : 24.38 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.20), residues: 1710 helix: 0.63 (0.22), residues: 612 sheet: -0.36 (0.26), residues: 383 loop : -1.22 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 248 TYR 0.016 0.001 TYR B 142 PHE 0.016 0.001 PHE C 193 TRP 0.010 0.001 TRP D 102 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00325 (14209) covalent geometry : angle 0.59976 (19229) hydrogen bonds : bond 0.03742 ( 651) hydrogen bonds : angle 4.75121 ( 1860) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 162 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7631 (mt) REVERT: A 510 PHE cc_start: 0.5021 (OUTLIER) cc_final: 0.4258 (t80) REVERT: A 601 GLU cc_start: 0.8299 (pm20) cc_final: 0.8090 (pm20) REVERT: B 360 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6492 (tm-30) REVERT: B 384 MET cc_start: 0.8047 (mtm) cc_final: 0.7563 (mmp) REVERT: C 75 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6921 (mt-10) REVERT: C 114 LEU cc_start: 0.7708 (mt) cc_final: 0.7451 (mp) REVERT: C 175 ASN cc_start: 0.6696 (OUTLIER) cc_final: 0.6170 (m-40) REVERT: C 183 ARG cc_start: 0.6458 (ptp90) cc_final: 0.6030 (mtm110) REVERT: C 556 LYS cc_start: 0.7386 (tttt) cc_final: 0.7012 (tttp) REVERT: C 649 GLN cc_start: 0.3908 (pt0) cc_final: 0.3277 (mm-40) REVERT: D 67 GLN cc_start: 0.8026 (mp10) cc_final: 0.7781 (mp10) outliers start: 68 outliers final: 54 residues processed: 216 average time/residue: 0.0948 time to fit residues: 31.7177 Evaluate side-chains 209 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 151 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 615 PHE Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain C residue 638 HIS Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 168 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 14 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 HIS ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 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 = 0.4568 r_free = 0.4568 target = 0.229696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.195804 restraints weight = 15076.265| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 1.62 r_work: 0.3847 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14209 Z= 0.132 Angle : 0.594 10.213 19229 Z= 0.303 Chirality : 0.044 0.237 2134 Planarity : 0.004 0.052 2478 Dihedral : 5.428 48.741 1900 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.42 % Allowed : 24.58 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.20), residues: 1710 helix: 0.67 (0.22), residues: 619 sheet: -0.34 (0.26), residues: 382 loop : -1.13 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 248 TYR 0.016 0.001 TYR B 142 PHE 0.015 0.001 PHE C 193 TRP 0.010 0.001 TRP D 102 HIS 0.006 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00310 (14209) covalent geometry : angle 0.59373 (19229) hydrogen bonds : bond 0.03723 ( 651) hydrogen bonds : angle 4.72927 ( 1860) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 153 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 ARG cc_start: 0.6626 (ptm160) cc_final: 0.6077 (mtm110) REVERT: A 466 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7660 (mt) REVERT: A 510 PHE cc_start: 0.5294 (OUTLIER) cc_final: 0.4426 (t80) REVERT: B 124 TYR cc_start: 0.6852 (m-80) cc_final: 0.6544 (m-10) REVERT: B 360 GLN cc_start: 0.6867 (OUTLIER) cc_final: 0.6631 (tm-30) REVERT: C 175 ASN cc_start: 0.6249 (OUTLIER) cc_final: 0.5817 (m110) REVERT: C 183 ARG cc_start: 0.6246 (ptp90) cc_final: 0.5912 (mtm110) REVERT: C 329 SER cc_start: 0.3720 (OUTLIER) cc_final: 0.2860 (m) REVERT: C 556 LYS cc_start: 0.7265 (tttt) cc_final: 0.6858 (tttp) REVERT: C 649 GLN cc_start: 0.3643 (pt0) cc_final: 0.3343 (mm-40) outliers start: 68 outliers final: 55 residues processed: 206 average time/residue: 0.1096 time to fit residues: 34.7535 Evaluate side-chains 209 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 149 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 615 PHE Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain C residue 638 HIS Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 168 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 42 optimal weight: 0.4980 chunk 137 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 5 optimal weight: 0.0270 chunk 141 optimal weight: 0.0870 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 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 = 0.4586 r_free = 0.4586 target = 0.231868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.194198 restraints weight = 15183.435| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 1.53 r_work: 0.3849 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14209 Z= 0.113 Angle : 0.587 9.170 19229 Z= 0.299 Chirality : 0.044 0.225 2134 Planarity : 0.004 0.051 2478 Dihedral : 5.332 48.799 1900 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.90 % Allowed : 25.75 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.20), residues: 1710 helix: 0.76 (0.22), residues: 621 sheet: -0.27 (0.26), residues: 377 loop : -1.07 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 447 TYR 0.017 0.001 TYR B 142 PHE 0.015 0.001 PHE C 193 TRP 0.010 0.001 TRP D 102 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00257 (14209) covalent geometry : angle 0.58701 (19229) hydrogen bonds : bond 0.03498 ( 651) hydrogen bonds : angle 4.65523 ( 1860) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 154 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ARG cc_start: 0.6720 (ptm160) cc_final: 0.6044 (mtm110) REVERT: A 387 MET cc_start: 0.8282 (tpp) cc_final: 0.8050 (tpt) REVERT: A 466 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7615 (mt) REVERT: A 510 PHE cc_start: 0.5040 (OUTLIER) cc_final: 0.4036 (t80) REVERT: B 360 GLN cc_start: 0.6830 (OUTLIER) cc_final: 0.6518 (tm-30) REVERT: B 384 MET cc_start: 0.7898 (mtm) cc_final: 0.7428 (mmp) REVERT: C 175 ASN cc_start: 0.6832 (OUTLIER) cc_final: 0.6270 (m110) REVERT: C 183 ARG cc_start: 0.6575 (ptp90) cc_final: 0.5954 (mtm110) REVERT: C 556 LYS cc_start: 0.7356 (tttt) cc_final: 0.6875 (tttp) REVERT: C 649 GLN cc_start: 0.3744 (pt0) cc_final: 0.3010 (mm-40) outliers start: 60 outliers final: 47 residues processed: 203 average time/residue: 0.1140 time to fit residues: 35.3442 Evaluate side-chains 199 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 148 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 396 GLN Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 615 PHE Chi-restraints excluded: chain C residue 622 ARG Chi-restraints excluded: chain C residue 638 HIS Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 168 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 107 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 148 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.231540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.198233 restraints weight = 15034.334| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 1.60 r_work: 0.3864 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14209 Z= 0.124 Angle : 0.603 10.146 19229 Z= 0.304 Chirality : 0.044 0.217 2134 Planarity : 0.004 0.051 2478 Dihedral : 5.315 48.083 1898 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.25 % Allowed : 26.27 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.20), residues: 1710 helix: 0.77 (0.22), residues: 621 sheet: -0.23 (0.26), residues: 385 loop : -1.02 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 248 TYR 0.016 0.001 TYR B 142 PHE 0.014 0.001 PHE A 385 TRP 0.009 0.001 TRP D 102 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00290 (14209) covalent geometry : angle 0.60307 (19229) hydrogen bonds : bond 0.03561 ( 651) hydrogen bonds : angle 4.67271 ( 1860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3048.98 seconds wall clock time: 53 minutes 14.89 seconds (3194.89 seconds total)