Starting phenix.real_space_refine on Tue Aug 26 00:53:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rn3_19385/08_2025/8rn3_19385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rn3_19385/08_2025/8rn3_19385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rn3_19385/08_2025/8rn3_19385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rn3_19385/08_2025/8rn3_19385.map" model { file = "/net/cci-nas-00/data/ceres_data/8rn3_19385/08_2025/8rn3_19385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rn3_19385/08_2025/8rn3_19385.cif" } resolution = 2.78 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= 0.104 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: 6 Type Number sf(0) Gaussians Mg 3 5.21 5 S 121 5.16 5 C 10193 2.51 5 N 2731 2.21 5 O 3010 1.98 5 H 16100 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32158 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 11326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 11326 Classifications: {'peptide': 706} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 26, 'TRANS': 679} Chain breaks: 1 Chain: "B" Number of atoms: 9957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 9957 Classifications: {'peptide': 636} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 33, 'TRANS': 602} Chain breaks: 2 Chain: "C" Number of atoms: 9818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 9818 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 21, 'TRANS': 591} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 480 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 574 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 3, 'TRANS': 30} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.81, per 1000 atoms: 0.18 Number of scatterers: 32158 At special positions: 0 Unit cell: (100.8, 130.2, 144.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 121 16.00 Mg 3 11.99 O 3010 8.00 N 2731 7.00 C 10193 6.00 H 16100 1.00 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: 2.97 Conformation dependent library (CDL) restraints added in 912.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3752 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 24 sheets defined 48.0% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 25 removed outlier: 3.549A pdb=" N GLU A 23 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 30 Processing helix chain 'A' and resid 31 through 52 removed outlier: 3.971A pdb=" N LEU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.547A pdb=" N MET A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 Processing helix chain 'A' and resid 163 through 184 Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 237 through 245 removed outlier: 3.541A pdb=" N ARG A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'A' and resid 358 through 366 removed outlier: 3.924A pdb=" N TRP A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 400 through 411 removed outlier: 4.236A pdb=" N GLN A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 447 Processing helix chain 'A' and resid 449 through 468 removed outlier: 3.646A pdb=" N THR A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 563 through 573 Processing helix chain 'A' and resid 575 through 595 removed outlier: 3.644A pdb=" N ILE A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 628 through 646 Processing helix chain 'A' and resid 648 through 671 removed outlier: 3.858A pdb=" N ARG A 659 " --> pdb=" O SER A 655 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 688 Processing helix chain 'A' and resid 693 through 716 removed outlier: 3.560A pdb=" N LYS A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.961A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 162 through 173 removed outlier: 3.584A pdb=" N PHE B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 264 removed outlier: 3.771A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 removed outlier: 4.064A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 3.539A pdb=" N ILE B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.599A pdb=" N ASN B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 376 removed outlier: 5.023A pdb=" N PHE B 374 " --> pdb=" O PRO B 371 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 413 through 426 Processing helix chain 'B' and resid 454 through 473 Processing helix chain 'B' and resid 517 through 536 removed outlier: 3.866A pdb=" N MET B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA B 523 " --> pdb=" O SER B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 559 Processing helix chain 'B' and resid 569 through 582 removed outlier: 3.901A pdb=" N ILE B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B 577 " --> pdb=" O LYS B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 588 Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 606 through 612 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.573A pdb=" N VAL C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 117 through 130 Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.514A pdb=" N GLU C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 255 through 274 removed outlier: 3.952A pdb=" N VAL C 274 " --> pdb=" O ARG C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 287 removed outlier: 3.574A pdb=" N LEU C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.743A pdb=" N ASP C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 318 Processing helix chain 'C' and resid 392 through 408 Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'C' and resid 431 through 443 Processing helix chain 'C' and resid 444 through 450 removed outlier: 3.751A pdb=" N GLN C 450 " --> pdb=" O ASP C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 534 through 541 removed outlier: 4.190A pdb=" N GLU C 539 " --> pdb=" O LYS C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 557 Processing helix chain 'C' and resid 557 through 566 Processing helix chain 'C' and resid 570 through 574 Processing helix chain 'C' and resid 575 through 583 removed outlier: 3.637A pdb=" N SER C 583 " --> pdb=" O GLU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 606 removed outlier: 4.695A pdb=" N GLY C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLN C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 620 through 623 removed outlier: 3.713A pdb=" N PHE C 623 " --> pdb=" O PRO C 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 620 through 623' Processing helix chain 'C' and resid 689 through 693 Processing helix chain 'C' and resid 713 through 720 Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'D' and resid 376 through 383 Processing helix chain 'E' and resid 377 through 381 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 256 removed outlier: 3.788A pdb=" N PHE B 446 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP B 445 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 295 removed outlier: 4.395A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS A 551 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER A 543 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 553 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 538 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 295 removed outlier: 4.395A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER A 492 " --> pdb=" O ASN A 487 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASN A 487 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP A 494 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL A 485 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU A 496 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ASN A 483 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY A 498 " --> pdb=" O ILE A 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 374 removed outlier: 5.757A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N GLN B 367 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 624 through 627 removed outlier: 3.549A pdb=" N GLY A 618 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY A 627 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N SER A 616 " --> pdb=" O GLY A 627 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 186 Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 244 removed outlier: 6.736A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 61 removed outlier: 4.333A pdb=" N GLN C 91 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AB5, first strand: chain 'C' and resid 131 through 137 removed outlier: 5.905A pdb=" N ILE C 245 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE C 135 " --> pdb=" O ARG C 243 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG C 243 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 294 through 295 Processing sheet with id=AB7, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AB8, first strand: chain 'C' and resid 325 through 327 removed outlier: 5.501A pdb=" N LEU C 332 " --> pdb=" O ARG C 368 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ARG C 368 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ARG C 334 " --> pdb=" O HIS C 366 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N HIS C 366 " --> pdb=" O ARG C 334 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ARG C 373 " --> pdb=" O ILE C 388 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE C 388 " --> pdb=" O ARG C 373 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE C 375 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU C 386 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS C 377 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL C 480 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU C 386 " --> pdb=" O VAL C 480 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 482 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE C 388 " --> pdb=" O THR C 482 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 342 through 347 Processing sheet with id=AC1, first strand: chain 'C' and resid 453 through 455 Processing sheet with id=AC2, first strand: chain 'C' and resid 498 through 499 removed outlier: 6.901A pdb=" N LEU C 505 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 639 through 641 Processing sheet with id=AC4, first strand: chain 'C' and resid 660 through 662 removed outlier: 3.751A pdb=" N VAL C 667 " --> pdb=" O ASN C 662 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 698 through 700 Processing sheet with id=AC6, first strand: chain 'D' and resid 373 through 374 removed outlier: 5.898A pdb=" N GLN D 373 " --> pdb=" O LYS E 365 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N GLN E 367 " --> pdb=" O GLN D 373 " (cutoff:3.500A) 767 hydrogen bonds defined for protein. 2091 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: 8.29 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16062 1.03 - 1.23: 47 1.23 - 1.42: 6675 1.42 - 1.62: 9477 1.62 - 1.81: 204 Bond restraints: 32465 Sorted by residual: bond pdb=" CB GLN C 587 " pdb=" CG GLN C 587 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CB VAL B 501 " pdb=" CG1 VAL B 501 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.54e-01 bond pdb=" C THR B 303 " pdb=" N GLY B 304 " ideal model delta sigma weight residual 1.330 1.343 -0.013 1.36e-02 5.41e+03 9.13e-01 bond pdb=" CB LYS A 605 " pdb=" CG LYS A 605 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.99e-01 bond pdb=" C GLY B 411 " pdb=" N MET B 412 " ideal model delta sigma weight residual 1.332 1.320 0.013 1.40e-02 5.10e+03 8.20e-01 ... (remaining 32460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 55074 1.05 - 2.10: 3464 2.10 - 3.15: 153 3.15 - 4.21: 66 4.21 - 5.26: 8 Bond angle restraints: 58765 Sorted by residual: angle pdb=" N ILE C 513 " pdb=" CA ILE C 513 " pdb=" C ILE C 513 " ideal model delta sigma weight residual 111.90 109.85 2.05 8.10e-01 1.52e+00 6.39e+00 angle pdb=" C ILE C 303 " pdb=" N ASP C 304 " pdb=" CA ASP C 304 " ideal model delta sigma weight residual 121.54 125.96 -4.42 1.91e+00 2.74e-01 5.36e+00 angle pdb=" N MET C 674 " pdb=" CA MET C 674 " pdb=" C MET C 674 " ideal model delta sigma weight residual 110.42 113.80 -3.38 1.46e+00 4.69e-01 5.34e+00 angle pdb=" CA TRP B 437 " pdb=" CB TRP B 437 " pdb=" CG TRP B 437 " ideal model delta sigma weight residual 113.60 117.91 -4.31 1.90e+00 2.77e-01 5.15e+00 angle pdb=" CB LYS A 605 " pdb=" CG LYS A 605 " pdb=" CD LYS A 605 " ideal model delta sigma weight residual 111.30 116.10 -4.80 2.30e+00 1.89e-01 4.35e+00 ... (remaining 58760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 13278 17.78 - 35.56: 1304 35.56 - 53.34: 442 53.34 - 71.12: 147 71.12 - 88.90: 21 Dihedral angle restraints: 15192 sinusoidal: 8410 harmonic: 6782 Sorted by residual: dihedral pdb=" CA ASP C 343 " pdb=" CB ASP C 343 " pdb=" CG ASP C 343 " pdb=" OD1 ASP C 343 " ideal model delta sinusoidal sigma weight residual -30.00 -88.20 58.20 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA LYS C 252 " pdb=" C LYS C 252 " pdb=" N LEU C 253 " pdb=" CA LEU C 253 " ideal model delta harmonic sigma weight residual 180.00 -163.19 -16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ASP C 707 " pdb=" CB ASP C 707 " pdb=" CG ASP C 707 " pdb=" OD1 ASP C 707 " ideal model delta sinusoidal sigma weight residual -30.00 -86.58 56.58 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 15189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1539 0.029 - 0.058: 617 0.058 - 0.087: 137 0.087 - 0.116: 91 0.116 - 0.145: 30 Chirality restraints: 2414 Sorted by residual: chirality pdb=" CA ILE B 348 " pdb=" N ILE B 348 " pdb=" C ILE B 348 " pdb=" CB ILE B 348 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE E 368 " pdb=" N ILE E 368 " pdb=" C ILE E 368 " pdb=" CB ILE E 368 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE C 291 " pdb=" N ILE C 291 " pdb=" C ILE C 291 " pdb=" CB ILE C 291 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 2411 not shown) Planarity restraints: 4758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 370 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO B 371 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 371 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 371 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 393 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.34e+00 pdb=" N PRO B 394 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 394 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 394 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 370 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO E 371 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO E 371 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 371 " -0.016 5.00e-02 4.00e+02 ... (remaining 4755 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1700 2.18 - 2.78: 64880 2.78 - 3.39: 91189 3.39 - 3.99: 121694 3.99 - 4.60: 189453 Nonbonded interactions: 468916 Sorted by model distance: nonbonded pdb=" O GLU B 518 " pdb=" HH TYR B 554 " model vdw 1.570 2.450 nonbonded pdb=" OD2 ASP B 521 " pdb=" HH TYR B 558 " model vdw 1.575 2.450 nonbonded pdb=" OE1 GLU C 716 " pdb=" H GLU C 716 " model vdw 1.584 2.450 nonbonded pdb="HH21 ARG C 257 " pdb=" OE1 GLU C 294 " model vdw 1.602 2.450 nonbonded pdb=" O LEU A 262 " pdb=" HZ2 LYS A 711 " model vdw 1.617 2.450 ... (remaining 468911 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: 10.630 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: 0.190 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.440 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:8.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16365 Z= 0.116 Angle : 0.485 5.257 22047 Z= 0.255 Chirality : 0.038 0.145 2414 Planarity : 0.003 0.039 2832 Dihedral : 17.479 88.899 6228 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 2.49 % Allowed : 22.73 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.19), residues: 2002 helix: 1.52 (0.18), residues: 841 sheet: -0.80 (0.33), residues: 237 loop : -0.65 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 574 TYR 0.012 0.001 TYR B 466 PHE 0.011 0.001 PHE C 340 TRP 0.012 0.001 TRP B 437 HIS 0.002 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00267 (16365) covalent geometry : angle 0.48507 (22047) hydrogen bonds : bond 0.13515 ( 762) hydrogen bonds : angle 5.31299 ( 2091) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 42 residues processed: 256 average time/residue: 1.3306 time to fit residues: 381.2657 Evaluate side-chains 255 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 557 ASN Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 707 ASP Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 739 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 389 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.178498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136920 restraints weight = 51447.542| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.90 r_work: 0.3501 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16365 Z= 0.143 Angle : 0.504 4.964 22047 Z= 0.267 Chirality : 0.039 0.150 2414 Planarity : 0.004 0.040 2832 Dihedral : 6.704 89.979 2232 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.75 % Favored : 95.15 % Rotamer: Outliers : 3.23 % Allowed : 20.92 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.19), residues: 2002 helix: 1.38 (0.18), residues: 845 sheet: -0.95 (0.32), residues: 250 loop : -0.70 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 417 TYR 0.012 0.001 TYR B 466 PHE 0.012 0.001 PHE C 365 TRP 0.013 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00331 (16365) covalent geometry : angle 0.50448 (22047) hydrogen bonds : bond 0.04344 ( 762) hydrogen bonds : angle 4.65304 ( 2091) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ARG cc_start: 0.8544 (ttp-170) cc_final: 0.8301 (ttp-170) REVERT: A 623 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7610 (mptt) REVERT: B 120 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7989 (p0) REVERT: C 496 LYS cc_start: 0.7413 (tttt) cc_final: 0.7112 (tptp) outliers start: 57 outliers final: 33 residues processed: 263 average time/residue: 1.2878 time to fit residues: 378.6265 Evaluate side-chains 248 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain E residue 356 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 150 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 172 optimal weight: 0.0870 chunk 117 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 389 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.179281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.137676 restraints weight = 51370.200| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.94 r_work: 0.3506 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16365 Z= 0.114 Angle : 0.471 4.687 22047 Z= 0.247 Chirality : 0.038 0.145 2414 Planarity : 0.003 0.032 2832 Dihedral : 6.088 88.933 2211 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 2.95 % Allowed : 21.09 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.19), residues: 2002 helix: 1.51 (0.18), residues: 847 sheet: -0.91 (0.32), residues: 249 loop : -0.72 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 673 TYR 0.013 0.001 TYR B 554 PHE 0.011 0.001 PHE C 365 TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00263 (16365) covalent geometry : angle 0.47129 (22047) hydrogen bonds : bond 0.03850 ( 762) hydrogen bonds : angle 4.45255 ( 2091) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 274 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 222 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6872 (tt) REVERT: B 120 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8027 (p0) REVERT: B 568 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: C 394 GLU cc_start: 0.7066 (pt0) cc_final: 0.6751 (mp0) REVERT: C 496 LYS cc_start: 0.7337 (tttt) cc_final: 0.7035 (tptp) outliers start: 52 outliers final: 31 residues processed: 259 average time/residue: 1.2325 time to fit residues: 356.5512 Evaluate side-chains 245 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain E residue 356 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 32 optimal weight: 0.5980 chunk 170 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN C 389 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.178051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.136362 restraints weight = 51139.920| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.89 r_work: 0.3494 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16365 Z= 0.147 Angle : 0.487 4.744 22047 Z= 0.256 Chirality : 0.039 0.147 2414 Planarity : 0.004 0.051 2832 Dihedral : 5.942 89.956 2203 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.65 % Favored : 95.25 % Rotamer: Outliers : 3.29 % Allowed : 21.32 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.19), residues: 2002 helix: 1.46 (0.18), residues: 847 sheet: -0.94 (0.32), residues: 249 loop : -0.73 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 417 TYR 0.013 0.001 TYR B 554 PHE 0.012 0.001 PHE B 550 TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00347 (16365) covalent geometry : angle 0.48691 (22047) hydrogen bonds : bond 0.03944 ( 762) hydrogen bonds : angle 4.42147 ( 2091) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 0.898 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 504 GLN cc_start: 0.5980 (OUTLIER) cc_final: 0.5648 (pt0) REVERT: A 623 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7611 (mptt) REVERT: B 120 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8019 (p0) REVERT: B 568 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: C 394 GLU cc_start: 0.7067 (pt0) cc_final: 0.6758 (mp0) REVERT: C 496 LYS cc_start: 0.7356 (tttt) cc_final: 0.7025 (tptp) outliers start: 58 outliers final: 36 residues processed: 259 average time/residue: 1.3366 time to fit residues: 389.4531 Evaluate side-chains 250 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain E residue 356 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 87 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 194 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 187 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 178 GLN B 292 ASN C 389 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.178872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137154 restraints weight = 51246.132| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.92 r_work: 0.3498 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16365 Z= 0.116 Angle : 0.471 5.083 22047 Z= 0.246 Chirality : 0.038 0.145 2414 Planarity : 0.003 0.034 2832 Dihedral : 5.768 89.630 2202 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.30 % Favored : 95.60 % Rotamer: Outliers : 3.23 % Allowed : 21.09 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.19), residues: 2002 helix: 1.54 (0.18), residues: 848 sheet: -0.89 (0.32), residues: 249 loop : -0.68 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 673 TYR 0.014 0.001 TYR B 554 PHE 0.011 0.001 PHE B 550 TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00272 (16365) covalent geometry : angle 0.47128 (22047) hydrogen bonds : bond 0.03674 ( 762) hydrogen bonds : angle 4.34354 ( 2091) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 279 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 222 time to evaluate : 0.880 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 287 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7952 (m-30) REVERT: A 382 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8114 (m-30) REVERT: A 504 GLN cc_start: 0.5982 (OUTLIER) cc_final: 0.5644 (pt0) REVERT: B 120 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7998 (p0) REVERT: B 367 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8621 (tt0) REVERT: B 568 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: C 381 MET cc_start: 0.7264 (mtt) cc_final: 0.6893 (mtt) REVERT: C 394 GLU cc_start: 0.7044 (pt0) cc_final: 0.6757 (mp0) REVERT: C 496 LYS cc_start: 0.7368 (tttt) cc_final: 0.7026 (tptp) REVERT: C 674 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.6190 (mpp) outliers start: 57 outliers final: 32 residues processed: 260 average time/residue: 1.1746 time to fit residues: 343.9759 Evaluate side-chains 253 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain E residue 356 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 185 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 389 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.177789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.136003 restraints weight = 51135.966| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.92 r_work: 0.3487 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16365 Z= 0.145 Angle : 0.485 5.034 22047 Z= 0.254 Chirality : 0.039 0.172 2414 Planarity : 0.003 0.036 2832 Dihedral : 5.588 89.015 2197 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.80 % Favored : 95.10 % Rotamer: Outliers : 3.00 % Allowed : 21.54 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.19), residues: 2002 helix: 1.49 (0.18), residues: 848 sheet: -0.92 (0.32), residues: 249 loop : -0.69 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 673 TYR 0.014 0.001 TYR B 554 PHE 0.012 0.001 PHE B 550 TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00344 (16365) covalent geometry : angle 0.48475 (22047) hydrogen bonds : bond 0.03851 ( 762) hydrogen bonds : angle 4.36171 ( 2091) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 274 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7956 (m-30) REVERT: A 504 GLN cc_start: 0.6011 (OUTLIER) cc_final: 0.5693 (pt0) REVERT: B 120 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8014 (p0) REVERT: B 227 MET cc_start: 0.7362 (mtp) cc_final: 0.7067 (mmm) REVERT: B 568 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: C 294 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.6063 (pt0) REVERT: C 364 GLU cc_start: 0.6076 (OUTLIER) cc_final: 0.5258 (tp30) REVERT: C 381 MET cc_start: 0.7301 (mtt) cc_final: 0.6958 (mtt) REVERT: C 394 GLU cc_start: 0.7023 (pt0) cc_final: 0.6742 (mp0) REVERT: C 496 LYS cc_start: 0.7319 (tttt) cc_final: 0.6979 (tptp) outliers start: 53 outliers final: 36 residues processed: 258 average time/residue: 1.2167 time to fit residues: 351.4376 Evaluate side-chains 257 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 502 ASN Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain E residue 356 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 132 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 73 optimal weight: 0.2980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 389 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.177368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.130334 restraints weight = 51464.474| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.15 r_work: 0.3486 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16365 Z= 0.154 Angle : 0.492 4.856 22047 Z= 0.258 Chirality : 0.039 0.148 2414 Planarity : 0.004 0.038 2832 Dihedral : 5.509 87.659 2196 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.75 % Favored : 95.15 % Rotamer: Outliers : 3.00 % Allowed : 21.66 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.19), residues: 2002 helix: 1.45 (0.18), residues: 848 sheet: -0.93 (0.32), residues: 249 loop : -0.70 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 673 TYR 0.014 0.001 TYR B 554 PHE 0.017 0.001 PHE C 440 TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00368 (16365) covalent geometry : angle 0.49212 (22047) hydrogen bonds : bond 0.03929 ( 762) hydrogen bonds : angle 4.37684 ( 2091) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 224 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: A 504 GLN cc_start: 0.6073 (OUTLIER) cc_final: 0.5767 (pt0) REVERT: A 623 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7652 (mptt) REVERT: B 120 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8024 (p0) REVERT: B 227 MET cc_start: 0.7431 (mtp) cc_final: 0.7129 (mmm) REVERT: B 568 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: C 381 MET cc_start: 0.7340 (mtt) cc_final: 0.7014 (mtt) REVERT: C 394 GLU cc_start: 0.6993 (pt0) cc_final: 0.6633 (mp0) REVERT: C 496 LYS cc_start: 0.7331 (tttt) cc_final: 0.7021 (tptp) REVERT: C 674 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.6183 (mpp) outliers start: 53 outliers final: 34 residues processed: 259 average time/residue: 1.1831 time to fit residues: 341.8869 Evaluate side-chains 256 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 502 ASN Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain E residue 356 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 83 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN B 292 ASN C 389 ASN C 463 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.177154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129164 restraints weight = 51347.281| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.01 r_work: 0.3486 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16365 Z= 0.163 Angle : 0.500 4.976 22047 Z= 0.262 Chirality : 0.039 0.148 2414 Planarity : 0.004 0.038 2832 Dihedral : 5.404 86.817 2192 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 3.12 % Allowed : 21.49 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.19), residues: 2002 helix: 1.41 (0.18), residues: 849 sheet: -0.94 (0.32), residues: 249 loop : -0.74 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 673 TYR 0.014 0.001 TYR B 554 PHE 0.015 0.001 PHE C 440 TRP 0.013 0.001 TRP B 437 HIS 0.006 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00390 (16365) covalent geometry : angle 0.50012 (22047) hydrogen bonds : bond 0.03993 ( 762) hydrogen bonds : angle 4.39732 ( 2091) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 222 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: A 504 GLN cc_start: 0.6022 (OUTLIER) cc_final: 0.5658 (pt0) REVERT: A 623 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7676 (mptt) REVERT: B 120 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8024 (p0) REVERT: B 344 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8630 (t80) REVERT: B 568 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: C 377 LYS cc_start: 0.7431 (tppt) cc_final: 0.7059 (ttmm) REVERT: C 381 MET cc_start: 0.7360 (mtt) cc_final: 0.7040 (mtt) REVERT: C 394 GLU cc_start: 0.6994 (pt0) cc_final: 0.6630 (mp0) REVERT: C 463 HIS cc_start: 0.5756 (OUTLIER) cc_final: 0.5210 (m-70) REVERT: C 496 LYS cc_start: 0.7346 (tttt) cc_final: 0.7033 (tptp) outliers start: 55 outliers final: 37 residues processed: 257 average time/residue: 1.3391 time to fit residues: 385.0304 Evaluate side-chains 264 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 220 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 502 ASN Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain E residue 356 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 190 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 0.0470 chunk 145 optimal weight: 0.0570 chunk 166 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 389 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.178577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.137449 restraints weight = 51000.077| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.96 r_work: 0.3498 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16365 Z= 0.109 Angle : 0.481 4.601 22047 Z= 0.252 Chirality : 0.038 0.145 2414 Planarity : 0.004 0.074 2832 Dihedral : 5.301 88.103 2191 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 2.32 % Allowed : 22.22 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.19), residues: 2002 helix: 1.54 (0.18), residues: 851 sheet: -0.89 (0.32), residues: 249 loop : -0.68 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 417 TYR 0.013 0.001 TYR B 554 PHE 0.014 0.001 PHE C 440 TRP 0.013 0.001 TRP B 437 HIS 0.005 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00252 (16365) covalent geometry : angle 0.48059 (22047) hydrogen bonds : bond 0.03588 ( 762) hydrogen bonds : angle 4.32638 ( 2091) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7930 (m-30) REVERT: A 504 GLN cc_start: 0.5963 (OUTLIER) cc_final: 0.5659 (pt0) REVERT: B 120 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8030 (p0) REVERT: C 377 LYS cc_start: 0.7399 (tppt) cc_final: 0.7039 (ttmm) REVERT: C 381 MET cc_start: 0.7305 (mtt) cc_final: 0.6997 (mtt) REVERT: C 394 GLU cc_start: 0.6984 (pt0) cc_final: 0.6688 (mp0) REVERT: C 496 LYS cc_start: 0.7337 (tttt) cc_final: 0.7003 (tptp) outliers start: 41 outliers final: 28 residues processed: 251 average time/residue: 1.3456 time to fit residues: 376.9684 Evaluate side-chains 245 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain E residue 356 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 106 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 0.0040 chunk 13 optimal weight: 4.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN B 292 ASN C 389 ASN C 463 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.178685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.130816 restraints weight = 51493.248| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.06 r_work: 0.3501 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16365 Z= 0.113 Angle : 0.479 4.789 22047 Z= 0.249 Chirality : 0.038 0.145 2414 Planarity : 0.004 0.072 2832 Dihedral : 5.139 88.647 2189 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.20 % Rotamer: Outliers : 1.93 % Allowed : 22.85 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.19), residues: 2002 helix: 1.58 (0.18), residues: 852 sheet: -0.86 (0.32), residues: 249 loop : -0.66 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 417 TYR 0.013 0.001 TYR B 554 PHE 0.015 0.001 PHE B 344 TRP 0.012 0.001 TRP B 437 HIS 0.007 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00267 (16365) covalent geometry : angle 0.47893 (22047) hydrogen bonds : bond 0.03544 ( 762) hydrogen bonds : angle 4.27725 ( 2091) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 240 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.623 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 287 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: A 504 GLN cc_start: 0.5837 (OUTLIER) cc_final: 0.5560 (pt0) REVERT: B 120 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8005 (p0) REVERT: B 494 MET cc_start: 0.9138 (ttm) cc_final: 0.8819 (ttm) REVERT: C 381 MET cc_start: 0.7312 (mtt) cc_final: 0.7002 (mtt) REVERT: C 394 GLU cc_start: 0.6986 (pt0) cc_final: 0.6684 (mp0) REVERT: C 496 LYS cc_start: 0.7314 (tttt) cc_final: 0.6995 (tptp) REVERT: C 627 LYS cc_start: 0.7583 (tptp) cc_final: 0.7236 (tptp) outliers start: 34 outliers final: 28 residues processed: 243 average time/residue: 1.1812 time to fit residues: 319.0024 Evaluate side-chains 250 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 219 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain E residue 356 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 35 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 120 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 389 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.178813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.138171 restraints weight = 51178.082| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.00 r_work: 0.3503 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16365 Z= 0.115 Angle : 0.477 4.898 22047 Z= 0.248 Chirality : 0.038 0.145 2414 Planarity : 0.004 0.070 2832 Dihedral : 5.082 88.578 2189 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 2.04 % Allowed : 22.56 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.19), residues: 2002 helix: 1.61 (0.18), residues: 853 sheet: -0.85 (0.32), residues: 249 loop : -0.64 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 417 TYR 0.013 0.001 TYR B 554 PHE 0.014 0.001 PHE B 344 TRP 0.013 0.001 TRP C 51 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00272 (16365) covalent geometry : angle 0.47696 (22047) hydrogen bonds : bond 0.03520 ( 762) hydrogen bonds : angle 4.24968 ( 2091) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11746.70 seconds wall clock time: 199 minutes 13.92 seconds (11953.92 seconds total)