Starting phenix.real_space_refine on Mon May 4 00:53:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xvp_67296/05_2026/9xvp_67296.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xvp_67296/05_2026/9xvp_67296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xvp_67296/05_2026/9xvp_67296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xvp_67296/05_2026/9xvp_67296.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xvp_67296/05_2026/9xvp_67296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xvp_67296/05_2026/9xvp_67296.map" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 10541 2.51 5 N 2793 2.21 5 O 3087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16512 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 6057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6057 Classifications: {'peptide': 764} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 721} Chain breaks: 2 Chain: "A" Number of atoms: 5793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5793 Classifications: {'peptide': 718} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 681} Chain: "B" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4662 Classifications: {'peptide': 572} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 545} Chain breaks: 7 Time building chain proxies: 3.84, per 1000 atoms: 0.23 Number of scatterers: 16512 At special positions: 0 Unit cell: (97.97, 105.73, 234.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 3087 8.00 N 2793 7.00 C 10541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 771.1 milliseconds 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3826 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 23 sheets defined 24.4% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'C' and resid 290 through 294 removed outlier: 4.219A pdb=" N LEU C 294 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 319 through 326 removed outlier: 4.338A pdb=" N VAL C 323 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA C 324 " --> pdb=" O PHE C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 334 Processing helix chain 'C' and resid 372 through 388 removed outlier: 4.050A pdb=" N ASN C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS C 379 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 380 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 426 removed outlier: 3.954A pdb=" N SER C 426 " --> pdb=" O ASN C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 452 Processing helix chain 'C' and resid 461 through 467 Processing helix chain 'C' and resid 477 through 485 removed outlier: 3.611A pdb=" N GLU C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 533 removed outlier: 3.824A pdb=" N ASN C 527 " --> pdb=" O ARG C 523 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 531 " --> pdb=" O ASN C 527 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG C 533 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 removed outlier: 3.972A pdb=" N CYS C 546 " --> pdb=" O ALA C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 577 removed outlier: 4.018A pdb=" N VAL C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 621 removed outlier: 3.910A pdb=" N GLN C 610 " --> pdb=" O ARG C 606 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ARG C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE C 614 " --> pdb=" O GLN C 610 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU C 615 " --> pdb=" O ILE C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 646 removed outlier: 3.710A pdb=" N SER C 645 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG C 646 " --> pdb=" O LEU C 643 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 642 through 646' Processing helix chain 'C' and resid 652 through 655 Processing helix chain 'C' and resid 656 through 673 removed outlier: 3.978A pdb=" N SER C 671 " --> pdb=" O SER C 667 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 672 " --> pdb=" O PHE C 668 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG C 673 " --> pdb=" O MET C 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.653A pdb=" N ARG A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 66' Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 181 through 186 removed outlier: 4.516A pdb=" N THR A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 removed outlier: 3.587A pdb=" N LYS A 192 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.619A pdb=" N VAL A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 removed outlier: 4.294A pdb=" N LEU A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 285 removed outlier: 4.054A pdb=" N ASN A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 319 removed outlier: 3.742A pdb=" N ASN A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N SER A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 360 removed outlier: 3.978A pdb=" N LEU A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET A 359 " --> pdb=" O TRP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 376 through 379 removed outlier: 3.633A pdb=" N TRP A 379 " --> pdb=" O SER A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 380 through 386 Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 446 through 458 removed outlier: 4.353A pdb=" N ARG A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 451 " --> pdb=" O GLY A 447 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 452 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 457 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.802A pdb=" N ALA A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 501 through 505 removed outlier: 3.566A pdb=" N THR A 504 " --> pdb=" O ASP A 501 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR A 505 " --> pdb=" O LEU A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 501 through 505' Processing helix chain 'A' and resid 537 through 556 removed outlier: 3.991A pdb=" N ARG A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE A 552 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 589 Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 602 through 616 Processing helix chain 'A' and resid 705 through 712 removed outlier: 3.630A pdb=" N GLN A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 198 through 205 removed outlier: 4.225A pdb=" N VAL B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 203 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 removed outlier: 4.253A pdb=" N LEU B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 284 removed outlier: 3.555A pdb=" N LYS B 276 " --> pdb=" O ILE B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.545A pdb=" N LEU B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 459 removed outlier: 3.950A pdb=" N ARG B 450 " --> pdb=" O ASN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 473 removed outlier: 3.633A pdb=" N GLY B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'B' and resid 500 through 504 Processing helix chain 'B' and resid 537 through 558 removed outlier: 3.545A pdb=" N LYS B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 583 removed outlier: 4.274A pdb=" N CYS B 582 " --> pdb=" O ASN B 579 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS B 583 " --> pdb=" O THR B 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 579 through 583' Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.514A pdb=" N TYR B 589 " --> pdb=" O TYR B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 598 Processing helix chain 'B' and resid 602 through 616 Processing helix chain 'B' and resid 705 through 719 removed outlier: 3.700A pdb=" N ALA B 709 " --> pdb=" O GLU B 705 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR B 713 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N HIS B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N PHE B 716 " --> pdb=" O GLN B 712 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 26 through 31 removed outlier: 3.767A pdb=" N SER C 50 " --> pdb=" O GLU C 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 99 through 102 removed outlier: 3.585A pdb=" N VAL C 71 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C 130 " --> pdb=" O MET C 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 99 through 102 removed outlier: 3.585A pdb=" N VAL C 71 " --> pdb=" O HIS C 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 178 through 181 removed outlier: 3.578A pdb=" N ALA C 220 " --> pdb=" O PHE C 178 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 205 through 206 removed outlier: 3.602A pdb=" N ASN C 187 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR C 233 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 230 through 231 removed outlier: 3.736A pdb=" N GLY C 271 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 296 through 299 removed outlier: 5.926A pdb=" N TYR C 297 " --> pdb=" O LEU C 339 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL C 338 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLU C 395 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU C 340 " --> pdb=" O GLU C 395 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 456 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU C 494 " --> pdb=" O ALA C 518 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU C 520 " --> pdb=" O LEU C 494 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA C 496 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLU C 519 " --> pdb=" O PHE C 562 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER C 561 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL C 626 " --> pdb=" O SER C 561 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASN C 563 " --> pdb=" O VAL C 626 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 692 through 694 removed outlier: 3.574A pdb=" N ALA C 712 " --> pdb=" O TYR C 694 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 739 " --> pdb=" O PHE C 805 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N CYS C 802 " --> pdb=" O ASP C 767 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ASP C 767 " --> pdb=" O CYS C 802 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU C 804 " --> pdb=" O LEU C 765 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 749 through 752 removed outlier: 3.687A pdb=" N VAL C 751 " --> pdb=" O TYR C 795 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 25 through 27 removed outlier: 3.510A pdb=" N VAL A 89 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 91 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AB3, first strand: chain 'A' and resid 108 through 109 Processing sheet with id=AB4, first strand: chain 'A' and resid 177 through 180 removed outlier: 6.465A pdb=" N TYR A 178 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE A 217 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ASP A 292 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU A 219 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY A 363 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 420 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N TRP A 445 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ALA A 422 " --> pdb=" O TRP A 445 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N GLU A 444 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER A 487 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N MET A 563 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN A 489 " --> pdb=" O MET A 563 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N TYR A 565 " --> pdb=" O ASN A 489 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 631 through 633 removed outlier: 3.508A pdb=" N GLN A 631 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A 650 " --> pdb=" O HIS A 633 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 663 " --> pdb=" O PHE A 651 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N SER A 729 " --> pdb=" O ASP A 689 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP A 689 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 731 " --> pdb=" O PHE A 687 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 672 through 675 Processing sheet with id=AB7, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.928A pdb=" N SER B 46 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 56 through 58 Processing sheet with id=AB9, first strand: chain 'B' and resid 99 through 100 removed outlier: 4.004A pdb=" N CYS B 151 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 150 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 177 through 179 removed outlier: 6.625A pdb=" N GLU B 444 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE B 490 " --> pdb=" O GLU B 444 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 363 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 223 through 225 removed outlier: 6.828A pdb=" N GLU B 224 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 233 through 234 Processing sheet with id=AC4, first strand: chain 'B' and resid 630 through 633 removed outlier: 3.525A pdb=" N ALA B 650 " --> pdb=" O HIS B 633 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU B 660 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 734 " --> pdb=" O GLU B 660 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER B 729 " --> pdb=" O ASP B 689 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP B 689 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE B 731 " --> pdb=" O PHE B 687 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 672 through 675 431 hydrogen bonds defined for protein. 1119 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: 3.01 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5358 1.34 - 1.46: 4107 1.46 - 1.58: 7358 1.58 - 1.70: 0 1.70 - 1.82: 139 Bond restraints: 16962 Sorted by residual: bond pdb=" C ASN B 266 " pdb=" N PHE B 267 " ideal model delta sigma weight residual 1.334 1.355 -0.021 1.24e-02 6.50e+03 2.86e+00 bond pdb=" SD MET A 359 " pdb=" CE MET A 359 " ideal model delta sigma weight residual 1.791 1.761 0.030 2.50e-02 1.60e+03 1.42e+00 bond pdb=" CA PHE B 267 " pdb=" CB PHE B 267 " ideal model delta sigma weight residual 1.516 1.534 -0.018 1.65e-02 3.67e+03 1.17e+00 bond pdb=" CG PRO C 773 " pdb=" CD PRO C 773 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.47e-01 bond pdb=" N VAL C 784 " pdb=" CA VAL C 784 " ideal model delta sigma weight residual 1.459 1.471 -0.012 1.25e-02 6.40e+03 9.41e-01 ... (remaining 16957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 22204 1.57 - 3.14: 653 3.14 - 4.72: 100 4.72 - 6.29: 23 6.29 - 7.86: 7 Bond angle restraints: 22987 Sorted by residual: angle pdb=" N ILE B 272 " pdb=" CA ILE B 272 " pdb=" C ILE B 272 " ideal model delta sigma weight residual 110.62 106.13 4.49 1.02e+00 9.61e-01 1.94e+01 angle pdb=" C ASN B 265 " pdb=" N ASN B 266 " pdb=" CA ASN B 266 " ideal model delta sigma weight residual 121.54 128.40 -6.86 1.91e+00 2.74e-01 1.29e+01 angle pdb=" N PHE C 775 " pdb=" CA PHE C 775 " pdb=" C PHE C 775 " ideal model delta sigma weight residual 110.80 118.43 -7.63 2.13e+00 2.20e-01 1.28e+01 angle pdb=" N VAL C 574 " pdb=" CA VAL C 574 " pdb=" C VAL C 574 " ideal model delta sigma weight residual 112.98 108.82 4.16 1.25e+00 6.40e-01 1.11e+01 angle pdb=" N LEU C 604 " pdb=" CA LEU C 604 " pdb=" C LEU C 604 " ideal model delta sigma weight residual 114.75 110.57 4.18 1.26e+00 6.30e-01 1.10e+01 ... (remaining 22982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8425 17.94 - 35.88: 1123 35.88 - 53.82: 374 53.82 - 71.76: 52 71.76 - 89.70: 18 Dihedral angle restraints: 9992 sinusoidal: 4039 harmonic: 5953 Sorted by residual: dihedral pdb=" CA GLY C 774 " pdb=" C GLY C 774 " pdb=" N PHE C 775 " pdb=" CA PHE C 775 " ideal model delta harmonic sigma weight residual 180.00 -151.44 -28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA VAL C 603 " pdb=" C VAL C 603 " pdb=" N LEU C 604 " pdb=" CA LEU C 604 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA ASN B 266 " pdb=" C ASN B 266 " pdb=" N PHE B 267 " pdb=" CA PHE B 267 " ideal model delta harmonic sigma weight residual 180.00 157.30 22.70 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 9989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1627 0.043 - 0.086: 595 0.086 - 0.130: 185 0.130 - 0.173: 10 0.173 - 0.216: 1 Chirality restraints: 2418 Sorted by residual: chirality pdb=" CA PHE C 775 " pdb=" N PHE C 775 " pdb=" C PHE C 775 " pdb=" CB PHE C 775 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA PHE C 772 " pdb=" N PHE C 772 " pdb=" C PHE C 772 " pdb=" CB PHE C 772 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" C PRO A 221 " pdb=" CB PRO A 221 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.66e-01 ... (remaining 2415 not shown) Planarity restraints: 2986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 351 " 0.039 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO C 352 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 352 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 352 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 544 " -0.214 9.50e-02 1.11e+02 9.58e-02 5.64e+00 pdb=" NE ARG C 544 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 544 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 544 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 544 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 647 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO C 648 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 648 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 648 " -0.028 5.00e-02 4.00e+02 ... (remaining 2983 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 7487 2.95 - 3.44: 14612 3.44 - 3.92: 25476 3.92 - 4.41: 29042 4.41 - 4.90: 48969 Nonbonded interactions: 125586 Sorted by model distance: nonbonded pdb=" O VAL C 783 " pdb=" O VAL C 784 " model vdw 2.461 3.040 nonbonded pdb=" OD1 ASP C 118 " pdb=" N GLY C 119 " model vdw 2.484 3.120 nonbonded pdb=" O ASN B 678 " pdb=" OD1 ASN B 678 " model vdw 2.495 3.040 nonbonded pdb=" N ASP B 593 " pdb=" OD1 ASP B 593 " model vdw 2.510 3.120 nonbonded pdb=" O ASP C 172 " pdb=" OD1 ASP C 172 " model vdw 2.511 3.040 ... (remaining 125581 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: 4.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.260 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16962 Z= 0.211 Angle : 0.650 7.858 22987 Z= 0.355 Chirality : 0.047 0.216 2418 Planarity : 0.005 0.096 2986 Dihedral : 18.153 89.700 6166 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.39 % Favored : 89.36 % Rotamer: Outliers : 4.94 % Allowed : 28.70 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.18), residues: 2030 helix: -0.45 (0.27), residues: 387 sheet: -1.05 (0.27), residues: 406 loop : -2.37 (0.16), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 523 TYR 0.018 0.002 TYR A 727 PHE 0.034 0.002 PHE C 775 TRP 0.027 0.002 TRP C 651 HIS 0.007 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00490 (16962) covalent geometry : angle 0.64988 (22987) hydrogen bonds : bond 0.24642 ( 420) hydrogen bonds : angle 7.86431 ( 1119) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 345 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 71 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8027 (t) REVERT: C 105 LYS cc_start: 0.8378 (mtpp) cc_final: 0.8148 (mtpt) REVERT: C 110 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6654 (tp30) REVERT: C 161 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.8148 (t70) REVERT: C 427 LYS cc_start: 0.4078 (OUTLIER) cc_final: 0.3560 (ptmm) REVERT: C 610 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.6929 (mp10) REVERT: C 620 ILE cc_start: 0.8492 (tp) cc_final: 0.8157 (tp) REVERT: C 687 LYS cc_start: 0.7910 (mmtp) cc_final: 0.7684 (mttt) REVERT: C 699 THR cc_start: 0.7530 (OUTLIER) cc_final: 0.7330 (p) REVERT: A 92 ARG cc_start: 0.8142 (ttm110) cc_final: 0.7665 (ttp-110) REVERT: A 230 TYR cc_start: 0.7230 (OUTLIER) cc_final: 0.6268 (p90) REVERT: A 241 ARG cc_start: 0.7137 (mtm110) cc_final: 0.6738 (tpp80) REVERT: A 267 PHE cc_start: 0.8794 (t80) cc_final: 0.8514 (t80) REVERT: A 324 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7837 (tppt) REVERT: A 348 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8093 (mt) REVERT: A 357 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8545 (p) REVERT: A 594 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7970 (mtmt) REVERT: A 611 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7594 (ttpp) REVERT: A 628 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7773 (tptt) REVERT: A 682 TYR cc_start: 0.8679 (m-80) cc_final: 0.8402 (m-80) REVERT: A 735 SER cc_start: 0.8932 (t) cc_final: 0.8554 (m) REVERT: B 98 MET cc_start: 0.5221 (mtp) cc_final: 0.4573 (mpp) REVERT: B 135 GLU cc_start: 0.6746 (pm20) cc_final: 0.6134 (mp0) REVERT: B 147 PRO cc_start: 0.7345 (Cg_endo) cc_final: 0.7012 (Cg_exo) REVERT: B 173 LYS cc_start: 0.7269 (pptt) cc_final: 0.6950 (pttm) REVERT: B 207 ASP cc_start: 0.8129 (p0) cc_final: 0.7858 (m-30) REVERT: B 280 LYS cc_start: 0.7236 (ttpt) cc_final: 0.7024 (ttpt) REVERT: B 469 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7310 (mm-30) REVERT: B 506 ASN cc_start: 0.6944 (p0) cc_final: 0.6464 (t0) REVERT: B 535 PHE cc_start: 0.8019 (t80) cc_final: 0.7717 (m-80) outliers start: 90 outliers final: 31 residues processed: 408 average time/residue: 0.1391 time to fit residues: 84.4944 Evaluate side-chains 266 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 610 GLN Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 690 ASN Chi-restraints excluded: chain C residue 699 THR Chi-restraints excluded: chain C residue 797 MET Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 230 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 703 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 400 HIS C 473 GLN C 661 GLN A 588 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 720 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.173814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130200 restraints weight = 18970.438| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.30 r_work: 0.3364 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16962 Z= 0.138 Angle : 0.592 9.432 22987 Z= 0.311 Chirality : 0.045 0.241 2418 Planarity : 0.005 0.073 2986 Dihedral : 7.229 59.511 2321 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.97 % Favored : 90.79 % Rotamer: Outliers : 5.27 % Allowed : 24.53 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.18), residues: 2030 helix: -0.22 (0.27), residues: 405 sheet: -0.88 (0.25), residues: 437 loop : -2.18 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 66 TYR 0.022 0.001 TYR C 125 PHE 0.017 0.001 PHE B 195 TRP 0.011 0.001 TRP A 425 HIS 0.005 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00328 (16962) covalent geometry : angle 0.59233 (22987) hydrogen bonds : bond 0.04235 ( 420) hydrogen bonds : angle 5.38492 ( 1119) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 217 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 105 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8180 (mmmt) REVERT: C 110 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6534 (tp30) REVERT: C 199 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: C 427 LYS cc_start: 0.4059 (OUTLIER) cc_final: 0.3482 (ptmm) REVERT: C 451 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7767 (mm-30) REVERT: C 610 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.6753 (mp10) REVERT: C 620 ILE cc_start: 0.8311 (tp) cc_final: 0.7751 (tp) REVERT: C 685 PHE cc_start: 0.8545 (m-10) cc_final: 0.8311 (m-10) REVERT: C 692 VAL cc_start: 0.7637 (t) cc_final: 0.7416 (t) REVERT: C 709 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7563 (ptmm) REVERT: A 92 ARG cc_start: 0.8196 (ttm110) cc_final: 0.7687 (ttp-110) REVERT: A 116 TYR cc_start: 0.8763 (m-80) cc_final: 0.8522 (m-80) REVERT: A 230 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6215 (p90) REVERT: A 241 ARG cc_start: 0.7362 (mtm110) cc_final: 0.6929 (tpp80) REVERT: A 348 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8401 (mt) REVERT: A 353 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8375 (mtt180) REVERT: A 611 LYS cc_start: 0.8216 (tttp) cc_final: 0.7897 (ttpp) REVERT: A 628 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7791 (tptt) REVERT: A 716 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: A 735 SER cc_start: 0.8647 (t) cc_final: 0.8129 (m) REVERT: B 98 MET cc_start: 0.5060 (mtp) cc_final: 0.4447 (mpp) REVERT: B 135 GLU cc_start: 0.6940 (pm20) cc_final: 0.6271 (mp0) REVERT: B 207 ASP cc_start: 0.8016 (p0) cc_final: 0.7522 (m-30) REVERT: B 359 MET cc_start: 0.6541 (mmm) cc_final: 0.6034 (mmt) REVERT: B 469 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7126 (mm-30) REVERT: B 535 PHE cc_start: 0.7898 (t80) cc_final: 0.7564 (m-80) outliers start: 96 outliers final: 57 residues processed: 291 average time/residue: 0.1377 time to fit residues: 60.2992 Evaluate side-chains 258 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 191 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 514 TRP Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 610 GLN Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 661 GLN Chi-restraints excluded: chain C residue 709 LYS Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 716 PHE Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 230 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 703 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 47 optimal weight: 4.9990 chunk 152 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 114 optimal weight: 0.2980 chunk 66 optimal weight: 0.2980 chunk 60 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 HIS C 161 HIS C 527 ASN C 661 GLN A 234 ASN B 81 ASN B 85 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.167666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122423 restraints weight = 20102.099| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.32 r_work: 0.3238 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16962 Z= 0.228 Angle : 0.657 9.201 22987 Z= 0.344 Chirality : 0.048 0.195 2418 Planarity : 0.005 0.072 2986 Dihedral : 6.799 56.336 2284 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.05 % Favored : 89.70 % Rotamer: Outliers : 5.43 % Allowed : 23.82 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.18), residues: 2030 helix: -0.28 (0.27), residues: 407 sheet: -0.85 (0.25), residues: 433 loop : -2.14 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 66 TYR 0.018 0.002 TYR C 125 PHE 0.021 0.002 PHE C 356 TRP 0.013 0.001 TRP B 527 HIS 0.006 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00561 (16962) covalent geometry : angle 0.65657 (22987) hydrogen bonds : bond 0.05557 ( 420) hydrogen bonds : angle 5.27454 ( 1119) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 194 time to evaluate : 0.693 Fit side-chains REVERT: C 105 LYS cc_start: 0.8648 (mtpp) cc_final: 0.8186 (mtpt) REVERT: C 110 GLU cc_start: 0.7008 (mp0) cc_final: 0.6425 (tp30) REVERT: C 312 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6867 (mp) REVERT: C 427 LYS cc_start: 0.4269 (OUTLIER) cc_final: 0.3047 (ptmm) REVERT: C 620 ILE cc_start: 0.8263 (tp) cc_final: 0.7756 (tp) REVERT: C 647 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7652 (mtpt) REVERT: C 654 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7196 (tt) REVERT: C 709 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7100 (ptmm) REVERT: A 92 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7596 (ttp-110) REVERT: A 116 TYR cc_start: 0.8820 (m-80) cc_final: 0.8525 (m-80) REVERT: A 230 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.6548 (p90) REVERT: A 241 ARG cc_start: 0.7416 (mtm110) cc_final: 0.7050 (mtm-85) REVERT: A 353 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8441 (mtt180) REVERT: A 534 ASP cc_start: 0.8859 (t0) cc_final: 0.8648 (t0) REVERT: A 611 LYS cc_start: 0.8070 (tttp) cc_final: 0.7699 (ttpp) REVERT: A 628 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7715 (tptt) REVERT: A 682 TYR cc_start: 0.8700 (m-80) cc_final: 0.8196 (m-80) REVERT: A 683 ARG cc_start: 0.8233 (ttp80) cc_final: 0.8011 (ttp-110) REVERT: A 735 SER cc_start: 0.8608 (t) cc_final: 0.8048 (m) REVERT: B 135 GLU cc_start: 0.6853 (pm20) cc_final: 0.6225 (mp0) REVERT: B 187 ARG cc_start: 0.7446 (tpt90) cc_final: 0.6677 (tpp-160) REVERT: B 247 TYR cc_start: 0.8371 (m-80) cc_final: 0.8125 (m-80) REVERT: B 359 MET cc_start: 0.6507 (mmm) cc_final: 0.5509 (mmt) REVERT: B 469 GLU cc_start: 0.8014 (mt-10) cc_final: 0.6907 (mm-30) REVERT: B 535 PHE cc_start: 0.8036 (t80) cc_final: 0.7374 (m-80) outliers start: 99 outliers final: 56 residues processed: 272 average time/residue: 0.1380 time to fit residues: 56.4970 Evaluate side-chains 242 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 178 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 514 TRP Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 605 GLN Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 647 LYS Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 709 LYS Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 230 TYR Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 685 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 162 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 HIS A 226 ASN B 208 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.170647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125826 restraints weight = 19878.654| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.27 r_work: 0.3312 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16962 Z= 0.160 Angle : 0.592 10.776 22987 Z= 0.308 Chirality : 0.045 0.197 2418 Planarity : 0.004 0.058 2986 Dihedral : 6.285 56.049 2272 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.51 % Favored : 90.30 % Rotamer: Outliers : 5.32 % Allowed : 23.44 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.18), residues: 2030 helix: -0.15 (0.27), residues: 408 sheet: -0.83 (0.25), residues: 433 loop : -2.07 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 80 TYR 0.015 0.001 TYR B 231 PHE 0.020 0.001 PHE B 267 TRP 0.011 0.001 TRP A 642 HIS 0.005 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00391 (16962) covalent geometry : angle 0.59206 (22987) hydrogen bonds : bond 0.04238 ( 420) hydrogen bonds : angle 4.87621 ( 1119) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 194 time to evaluate : 0.648 Fit side-chains REVERT: C 37 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7365 (mp) REVERT: C 105 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8156 (mmmt) REVERT: C 110 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6324 (tp30) REVERT: C 280 ASP cc_start: 0.7674 (p0) cc_final: 0.7229 (p0) REVERT: C 312 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6944 (mt) REVERT: C 427 LYS cc_start: 0.4196 (OUTLIER) cc_final: 0.2904 (ptmm) REVERT: C 467 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7794 (ttm110) REVERT: C 595 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.5683 (pt0) REVERT: C 610 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.6636 (mp10) REVERT: C 620 ILE cc_start: 0.8257 (tp) cc_final: 0.7784 (tp) REVERT: C 647 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7671 (mtpt) REVERT: C 654 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7035 (tt) REVERT: A 92 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7495 (ttp-110) REVERT: A 116 TYR cc_start: 0.8810 (m-80) cc_final: 0.8448 (m-80) REVERT: A 230 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.6340 (p90) REVERT: A 241 ARG cc_start: 0.7528 (mtm110) cc_final: 0.7191 (mtm-85) REVERT: A 295 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8865 (pp) REVERT: A 353 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8398 (mtt180) REVERT: A 535 PHE cc_start: 0.8652 (m-10) cc_final: 0.8294 (t80) REVERT: A 563 MET cc_start: 0.9211 (ttm) cc_final: 0.8903 (ttt) REVERT: A 611 LYS cc_start: 0.8024 (tttp) cc_final: 0.7662 (ttpp) REVERT: A 628 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7752 (tptt) REVERT: A 682 TYR cc_start: 0.8747 (m-80) cc_final: 0.8331 (m-80) REVERT: A 683 ARG cc_start: 0.8247 (ttp80) cc_final: 0.8018 (ttp-110) REVERT: B 41 ASP cc_start: 0.6438 (OUTLIER) cc_final: 0.5907 (p0) REVERT: B 104 PHE cc_start: 0.6325 (m-80) cc_final: 0.6028 (m-80) REVERT: B 135 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6122 (mp0) REVERT: B 187 ARG cc_start: 0.7579 (tpt90) cc_final: 0.6811 (tpp-160) REVERT: B 228 LEU cc_start: 0.6945 (mm) cc_final: 0.6704 (mm) REVERT: B 247 TYR cc_start: 0.8347 (m-80) cc_final: 0.7781 (m-80) REVERT: B 359 MET cc_start: 0.6577 (mmm) cc_final: 0.5840 (mmt) REVERT: B 535 PHE cc_start: 0.8079 (t80) cc_final: 0.7426 (m-80) REVERT: B 710 MET cc_start: 0.8188 (mmm) cc_final: 0.7912 (mmm) outliers start: 97 outliers final: 62 residues processed: 275 average time/residue: 0.1369 time to fit residues: 56.5521 Evaluate side-chains 257 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 180 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 514 TRP Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 605 GLN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 GLN Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 647 LYS Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 685 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 163 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 HIS C 613 ASN A 432 GLN B 188 HIS ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.167037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.122203 restraints weight = 19972.995| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.24 r_work: 0.3242 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16962 Z= 0.249 Angle : 0.669 9.551 22987 Z= 0.349 Chirality : 0.048 0.183 2418 Planarity : 0.005 0.060 2986 Dihedral : 6.506 59.716 2270 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.69 % Favored : 89.11 % Rotamer: Outliers : 5.98 % Allowed : 23.00 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.18), residues: 2030 helix: -0.31 (0.26), residues: 414 sheet: -1.01 (0.25), residues: 427 loop : -2.16 (0.16), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 241 TYR 0.016 0.002 TYR C 125 PHE 0.020 0.002 PHE C 356 TRP 0.014 0.002 TRP A 642 HIS 0.006 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00615 (16962) covalent geometry : angle 0.66864 (22987) hydrogen bonds : bond 0.05464 ( 420) hydrogen bonds : angle 5.08374 ( 1119) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 190 time to evaluate : 0.611 Fit side-chains REVERT: C 37 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7585 (mp) REVERT: C 92 GLN cc_start: 0.6153 (OUTLIER) cc_final: 0.5533 (tp-100) REVERT: C 105 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8437 (mtpp) REVERT: C 110 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6546 (tp30) REVERT: C 280 ASP cc_start: 0.7849 (p0) cc_final: 0.7393 (p0) REVERT: C 312 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7115 (mt) REVERT: C 427 LYS cc_start: 0.4318 (OUTLIER) cc_final: 0.2767 (ptmm) REVERT: C 467 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7978 (ttm110) REVERT: C 595 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6074 (pt0) REVERT: C 610 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.6794 (mp10) REVERT: C 620 ILE cc_start: 0.8507 (tp) cc_final: 0.7999 (tp) REVERT: C 647 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7725 (mtmt) REVERT: C 709 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7750 (ptpt) REVERT: A 116 TYR cc_start: 0.8860 (m-80) cc_final: 0.8520 (m-80) REVERT: A 173 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8372 (pttm) REVERT: A 209 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8498 (mp) REVERT: A 230 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.6499 (p90) REVERT: A 241 ARG cc_start: 0.7633 (mtm110) cc_final: 0.7336 (mtm-85) REVERT: A 295 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8917 (pp) REVERT: A 353 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8600 (mtt180) REVERT: A 563 MET cc_start: 0.9172 (ttm) cc_final: 0.8862 (ttt) REVERT: A 611 LYS cc_start: 0.8282 (tttp) cc_final: 0.7972 (ttpp) REVERT: A 628 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7825 (tptt) REVERT: A 682 TYR cc_start: 0.8787 (m-80) cc_final: 0.8381 (m-80) REVERT: B 41 ASP cc_start: 0.6320 (OUTLIER) cc_final: 0.5960 (p0) REVERT: B 104 PHE cc_start: 0.6821 (m-80) cc_final: 0.6179 (m-80) REVERT: B 135 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6246 (mp0) REVERT: B 187 ARG cc_start: 0.7706 (tpt90) cc_final: 0.6969 (tpp-160) REVERT: B 359 MET cc_start: 0.6676 (mmm) cc_final: 0.5483 (mmm) REVERT: B 408 MET cc_start: 0.4282 (tpt) cc_final: 0.4022 (mtt) REVERT: B 535 PHE cc_start: 0.7971 (t80) cc_final: 0.7397 (m-80) REVERT: B 597 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6533 (mt-10) REVERT: B 710 MET cc_start: 0.8390 (mmm) cc_final: 0.8063 (mmm) outliers start: 109 outliers final: 75 residues processed: 279 average time/residue: 0.1322 time to fit residues: 55.9556 Evaluate side-chains 273 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 180 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 514 TRP Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 GLN Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 647 LYS Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 709 LYS Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 743 ASN Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 694 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 118 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 198 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 HIS C 613 ASN B 44 ASN B 188 HIS ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.171136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128335 restraints weight = 19866.523| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.37 r_work: 0.3319 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16962 Z= 0.121 Angle : 0.568 9.523 22987 Z= 0.294 Chirality : 0.044 0.172 2418 Planarity : 0.004 0.049 2986 Dihedral : 6.066 56.210 2268 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.11 % Favored : 90.69 % Rotamer: Outliers : 4.34 % Allowed : 25.19 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.18), residues: 2030 helix: -0.07 (0.26), residues: 416 sheet: -0.85 (0.25), residues: 431 loop : -2.03 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 80 TYR 0.010 0.001 TYR C 125 PHE 0.019 0.001 PHE C 775 TRP 0.010 0.001 TRP A 642 HIS 0.020 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00286 (16962) covalent geometry : angle 0.56757 (22987) hydrogen bonds : bond 0.03721 ( 420) hydrogen bonds : angle 4.70967 ( 1119) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 185 time to evaluate : 0.696 Fit side-chains REVERT: C 37 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7498 (mp) REVERT: C 92 GLN cc_start: 0.5991 (OUTLIER) cc_final: 0.5435 (tp-100) REVERT: C 105 LYS cc_start: 0.8660 (mtpp) cc_final: 0.7855 (mtpt) REVERT: C 110 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6406 (tp30) REVERT: C 312 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.7027 (mt) REVERT: C 427 LYS cc_start: 0.3983 (OUTLIER) cc_final: 0.2579 (ptmm) REVERT: C 595 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6188 (pt0) REVERT: C 610 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.6576 (mp10) REVERT: C 620 ILE cc_start: 0.8363 (tp) cc_final: 0.7865 (tp) REVERT: C 709 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7351 (ptmm) REVERT: A 92 ARG cc_start: 0.8218 (ttp-110) cc_final: 0.7998 (ttm110) REVERT: A 116 TYR cc_start: 0.8802 (m-80) cc_final: 0.8388 (m-80) REVERT: A 230 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.6564 (p90) REVERT: A 241 ARG cc_start: 0.7570 (mtm110) cc_final: 0.7276 (mtm-85) REVERT: A 295 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8868 (pp) REVERT: A 353 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8398 (mtt180) REVERT: A 563 MET cc_start: 0.9186 (ttm) cc_final: 0.8886 (ttt) REVERT: A 611 LYS cc_start: 0.8157 (tttp) cc_final: 0.7821 (ttpp) REVERT: A 628 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7816 (tptt) REVERT: A 682 TYR cc_start: 0.8712 (m-80) cc_final: 0.8310 (m-80) REVERT: B 104 PHE cc_start: 0.6913 (m-80) cc_final: 0.6383 (m-80) REVERT: B 135 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.5981 (mp0) REVERT: B 149 MET cc_start: 0.5105 (pmm) cc_final: 0.3131 (tpp) REVERT: B 187 ARG cc_start: 0.7579 (tpt90) cc_final: 0.7120 (tpp-160) REVERT: B 207 ASP cc_start: 0.7993 (p0) cc_final: 0.7260 (m-30) REVERT: B 240 HIS cc_start: 0.6373 (OUTLIER) cc_final: 0.5412 (t-90) REVERT: B 535 PHE cc_start: 0.7997 (t80) cc_final: 0.7431 (m-80) REVERT: B 710 MET cc_start: 0.8199 (mmm) cc_final: 0.7907 (mmm) outliers start: 79 outliers final: 52 residues processed: 248 average time/residue: 0.1340 time to fit residues: 50.4086 Evaluate side-chains 240 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 174 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 514 TRP Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 GLN Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 709 LYS Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 743 ASN Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 352 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 165 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 52 optimal weight: 0.0570 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 HIS C 613 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.164684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120018 restraints weight = 20093.321| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.23 r_work: 0.3226 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 16962 Z= 0.316 Angle : 0.727 10.269 22987 Z= 0.379 Chirality : 0.051 0.175 2418 Planarity : 0.005 0.059 2986 Dihedral : 6.564 56.930 2266 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.38 % Favored : 88.42 % Rotamer: Outliers : 6.20 % Allowed : 23.77 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.18), residues: 2030 helix: -0.30 (0.26), residues: 414 sheet: -1.09 (0.25), residues: 432 loop : -2.17 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 80 TYR 0.020 0.002 TYR C 125 PHE 0.026 0.002 PHE C 356 TRP 0.016 0.002 TRP A 642 HIS 0.007 0.002 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00781 (16962) covalent geometry : angle 0.72664 (22987) hydrogen bonds : bond 0.06242 ( 420) hydrogen bonds : angle 5.21377 ( 1119) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 170 time to evaluate : 0.599 Fit side-chains REVERT: C 37 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7577 (mp) REVERT: C 92 GLN cc_start: 0.6063 (OUTLIER) cc_final: 0.5449 (tp-100) REVERT: C 105 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8414 (mtpp) REVERT: C 110 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6548 (tt0) REVERT: C 195 ASP cc_start: 0.7631 (t70) cc_final: 0.6101 (p0) REVERT: C 467 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7974 (ttm110) REVERT: C 595 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6187 (pt0) REVERT: C 610 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.6915 (mp10) REVERT: C 620 ILE cc_start: 0.8488 (tp) cc_final: 0.8243 (tp) REVERT: C 709 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7789 (ptpt) REVERT: A 116 TYR cc_start: 0.8828 (m-80) cc_final: 0.8449 (m-80) REVERT: A 173 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8377 (pttm) REVERT: A 230 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.6379 (p90) REVERT: A 241 ARG cc_start: 0.7800 (mtm110) cc_final: 0.7454 (mtm-85) REVERT: A 295 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8970 (pp) REVERT: A 326 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: A 353 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8585 (mtt180) REVERT: A 563 MET cc_start: 0.9207 (ttm) cc_final: 0.8890 (ttp) REVERT: A 611 LYS cc_start: 0.8286 (tttp) cc_final: 0.7964 (ttpp) REVERT: A 628 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7841 (tptt) REVERT: A 682 TYR cc_start: 0.8774 (m-80) cc_final: 0.8398 (m-80) REVERT: B 41 ASP cc_start: 0.6142 (OUTLIER) cc_final: 0.5917 (p0) REVERT: B 91 LEU cc_start: 0.4110 (OUTLIER) cc_final: 0.3831 (mm) REVERT: B 104 PHE cc_start: 0.7194 (m-80) cc_final: 0.6901 (m-80) REVERT: B 135 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6223 (mp0) REVERT: B 187 ARG cc_start: 0.7685 (tpt90) cc_final: 0.7079 (tpp-160) REVERT: B 240 HIS cc_start: 0.6546 (OUTLIER) cc_final: 0.5579 (t-90) REVERT: B 535 PHE cc_start: 0.7914 (t80) cc_final: 0.7339 (m-80) REVERT: B 710 MET cc_start: 0.8463 (mmm) cc_final: 0.8058 (mmm) outliers start: 113 outliers final: 80 residues processed: 265 average time/residue: 0.1325 time to fit residues: 52.9721 Evaluate side-chains 259 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 162 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain C residue 514 TRP Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 GLN Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 709 LYS Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 743 ASN Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 694 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 130 optimal weight: 0.7980 chunk 160 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 77 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN A 506 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.170264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125773 restraints weight = 19892.290| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.26 r_work: 0.3319 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16962 Z= 0.121 Angle : 0.572 9.876 22987 Z= 0.295 Chirality : 0.044 0.168 2418 Planarity : 0.004 0.048 2986 Dihedral : 6.084 57.378 2266 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.26 % Favored : 90.54 % Rotamer: Outliers : 4.39 % Allowed : 25.52 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.18), residues: 2030 helix: -0.00 (0.27), residues: 415 sheet: -0.87 (0.26), residues: 420 loop : -2.05 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 80 TYR 0.017 0.001 TYR B 586 PHE 0.015 0.001 PHE C 775 TRP 0.011 0.001 TRP A 425 HIS 0.010 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00287 (16962) covalent geometry : angle 0.57185 (22987) hydrogen bonds : bond 0.03649 ( 420) hydrogen bonds : angle 4.71755 ( 1119) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 184 time to evaluate : 0.783 Fit side-chains REVERT: C 37 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7327 (mp) REVERT: C 92 GLN cc_start: 0.5842 (OUTLIER) cc_final: 0.5415 (tp-100) REVERT: C 105 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8376 (mtpp) REVERT: C 110 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6266 (tp30) REVERT: C 427 LYS cc_start: 0.3911 (OUTLIER) cc_final: 0.2238 (ptmm) REVERT: C 595 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6151 (pt0) REVERT: C 610 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.6433 (mp10) REVERT: C 620 ILE cc_start: 0.8206 (tp) cc_final: 0.7740 (tp) REVERT: C 709 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7178 (ptmm) REVERT: A 116 TYR cc_start: 0.8782 (m-80) cc_final: 0.8326 (m-80) REVERT: A 209 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8303 (mp) REVERT: A 230 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.6531 (p90) REVERT: A 241 ARG cc_start: 0.7650 (mtm110) cc_final: 0.7336 (mtm-85) REVERT: A 295 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8810 (pp) REVERT: A 353 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8201 (mtt180) REVERT: A 528 ASN cc_start: 0.8770 (p0) cc_final: 0.8465 (p0) REVERT: A 611 LYS cc_start: 0.8008 (tttp) cc_final: 0.7653 (ttpp) REVERT: A 628 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7755 (tptt) REVERT: A 682 TYR cc_start: 0.8691 (m-80) cc_final: 0.8296 (m-80) REVERT: B 91 LEU cc_start: 0.3694 (OUTLIER) cc_final: 0.3431 (mm) REVERT: B 104 PHE cc_start: 0.7279 (m-80) cc_final: 0.6988 (m-80) REVERT: B 135 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6129 (mp0) REVERT: B 149 MET cc_start: 0.4911 (pmm) cc_final: 0.3044 (tpp) REVERT: B 207 ASP cc_start: 0.7939 (p0) cc_final: 0.7193 (m-30) REVERT: B 535 PHE cc_start: 0.7836 (t80) cc_final: 0.7274 (m-80) REVERT: B 595 LYS cc_start: 0.6912 (tptp) cc_final: 0.6416 (tptm) REVERT: B 710 MET cc_start: 0.8127 (mmm) cc_final: 0.7784 (mmm) outliers start: 80 outliers final: 63 residues processed: 249 average time/residue: 0.1297 time to fit residues: 49.1300 Evaluate side-chains 256 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 179 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 514 TRP Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 GLN Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 709 LYS Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 743 ASN Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 694 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 183 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 HIS ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.168684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123583 restraints weight = 19918.206| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.20 r_work: 0.3310 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16962 Z= 0.162 Angle : 0.599 9.303 22987 Z= 0.310 Chirality : 0.045 0.179 2418 Planarity : 0.004 0.050 2986 Dihedral : 6.067 58.775 2266 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.25 % Favored : 89.56 % Rotamer: Outliers : 4.56 % Allowed : 25.14 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.18), residues: 2030 helix: 0.06 (0.27), residues: 414 sheet: -0.85 (0.26), residues: 421 loop : -2.02 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 80 TYR 0.014 0.001 TYR B 586 PHE 0.015 0.001 PHE C 775 TRP 0.011 0.001 TRP A 87 HIS 0.009 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00395 (16962) covalent geometry : angle 0.59861 (22987) hydrogen bonds : bond 0.04330 ( 420) hydrogen bonds : angle 4.74033 ( 1119) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 181 time to evaluate : 0.744 Fit side-chains REVERT: C 37 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7419 (mp) REVERT: C 92 GLN cc_start: 0.5997 (OUTLIER) cc_final: 0.5588 (tp-100) REVERT: C 105 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8420 (mtpp) REVERT: C 110 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6438 (tp30) REVERT: C 427 LYS cc_start: 0.4040 (OUTLIER) cc_final: 0.2362 (ptmm) REVERT: C 467 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7770 (ttm110) REVERT: C 595 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6273 (pt0) REVERT: C 610 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.6565 (mp10) REVERT: C 620 ILE cc_start: 0.8325 (tp) cc_final: 0.7831 (tp) REVERT: C 709 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7553 (ptpt) REVERT: A 116 TYR cc_start: 0.8800 (m-80) cc_final: 0.8342 (m-80) REVERT: A 230 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.6548 (p90) REVERT: A 241 ARG cc_start: 0.7706 (mtm110) cc_final: 0.7411 (mtm-85) REVERT: A 295 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8870 (pp) REVERT: A 353 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8407 (mtt180) REVERT: A 611 LYS cc_start: 0.8133 (tttp) cc_final: 0.7771 (ttpp) REVERT: A 628 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7776 (tptt) REVERT: A 682 TYR cc_start: 0.8702 (m-80) cc_final: 0.8319 (m-80) REVERT: B 104 PHE cc_start: 0.7466 (m-80) cc_final: 0.7188 (m-80) REVERT: B 135 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6057 (mp0) REVERT: B 149 MET cc_start: 0.4995 (pmm) cc_final: 0.3131 (tpp) REVERT: B 174 ASP cc_start: 0.7930 (t0) cc_final: 0.7647 (t0) REVERT: B 207 ASP cc_start: 0.7943 (p0) cc_final: 0.7185 (m-30) REVERT: B 535 PHE cc_start: 0.7817 (t80) cc_final: 0.7330 (m-80) REVERT: B 595 LYS cc_start: 0.7062 (tptp) cc_final: 0.6554 (tptm) REVERT: B 710 MET cc_start: 0.8210 (mmm) cc_final: 0.7870 (mmm) outliers start: 83 outliers final: 65 residues processed: 247 average time/residue: 0.1381 time to fit residues: 51.3593 Evaluate side-chains 255 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 177 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 514 TRP Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 GLN Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 709 LYS Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 743 ASN Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 694 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 85 optimal weight: 0.0370 chunk 20 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.167221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122551 restraints weight = 19906.596| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.21 r_work: 0.3279 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16962 Z= 0.213 Angle : 0.642 9.240 22987 Z= 0.333 Chirality : 0.047 0.196 2418 Planarity : 0.005 0.050 2986 Dihedral : 6.218 56.391 2266 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.44 % Favored : 89.36 % Rotamer: Outliers : 4.67 % Allowed : 25.25 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.18), residues: 2030 helix: -0.03 (0.27), residues: 413 sheet: -0.96 (0.26), residues: 422 loop : -2.04 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 92 TYR 0.015 0.002 TYR C 125 PHE 0.018 0.002 PHE C 356 TRP 0.012 0.001 TRP A 87 HIS 0.006 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00525 (16962) covalent geometry : angle 0.64238 (22987) hydrogen bonds : bond 0.04919 ( 420) hydrogen bonds : angle 4.88183 ( 1119) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 173 time to evaluate : 0.698 Fit side-chains REVERT: C 37 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7398 (mp) REVERT: C 67 ARG cc_start: 0.5964 (ptt180) cc_final: 0.5631 (ptt-90) REVERT: C 92 GLN cc_start: 0.5853 (OUTLIER) cc_final: 0.5460 (tp-100) REVERT: C 105 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8411 (mtpp) REVERT: C 110 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6389 (tp30) REVERT: C 467 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7814 (ttm110) REVERT: C 595 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6217 (pt0) REVERT: C 610 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.6517 (mp10) REVERT: C 620 ILE cc_start: 0.8324 (tp) cc_final: 0.7829 (tp) REVERT: C 709 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7600 (ptpt) REVERT: A 116 TYR cc_start: 0.8822 (m-80) cc_final: 0.8425 (m-80) REVERT: A 230 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.6607 (p90) REVERT: A 241 ARG cc_start: 0.7704 (mtm110) cc_final: 0.7378 (mtm-85) REVERT: A 295 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8855 (pp) REVERT: A 353 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8464 (mtt180) REVERT: A 611 LYS cc_start: 0.8057 (tttp) cc_final: 0.7705 (ttpp) REVERT: A 628 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7772 (tptt) REVERT: A 682 TYR cc_start: 0.8712 (m-80) cc_final: 0.8323 (m-80) REVERT: B 104 PHE cc_start: 0.7479 (m-80) cc_final: 0.7161 (m-80) REVERT: B 135 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6041 (mp0) REVERT: B 149 MET cc_start: 0.4895 (pmm) cc_final: 0.3065 (tpp) REVERT: B 535 PHE cc_start: 0.7902 (t80) cc_final: 0.7281 (m-80) REVERT: B 595 LYS cc_start: 0.6921 (tptp) cc_final: 0.6417 (tptm) REVERT: B 710 MET cc_start: 0.8312 (mmm) cc_final: 0.7920 (mmm) outliers start: 85 outliers final: 70 residues processed: 243 average time/residue: 0.1344 time to fit residues: 49.5940 Evaluate side-chains 255 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 173 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 514 TRP Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 610 GLN Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 709 LYS Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 743 ASN Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 694 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.170305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126046 restraints weight = 19804.674| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.24 r_work: 0.3316 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16962 Z= 0.125 Angle : 0.576 9.658 22987 Z= 0.298 Chirality : 0.044 0.188 2418 Planarity : 0.004 0.046 2986 Dihedral : 5.998 59.939 2266 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.61 % Favored : 90.25 % Rotamer: Outliers : 4.28 % Allowed : 25.52 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.18), residues: 2030 helix: 0.17 (0.27), residues: 412 sheet: -0.81 (0.26), residues: 421 loop : -1.96 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 80 TYR 0.015 0.001 TYR B 586 PHE 0.015 0.001 PHE C 775 TRP 0.010 0.001 TRP A 425 HIS 0.005 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00299 (16962) covalent geometry : angle 0.57593 (22987) hydrogen bonds : bond 0.03734 ( 420) hydrogen bonds : angle 4.64269 ( 1119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4704.57 seconds wall clock time: 81 minutes 6.07 seconds (4866.07 seconds total)