Starting phenix.real_space_refine on Tue Mar 3 22:29:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6og2_20050/03_2026/6og2_20050.cif Found real_map, /net/cci-nas-00/data/ceres_data/6og2_20050/03_2026/6og2_20050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6og2_20050/03_2026/6og2_20050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6og2_20050/03_2026/6og2_20050.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6og2_20050/03_2026/6og2_20050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6og2_20050/03_2026/6og2_20050.map" } resolution = 4.1 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= 0.004 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 30 5.16 5 C 5535 2.51 5 N 1608 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8847 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4426 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 20, 'TRANS': 537} Chain breaks: 3 Chain: "A" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4340 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 21, 'TRANS': 526} Chain breaks: 2 Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.98, per 1000 atoms: 0.22 Number of scatterers: 8847 At special positions: 0 Unit cell: (107.328, 121.776, 108.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 6 15.00 O 1668 8.00 N 1608 7.00 C 5535 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 324.6 milliseconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2056 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 45.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'F' and resid 169 through 174 removed outlier: 4.730A pdb=" N GLN F 174 " --> pdb=" O GLU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 194 removed outlier: 3.526A pdb=" N ILE F 187 " --> pdb=" O ARG F 183 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 191 " --> pdb=" O ILE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 221 removed outlier: 4.664A pdb=" N VAL F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN F 221 " --> pdb=" O GLU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 245 No H-bonds generated for 'chain 'F' and resid 242 through 245' Processing helix chain 'F' and resid 258 through 264 removed outlier: 4.964A pdb=" N VAL F 262 " --> pdb=" O ARG F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 306 removed outlier: 6.076A pdb=" N ALA F 302 " --> pdb=" O MET F 298 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU F 303 " --> pdb=" O LEU F 299 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ALA F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ARG F 305 " --> pdb=" O PRO F 301 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY F 306 " --> pdb=" O ALA F 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 298 through 306' Processing helix chain 'F' and resid 316 through 320 removed outlier: 3.680A pdb=" N ARG F 320 " --> pdb=" O LEU F 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 316 through 320' Processing helix chain 'F' and resid 342 through 353 removed outlier: 3.865A pdb=" N LEU F 350 " --> pdb=" O THR F 346 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY F 352 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU F 353 " --> pdb=" O ILE F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 376 removed outlier: 5.681A pdb=" N ILE F 370 " --> pdb=" O THR F 366 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL F 371 " --> pdb=" O ASP F 367 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA F 372 " --> pdb=" O PRO F 368 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA F 373 " --> pdb=" O ALA F 369 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 406 removed outlier: 4.341A pdb=" N ILE F 391 " --> pdb=" O PRO F 387 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU F 396 " --> pdb=" O ASP F 392 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA F 397 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE F 401 " --> pdb=" O ALA F 397 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG F 402 " --> pdb=" O ALA F 398 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N MET F 403 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLN F 404 " --> pdb=" O SER F 400 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE F 405 " --> pdb=" O ILE F 401 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP F 406 " --> pdb=" O ARG F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 545 removed outlier: 3.778A pdb=" N ARG F 542 " --> pdb=" O GLU F 538 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 552 removed outlier: 3.951A pdb=" N MET F 551 " --> pdb=" O PRO F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 559 Processing helix chain 'F' and resid 561 through 568 removed outlier: 3.989A pdb=" N GLU F 565 " --> pdb=" O ARG F 561 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU F 566 " --> pdb=" O MET F 562 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N HIS F 567 " --> pdb=" O GLU F 563 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N HIS F 568 " --> pdb=" O GLN F 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 561 through 568' Processing helix chain 'F' and resid 578 through 586 removed outlier: 4.086A pdb=" N ASN F 582 " --> pdb=" O ASP F 578 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ALA F 583 " --> pdb=" O ALA F 579 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE F 584 " --> pdb=" O VAL F 580 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG F 585 " --> pdb=" O SER F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 618 removed outlier: 5.018A pdb=" N LEU F 618 " --> pdb=" O LEU F 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 614 through 618' Processing helix chain 'F' and resid 640 through 646 removed outlier: 6.912A pdb=" N SER F 644 " --> pdb=" O LYS F 640 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ARG F 645 " --> pdb=" O HIS F 641 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU F 646 " --> pdb=" O SER F 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 640 through 646' Processing helix chain 'F' and resid 661 through 665 removed outlier: 4.506A pdb=" N ALA F 665 " --> pdb=" O TYR F 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 661 through 665' Processing helix chain 'F' and resid 686 through 691 removed outlier: 3.760A pdb=" N LEU F 690 " --> pdb=" O VAL F 686 " (cutoff:3.500A) Processing helix chain 'F' and resid 708 through 712 Processing helix chain 'F' and resid 722 through 728 removed outlier: 5.921A pdb=" N GLN F 726 " --> pdb=" O SER F 722 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLU F 727 " --> pdb=" O ASP F 723 " (cutoff:3.500A) removed outlier: 11.720A pdb=" N ARG F 728 " --> pdb=" O LEU F 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 722 through 728' Processing helix chain 'F' and resid 734 through 748 removed outlier: 7.194A pdb=" N LYS F 738 " --> pdb=" O TYR F 734 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N GLU F 739 " --> pdb=" O ALA F 735 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU F 740 " --> pdb=" O HIS F 736 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N VAL F 741 " --> pdb=" O MET F 737 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N LEU F 742 " --> pdb=" O LYS F 738 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLY F 743 " --> pdb=" O GLU F 739 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL F 744 " --> pdb=" O LEU F 740 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VAL F 745 " --> pdb=" O VAL F 741 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER F 746 " --> pdb=" O LEU F 742 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N HIS F 747 " --> pdb=" O GLY F 743 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASN F 748 " --> pdb=" O VAL F 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 734 through 748' Processing helix chain 'F' and resid 750 through 756 removed outlier: 4.169A pdb=" N ILE F 754 " --> pdb=" O ARG F 750 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG F 756 " --> pdb=" O GLU F 752 " (cutoff:3.500A) Processing helix chain 'F' and resid 769 through 775 removed outlier: 5.988A pdb=" N SER F 773 " --> pdb=" O GLN F 769 " (cutoff:3.500A) Processing helix chain 'F' and resid 779 through 787 removed outlier: 3.609A pdb=" N TYR F 783 " --> pdb=" O LEU F 779 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG F 785 " --> pdb=" O ARG F 781 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU F 786 " --> pdb=" O LEU F 782 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLU F 787 " --> pdb=" O TYR F 783 " (cutoff:3.500A) Processing helix chain 'F' and resid 792 through 805 removed outlier: 10.096A pdb=" N SER F 796 " --> pdb=" O GLU F 792 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N ASP F 797 " --> pdb=" O ILE F 793 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N GLU F 798 " --> pdb=" O HIS F 794 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA F 799 " --> pdb=" O ILE F 795 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU F 802 " --> pdb=" O GLU F 798 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU F 803 " --> pdb=" O ALA F 799 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER F 804 " --> pdb=" O LEU F 800 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLU F 805 " --> pdb=" O LYS F 801 " (cutoff:3.500A) Processing helix chain 'F' and resid 815 through 821 removed outlier: 3.530A pdb=" N ILE F 821 " --> pdb=" O LEU F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 826 through 833 removed outlier: 5.430A pdb=" N GLN F 832 " --> pdb=" O PRO F 828 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE F 833 " --> pdb=" O LEU F 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 removed outlier: 3.507A pdb=" N ARG A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 removed outlier: 4.583A pdb=" N GLN A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG A 196 " --> pdb=" O GLN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 225 removed outlier: 3.863A pdb=" N ILE A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN A 225 " --> pdb=" O GLN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'A' and resid 259 through 269 removed outlier: 3.776A pdb=" N ASN A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 5.123A pdb=" N ARG A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.914A pdb=" N THR A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 3.927A pdb=" N HIS A 361 " --> pdb=" O TYR A 357 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 362' Processing helix chain 'A' and resid 367 through 381 removed outlier: 3.892A pdb=" N VAL A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 407 removed outlier: 3.682A pdb=" N ALA A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE A 391 " --> pdb=" O PRO A 387 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 544 removed outlier: 3.648A pdb=" N ILE A 536 " --> pdb=" O THR A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 568 removed outlier: 3.561A pdb=" N LEU A 560 " --> pdb=" O ARG A 556 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLN A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 588 removed outlier: 7.123A pdb=" N ALA A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 622 removed outlier: 4.962A pdb=" N CYS A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 616 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 617 " --> pdb=" O GLU A 613 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 619 " --> pdb=" O CYS A 615 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 646 removed outlier: 6.248A pdb=" N SER A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG A 645 " --> pdb=" O HIS A 641 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU A 646 " --> pdb=" O SER A 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 640 through 646' Processing helix chain 'A' and resid 660 through 668 removed outlier: 3.851A pdb=" N GLU A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 682 removed outlier: 5.271A pdb=" N ALA A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 678 through 682' Processing helix chain 'A' and resid 688 through 696 removed outlier: 4.824A pdb=" N GLN A 692 " --> pdb=" O ASN A 688 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL A 693 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 728 removed outlier: 7.703A pdb=" N GLN A 726 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 722 through 728' Processing helix chain 'A' and resid 734 through 748 removed outlier: 4.568A pdb=" N LYS A 738 " --> pdb=" O TYR A 734 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU A 740 " --> pdb=" O HIS A 736 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A 741 " --> pdb=" O MET A 737 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 743 " --> pdb=" O GLU A 739 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 744 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N SER A 746 " --> pdb=" O LEU A 742 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASN A 748 " --> pdb=" O VAL A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 757 removed outlier: 3.829A pdb=" N ILE A 754 " --> pdb=" O ARG A 750 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN A 755 " --> pdb=" O PRO A 751 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ARG A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE A 757 " --> pdb=" O PHE A 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 750 through 757' Processing helix chain 'A' and resid 767 through 776 removed outlier: 3.700A pdb=" N ILE A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA A 772 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER A 773 " --> pdb=" O GLN A 769 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE A 774 " --> pdb=" O HIS A 770 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 785 Processing helix chain 'A' and resid 792 through 795 No H-bonds generated for 'chain 'A' and resid 792 through 795' Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.425A pdb=" N GLU A 805 " --> pdb=" O LYS A 801 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 801 through 805' Processing helix chain 'A' and resid 817 through 821 removed outlier: 5.340A pdb=" N ILE A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 817 through 821' Processing helix chain 'A' and resid 825 through 833 removed outlier: 4.327A pdb=" N ALA A 830 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN A 831 " --> pdb=" O ASN A 827 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLN A 832 " --> pdb=" O PRO A 828 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE A 833 " --> pdb=" O LEU A 829 " (cutoff:3.500A) 112 hydrogen bonds defined for protein. 336 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: 1.09 Time building geometry restraints manager: 0.83 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: 3029 1.34 - 1.46: 1555 1.46 - 1.58: 4330 1.58 - 1.70: 9 1.70 - 1.82: 56 Bond restraints: 8979 Sorted by residual: bond pdb=" CB ILE F 825 " pdb=" CG2 ILE F 825 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.82e+00 bond pdb=" CB GLU F 254 " pdb=" CG GLU F 254 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.75e+00 bond pdb=" C GLU F 207 " pdb=" N PRO F 208 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.41e+00 bond pdb=" CB ASN A 200 " pdb=" CG ASN A 200 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.37e+00 bond pdb=" CB THR A 700 " pdb=" CG2 THR A 700 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.35e+00 ... (remaining 8974 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 11339 1.98 - 3.96: 622 3.96 - 5.94: 112 5.94 - 7.92: 43 7.92 - 9.90: 7 Bond angle restraints: 12123 Sorted by residual: angle pdb=" N ILE A 793 " pdb=" CA ILE A 793 " pdb=" C ILE A 793 " ideal model delta sigma weight residual 111.88 104.51 7.37 1.06e+00 8.90e-01 4.83e+01 angle pdb=" N PHE A 601 " pdb=" CA PHE A 601 " pdb=" C PHE A 601 " ideal model delta sigma weight residual 108.34 114.40 -6.06 1.31e+00 5.83e-01 2.14e+01 angle pdb=" N VAL F 745 " pdb=" CA VAL F 745 " pdb=" C VAL F 745 " ideal model delta sigma weight residual 112.12 108.45 3.67 8.40e-01 1.42e+00 1.91e+01 angle pdb=" N GLY F 730 " pdb=" CA GLY F 730 " pdb=" C GLY F 730 " ideal model delta sigma weight residual 113.18 123.08 -9.90 2.37e+00 1.78e-01 1.74e+01 angle pdb=" N THR F 712 " pdb=" CA THR F 712 " pdb=" C THR F 712 " ideal model delta sigma weight residual 109.94 103.45 6.49 1.57e+00 4.06e-01 1.71e+01 ... (remaining 12118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.58: 5217 29.58 - 59.16: 279 59.16 - 88.75: 28 88.75 - 118.33: 1 118.33 - 147.91: 2 Dihedral angle restraints: 5527 sinusoidal: 2344 harmonic: 3183 Sorted by residual: dihedral pdb=" O2A ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PA ADP A 901 " pdb=" PB ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 87.91 -147.91 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 72.36 -132.37 1 2.00e+01 2.50e-03 4.02e+01 dihedral pdb=" CA TYR F 783 " pdb=" C TYR F 783 " pdb=" N LYS F 784 " pdb=" CA LYS F 784 " ideal model delta harmonic sigma weight residual 180.00 150.63 29.37 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 5524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1024 0.063 - 0.127: 282 0.127 - 0.190: 54 0.190 - 0.253: 9 0.253 - 0.316: 3 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CB ILE F 166 " pdb=" CA ILE F 166 " pdb=" CG1 ILE F 166 " pdb=" CG2 ILE F 166 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB VAL A 577 " pdb=" CA VAL A 577 " pdb=" CG1 VAL A 577 " pdb=" CG2 VAL A 577 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ASN F 827 " pdb=" N ASN F 827 " pdb=" C ASN F 827 " pdb=" CB ASN F 827 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1369 not shown) Planarity restraints: 1581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 340 " 0.051 5.00e-02 4.00e+02 7.75e-02 9.60e+00 pdb=" N PRO A 341 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 683 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO F 684 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO F 684 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 684 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 300 " 0.047 5.00e-02 4.00e+02 7.07e-02 8.00e+00 pdb=" N PRO A 301 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " 0.040 5.00e-02 4.00e+02 ... (remaining 1578 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 965 2.75 - 3.29: 8069 3.29 - 3.82: 14471 3.82 - 4.36: 17175 4.36 - 4.90: 27750 Nonbonded interactions: 68430 Sorted by model distance: nonbonded pdb=" O LEU F 724 " pdb=" CG1 ILE F 725 " model vdw 2.211 3.440 nonbonded pdb=" OD1 ASP A 167 " pdb=" OG1 THR A 169 " model vdw 2.259 3.040 nonbonded pdb=" CD2 LEU F 802 " pdb=" CD1 LEU F 803 " model vdw 2.266 3.880 nonbonded pdb=" O PRO F 765 " pdb=" O LEU F 766 " model vdw 2.278 3.040 nonbonded pdb=" OE1 GLN F 726 " pdb=" OH TYR F 808 " model vdw 2.287 3.040 ... (remaining 68425 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 161 through 648 or resid 661 through 835 or resid 902)) selection = (chain 'F' and (resid 161 through 835 or resid 901)) } 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 group one per residue 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: 0.980 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.770 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.010 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5043 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8979 Z= 0.257 Angle : 1.113 9.900 12123 Z= 0.599 Chirality : 0.061 0.316 1372 Planarity : 0.007 0.077 1581 Dihedral : 17.539 147.910 3471 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.27 % Favored : 87.55 % Rotamer: Outliers : 0.43 % Allowed : 14.39 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.21 (0.19), residues: 1092 helix: -4.86 (0.13), residues: 292 sheet: -2.55 (0.50), residues: 78 loop : -3.13 (0.19), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 631 TYR 0.022 0.003 TYR A 653 PHE 0.020 0.003 PHE F 763 TRP 0.008 0.002 TRP F 543 HIS 0.007 0.002 HIS F 770 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 8979) covalent geometry : angle 1.11342 (12123) hydrogen bonds : bond 0.30979 ( 112) hydrogen bonds : angle 12.86247 ( 336) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 267 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 191 ILE cc_start: 0.8494 (pt) cc_final: 0.7785 (pt) REVERT: F 205 ILE cc_start: 0.7985 (mt) cc_final: 0.7778 (mt) REVERT: F 238 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7301 (mp) REVERT: F 278 ASP cc_start: 0.7920 (t0) cc_final: 0.7629 (t0) REVERT: F 279 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7531 (pt0) REVERT: F 401 ILE cc_start: 0.8335 (mt) cc_final: 0.8008 (tp) REVERT: F 712 THR cc_start: 0.6400 (m) cc_final: 0.6143 (p) REVERT: A 185 GLU cc_start: 0.7145 (pm20) cc_final: 0.5975 (mp0) REVERT: A 204 LEU cc_start: 0.7168 (mp) cc_final: 0.6764 (mt) REVERT: A 299 LEU cc_start: 0.7753 (mm) cc_final: 0.7516 (tp) REVERT: A 314 THR cc_start: 0.6811 (t) cc_final: 0.6586 (t) REVERT: A 564 GLN cc_start: 0.7585 (mp10) cc_final: 0.7129 (tt0) REVERT: A 656 TYR cc_start: 0.7192 (t80) cc_final: 0.6947 (t80) REVERT: A 713 VAL cc_start: 0.6134 (t) cc_final: 0.5831 (t) outliers start: 4 outliers final: 1 residues processed: 271 average time/residue: 0.1349 time to fit residues: 46.5791 Evaluate side-chains 158 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 711 ASN ** F 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 857 GLN A 174 GLN A 281 HIS A 361 HIS A 385 GLN A 711 ASN A 736 HIS A 770 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.210426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.180967 restraints weight = 23350.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.184559 restraints weight = 15781.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.187080 restraints weight = 11551.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.188889 restraints weight = 9069.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.190264 restraints weight = 7431.719| |-----------------------------------------------------------------------------| r_work (final): 0.4607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5749 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8979 Z= 0.133 Angle : 0.757 7.964 12123 Z= 0.378 Chirality : 0.047 0.175 1372 Planarity : 0.006 0.062 1581 Dihedral : 9.167 144.586 1256 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.21), residues: 1092 helix: -3.93 (0.18), residues: 336 sheet: -2.07 (0.58), residues: 70 loop : -2.72 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 196 TYR 0.010 0.001 TYR F 319 PHE 0.018 0.001 PHE A 623 TRP 0.003 0.001 TRP F 543 HIS 0.006 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8979) covalent geometry : angle 0.75719 (12123) hydrogen bonds : bond 0.03934 ( 112) hydrogen bonds : angle 7.51953 ( 336) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 188 ARG cc_start: 0.7131 (mtm-85) cc_final: 0.6720 (mtp180) REVERT: F 399 SER cc_start: 0.7920 (t) cc_final: 0.7559 (p) REVERT: F 401 ILE cc_start: 0.8441 (mt) cc_final: 0.8096 (tp) REVERT: F 629 MET cc_start: 0.6197 (pmm) cc_final: 0.5930 (pmm) REVERT: F 712 THR cc_start: 0.5886 (m) cc_final: 0.5584 (p) REVERT: A 179 PRO cc_start: 0.6038 (Cg_exo) cc_final: 0.5779 (Cg_endo) REVERT: A 275 LEU cc_start: 0.7847 (tt) cc_final: 0.7569 (tt) REVERT: A 310 CYS cc_start: 0.6048 (t) cc_final: 0.5497 (p) REVERT: A 353 LEU cc_start: 0.8355 (tp) cc_final: 0.8040 (tp) REVERT: A 634 MET cc_start: 0.7415 (mmm) cc_final: 0.6759 (mmp) REVERT: A 646 LEU cc_start: 0.7524 (pt) cc_final: 0.7217 (mp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1320 time to fit residues: 33.4549 Evaluate side-chains 139 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 96 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 93 optimal weight: 0.0980 chunk 48 optimal weight: 0.0570 chunk 92 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 106 optimal weight: 0.0170 chunk 107 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 0.0980 chunk 1 optimal weight: 0.9980 overall best weight: 0.1736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 264 ASN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 776 GLN A 269 GLN A 595 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.207954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.178962 restraints weight = 23821.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.182074 restraints weight = 16377.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.184535 restraints weight = 12296.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.185930 restraints weight = 9811.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.187372 restraints weight = 8320.789| |-----------------------------------------------------------------------------| r_work (final): 0.4596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8979 Z= 0.118 Angle : 0.706 7.263 12123 Z= 0.350 Chirality : 0.046 0.175 1372 Planarity : 0.005 0.047 1581 Dihedral : 8.594 141.614 1256 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.21 % Allowed : 3.62 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.11 (0.22), residues: 1092 helix: -3.43 (0.21), residues: 354 sheet: -1.71 (0.57), residues: 81 loop : -2.53 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 351 TYR 0.015 0.001 TYR F 319 PHE 0.010 0.001 PHE A 276 TRP 0.003 0.001 TRP F 543 HIS 0.007 0.001 HIS F 770 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8979) covalent geometry : angle 0.70567 (12123) hydrogen bonds : bond 0.03278 ( 112) hydrogen bonds : angle 6.73874 ( 336) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 188 ARG cc_start: 0.7196 (mtm-85) cc_final: 0.6851 (mtp180) REVERT: F 399 SER cc_start: 0.8218 (t) cc_final: 0.7866 (p) REVERT: F 401 ILE cc_start: 0.8404 (mt) cc_final: 0.8136 (mm) REVERT: F 528 ARG cc_start: 0.5426 (tpm170) cc_final: 0.3207 (mpp-170) REVERT: F 622 MET cc_start: 0.3607 (tpt) cc_final: 0.2162 (mmm) REVERT: F 712 THR cc_start: 0.5951 (m) cc_final: 0.5722 (p) REVERT: F 716 MET cc_start: 0.6194 (ptm) cc_final: 0.5598 (ppp) REVERT: A 177 LEU cc_start: 0.8115 (mt) cc_final: 0.7783 (mt) REVERT: A 179 PRO cc_start: 0.5751 (Cg_exo) cc_final: 0.5445 (Cg_endo) REVERT: A 310 CYS cc_start: 0.5810 (t) cc_final: 0.5081 (p) REVERT: A 353 LEU cc_start: 0.8390 (tp) cc_final: 0.8152 (tp) REVERT: A 393 LEU cc_start: 0.9369 (tp) cc_final: 0.9163 (tp) REVERT: A 801 LYS cc_start: 0.7355 (mmpt) cc_final: 0.6796 (ttpt) outliers start: 2 outliers final: 0 residues processed: 180 average time/residue: 0.1214 time to fit residues: 28.4323 Evaluate side-chains 128 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 0.0060 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 364 GLN ** F 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN A 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.206429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.177610 restraints weight = 24255.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.180224 restraints weight = 17063.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.181373 restraints weight = 13101.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.182353 restraints weight = 11087.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.182537 restraints weight = 10343.496| |-----------------------------------------------------------------------------| r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8979 Z= 0.122 Angle : 0.686 7.015 12123 Z= 0.340 Chirality : 0.045 0.171 1372 Planarity : 0.004 0.040 1581 Dihedral : 8.229 138.253 1256 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.11 % Allowed : 4.69 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.23), residues: 1092 helix: -3.01 (0.22), residues: 374 sheet: -1.44 (0.61), residues: 75 loop : -2.41 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 781 TYR 0.015 0.001 TYR F 319 PHE 0.011 0.001 PHE F 763 TRP 0.005 0.001 TRP F 543 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8979) covalent geometry : angle 0.68564 (12123) hydrogen bonds : bond 0.02839 ( 112) hydrogen bonds : angle 6.04110 ( 336) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 188 ARG cc_start: 0.7123 (mtm-85) cc_final: 0.6908 (mtp180) REVERT: F 399 SER cc_start: 0.8507 (t) cc_final: 0.8165 (p) REVERT: F 401 ILE cc_start: 0.8377 (mt) cc_final: 0.8051 (mm) REVERT: F 528 ARG cc_start: 0.5872 (tpm170) cc_final: 0.3673 (mpp-170) REVERT: F 622 MET cc_start: 0.3640 (tpt) cc_final: 0.2566 (mmm) REVERT: F 629 MET cc_start: 0.6637 (pmm) cc_final: 0.6332 (pmm) REVERT: F 716 MET cc_start: 0.6301 (ptm) cc_final: 0.5840 (ppp) REVERT: A 179 PRO cc_start: 0.6224 (Cg_exo) cc_final: 0.5430 (Cg_endo) REVERT: A 315 THR cc_start: 0.7885 (p) cc_final: 0.7681 (p) REVERT: A 713 VAL cc_start: 0.7084 (t) cc_final: 0.5828 (t) REVERT: A 801 LYS cc_start: 0.7552 (mmpt) cc_final: 0.6943 (ttpt) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.1069 time to fit residues: 24.9069 Evaluate side-chains 132 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 20 optimal weight: 7.9990 chunk 102 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN ** F 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 776 GLN F 857 GLN A 309 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.204306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.173423 restraints weight = 23789.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.176781 restraints weight = 16387.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.179047 restraints weight = 12184.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.180932 restraints weight = 9798.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.182088 restraints weight = 8210.601| |-----------------------------------------------------------------------------| r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.6219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8979 Z= 0.124 Angle : 0.679 6.923 12123 Z= 0.337 Chirality : 0.046 0.175 1372 Planarity : 0.004 0.053 1581 Dihedral : 8.156 134.468 1256 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.23), residues: 1092 helix: -2.91 (0.23), residues: 371 sheet: -1.69 (0.58), residues: 80 loop : -2.17 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 645 TYR 0.010 0.001 TYR F 783 PHE 0.012 0.001 PHE F 763 TRP 0.007 0.001 TRP F 543 HIS 0.005 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8979) covalent geometry : angle 0.67878 (12123) hydrogen bonds : bond 0.03030 ( 112) hydrogen bonds : angle 6.07558 ( 336) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 196 ARG cc_start: 0.7478 (mtp180) cc_final: 0.7271 (mtp180) REVERT: A 310 CYS cc_start: 0.6409 (t) cc_final: 0.6190 (p) REVERT: A 315 THR cc_start: 0.8037 (p) cc_final: 0.7763 (p) REVERT: A 561 ARG cc_start: 0.7105 (ptt90) cc_final: 0.6635 (ppt90) REVERT: A 595 ASN cc_start: 0.7762 (t0) cc_final: 0.7311 (t0) REVERT: A 653 TYR cc_start: 0.5507 (t80) cc_final: 0.4920 (m-80) REVERT: A 713 VAL cc_start: 0.7423 (t) cc_final: 0.5979 (t) REVERT: A 801 LYS cc_start: 0.7594 (mmpt) cc_final: 0.7031 (ttpt) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1064 time to fit residues: 23.5140 Evaluate side-chains 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 0.0270 chunk 86 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 0.0570 chunk 82 optimal weight: 4.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN F 764 HIS F 769 GLN ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS A 711 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.205721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.173618 restraints weight = 23645.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.177281 restraints weight = 15776.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.179904 restraints weight = 11599.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.181645 restraints weight = 9154.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.182925 restraints weight = 7628.397| |-----------------------------------------------------------------------------| r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8979 Z= 0.122 Angle : 0.684 7.202 12123 Z= 0.338 Chirality : 0.046 0.177 1372 Planarity : 0.004 0.043 1581 Dihedral : 8.055 132.341 1256 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 0.11 % Allowed : 2.77 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.24), residues: 1092 helix: -2.75 (0.23), residues: 371 sheet: -1.72 (0.66), residues: 61 loop : -2.00 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 645 TYR 0.013 0.001 TYR F 734 PHE 0.013 0.001 PHE F 763 TRP 0.005 0.001 TRP F 543 HIS 0.007 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8979) covalent geometry : angle 0.68433 (12123) hydrogen bonds : bond 0.02688 ( 112) hydrogen bonds : angle 5.82588 ( 336) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 401 ILE cc_start: 0.8409 (mt) cc_final: 0.8083 (mm) REVERT: F 528 ARG cc_start: 0.5743 (tpm170) cc_final: 0.3575 (mpp-170) REVERT: F 629 MET cc_start: 0.6936 (pmm) cc_final: 0.6518 (pmm) REVERT: A 177 LEU cc_start: 0.8083 (mm) cc_final: 0.7844 (mm) REVERT: A 315 THR cc_start: 0.8063 (p) cc_final: 0.7775 (p) REVERT: A 353 LEU cc_start: 0.8340 (tp) cc_final: 0.8130 (tp) REVERT: A 561 ARG cc_start: 0.7370 (ptt90) cc_final: 0.6915 (ppt90) REVERT: A 595 ASN cc_start: 0.7783 (t0) cc_final: 0.7455 (t0) REVERT: A 653 TYR cc_start: 0.5607 (t80) cc_final: 0.4882 (m-80) REVERT: A 664 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6625 (tm-30) REVERT: A 713 VAL cc_start: 0.7739 (t) cc_final: 0.7059 (t) REVERT: A 801 LYS cc_start: 0.7588 (mmpt) cc_final: 0.7107 (ttpt) outliers start: 1 outliers final: 1 residues processed: 164 average time/residue: 0.0961 time to fit residues: 21.9942 Evaluate side-chains 133 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 4.9990 chunk 103 optimal weight: 0.0010 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 107 optimal weight: 0.3980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.205307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.173403 restraints weight = 23338.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.177169 restraints weight = 15545.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.179539 restraints weight = 11318.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.181542 restraints weight = 8930.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.182727 restraints weight = 7414.389| |-----------------------------------------------------------------------------| r_work (final): 0.4470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.7123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8979 Z= 0.114 Angle : 0.683 8.093 12123 Z= 0.335 Chirality : 0.046 0.200 1372 Planarity : 0.004 0.041 1581 Dihedral : 7.893 130.506 1256 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.24), residues: 1092 helix: -2.64 (0.23), residues: 374 sheet: -2.03 (0.61), residues: 70 loop : -1.91 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 550 TYR 0.009 0.001 TYR F 783 PHE 0.012 0.001 PHE A 276 TRP 0.006 0.001 TRP F 543 HIS 0.005 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8979) covalent geometry : angle 0.68349 (12123) hydrogen bonds : bond 0.02700 ( 112) hydrogen bonds : angle 5.96243 ( 336) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 629 MET cc_start: 0.6740 (pmm) cc_final: 0.6312 (pmm) REVERT: A 315 THR cc_start: 0.8072 (p) cc_final: 0.7830 (p) REVERT: A 353 LEU cc_start: 0.8343 (tp) cc_final: 0.8077 (tp) REVERT: A 394 ILE cc_start: 0.8647 (mm) cc_final: 0.8300 (mm) REVERT: A 561 ARG cc_start: 0.7374 (ptt90) cc_final: 0.6996 (ppt90) REVERT: A 595 ASN cc_start: 0.7633 (t0) cc_final: 0.7219 (t0) REVERT: A 664 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6675 (tm-30) REVERT: A 713 VAL cc_start: 0.7712 (t) cc_final: 0.6947 (t) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.0962 time to fit residues: 20.4286 Evaluate side-chains 115 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 8 optimal weight: 8.9990 chunk 103 optimal weight: 0.0050 chunk 35 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 37 optimal weight: 0.0060 chunk 21 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 0.3980 overall best weight: 0.4210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 269 GLN ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN A 404 GLN A 711 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.200123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.168445 restraints weight = 23970.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.171888 restraints weight = 16097.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.174323 restraints weight = 11898.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.176073 restraints weight = 9410.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.177075 restraints weight = 7938.706| |-----------------------------------------------------------------------------| r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.7477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8979 Z= 0.115 Angle : 0.693 8.722 12123 Z= 0.341 Chirality : 0.046 0.167 1372 Planarity : 0.004 0.038 1581 Dihedral : 7.734 129.396 1256 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.11 % Allowed : 1.07 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.24), residues: 1092 helix: -2.55 (0.24), residues: 366 sheet: -2.17 (0.60), residues: 70 loop : -1.83 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 332 TYR 0.008 0.001 TYR F 808 PHE 0.012 0.001 PHE F 763 TRP 0.005 0.001 TRP F 543 HIS 0.003 0.001 HIS F 770 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8979) covalent geometry : angle 0.69266 (12123) hydrogen bonds : bond 0.02780 ( 112) hydrogen bonds : angle 5.80812 ( 336) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 217 GLU cc_start: 0.9254 (pm20) cc_final: 0.9022 (pm20) REVERT: F 401 ILE cc_start: 0.8391 (mt) cc_final: 0.8065 (mm) REVERT: F 629 MET cc_start: 0.6769 (pmm) cc_final: 0.6382 (pmm) REVERT: A 279 GLU cc_start: 0.6636 (tp30) cc_final: 0.6372 (tp30) REVERT: A 315 THR cc_start: 0.8085 (p) cc_final: 0.7822 (p) REVERT: A 394 ILE cc_start: 0.8573 (mm) cc_final: 0.8313 (mm) REVERT: A 561 ARG cc_start: 0.7328 (ptt90) cc_final: 0.7029 (ppt90) REVERT: A 595 ASN cc_start: 0.7688 (t0) cc_final: 0.7449 (t0) REVERT: A 664 GLU cc_start: 0.6808 (tm-30) cc_final: 0.6585 (tm-30) REVERT: A 713 VAL cc_start: 0.7759 (t) cc_final: 0.6986 (t) outliers start: 1 outliers final: 1 residues processed: 150 average time/residue: 0.0961 time to fit residues: 19.9229 Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 0.0570 chunk 37 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 89 optimal weight: 0.0670 chunk 66 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 44 optimal weight: 0.0670 chunk 54 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN F 769 GLN ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN A 297 ASN A 641 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.205000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.173898 restraints weight = 23479.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.177228 restraints weight = 15751.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.179827 restraints weight = 11615.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.181204 restraints weight = 9121.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.182794 restraints weight = 7740.686| |-----------------------------------------------------------------------------| r_work (final): 0.4459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.7769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8979 Z= 0.110 Angle : 0.676 7.217 12123 Z= 0.330 Chirality : 0.046 0.162 1372 Planarity : 0.004 0.038 1581 Dihedral : 7.641 127.487 1256 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.24), residues: 1092 helix: -2.54 (0.24), residues: 366 sheet: -2.11 (0.60), residues: 68 loop : -1.79 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 550 TYR 0.010 0.001 TYR F 319 PHE 0.012 0.001 PHE F 763 TRP 0.006 0.002 TRP F 543 HIS 0.007 0.001 HIS F 281 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8979) covalent geometry : angle 0.67636 (12123) hydrogen bonds : bond 0.02702 ( 112) hydrogen bonds : angle 5.85171 ( 336) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 401 ILE cc_start: 0.8476 (mt) cc_final: 0.8140 (mm) REVERT: F 629 MET cc_start: 0.6689 (pmm) cc_final: 0.6304 (pmm) REVERT: A 273 VAL cc_start: 0.9321 (m) cc_final: 0.9079 (t) REVERT: A 353 LEU cc_start: 0.8218 (tp) cc_final: 0.7935 (tp) REVERT: A 394 ILE cc_start: 0.8608 (mm) cc_final: 0.8350 (mm) REVERT: A 653 TYR cc_start: 0.5888 (t80) cc_final: 0.4709 (m-80) REVERT: A 664 GLU cc_start: 0.6757 (tm-30) cc_final: 0.6502 (tm-30) REVERT: A 713 VAL cc_start: 0.7460 (t) cc_final: 0.6896 (t) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.0980 time to fit residues: 20.8861 Evaluate side-chains 118 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 63 optimal weight: 4.9990 chunk 97 optimal weight: 0.0970 chunk 82 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.0000 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 0.0060 overall best weight: 0.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN A 711 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.206121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.175309 restraints weight = 23718.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.178814 restraints weight = 15897.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.181202 restraints weight = 11623.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.183085 restraints weight = 9199.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.184054 restraints weight = 7689.257| |-----------------------------------------------------------------------------| r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.7952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8979 Z= 0.115 Angle : 0.716 7.405 12123 Z= 0.349 Chirality : 0.047 0.187 1372 Planarity : 0.004 0.039 1581 Dihedral : 7.423 123.119 1256 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.11 % Allowed : 0.21 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.25), residues: 1092 helix: -2.46 (0.24), residues: 381 sheet: -2.27 (0.60), residues: 68 loop : -1.62 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 550 TYR 0.009 0.001 TYR F 319 PHE 0.012 0.001 PHE F 763 TRP 0.004 0.001 TRP F 543 HIS 0.013 0.001 HIS F 770 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8979) covalent geometry : angle 0.71572 (12123) hydrogen bonds : bond 0.02780 ( 112) hydrogen bonds : angle 5.68665 ( 336) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 401 ILE cc_start: 0.8406 (mt) cc_final: 0.8067 (mm) REVERT: F 629 MET cc_start: 0.6672 (pmm) cc_final: 0.6241 (pmm) REVERT: A 394 ILE cc_start: 0.8659 (mm) cc_final: 0.8371 (mm) REVERT: A 664 GLU cc_start: 0.6694 (tm-30) cc_final: 0.6489 (tm-30) REVERT: A 713 VAL cc_start: 0.7613 (t) cc_final: 0.6973 (t) outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.0960 time to fit residues: 20.7996 Evaluate side-chains 120 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 105 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 0.0870 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.202089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.170215 restraints weight = 23628.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.173672 restraints weight = 15996.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.176003 restraints weight = 11780.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.177852 restraints weight = 9387.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.179139 restraints weight = 7888.579| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.8326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8979 Z= 0.126 Angle : 0.720 8.090 12123 Z= 0.353 Chirality : 0.047 0.158 1372 Planarity : 0.004 0.038 1581 Dihedral : 7.435 123.599 1256 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.25), residues: 1092 helix: -2.45 (0.24), residues: 376 sheet: -2.13 (0.62), residues: 68 loop : -1.65 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 332 TYR 0.008 0.001 TYR F 783 PHE 0.020 0.002 PHE A 729 TRP 0.004 0.001 TRP F 543 HIS 0.012 0.001 HIS F 770 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8979) covalent geometry : angle 0.72036 (12123) hydrogen bonds : bond 0.02843 ( 112) hydrogen bonds : angle 5.74047 ( 336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1725.15 seconds wall clock time: 30 minutes 17.23 seconds (1817.23 seconds total)