Starting phenix.real_space_refine on Sun Jul 27 03:24:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6og2_20050/07_2025/6og2_20050.cif Found real_map, /net/cci-nas-00/data/ceres_data/6og2_20050/07_2025/6og2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6og2_20050/07_2025/6og2_20050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6og2_20050/07_2025/6og2_20050.map" model { file = "/net/cci-nas-00/data/ceres_data/6og2_20050/07_2025/6og2_20050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6og2_20050/07_2025/6og2_20050.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.17, per 1000 atoms: 0.58 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: 1.95 Conformation dependent library (CDL) restraints added in 948.8 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: 0.76 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: 1.71 Time building geometry restraints manager: 2.35 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: 0.730 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.570 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.870 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.002 TRP F 543 HIS 0.007 0.002 HIS F 770 PHE 0.020 0.003 PHE F 763 TYR 0.022 0.003 TYR A 653 ARG 0.009 0.001 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.30979 ( 112) hydrogen bonds : angle 12.86247 ( 336) covalent geometry : bond 0.00554 ( 8979) covalent geometry : angle 1.11342 (12123) *********************** 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 : 0.899 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: F 191 ILE cc_start: 0.8494 (pt) cc_final: 0.7791 (pt) REVERT: F 205 ILE cc_start: 0.7985 (mt) cc_final: 0.7782 (mt) REVERT: F 238 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7302 (mp) REVERT: F 278 ASP cc_start: 0.7920 (t0) cc_final: 0.7630 (t0) REVERT: F 279 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7532 (pt0) REVERT: F 401 ILE cc_start: 0.8335 (mt) cc_final: 0.8001 (tp) REVERT: F 712 THR cc_start: 0.6400 (m) cc_final: 0.6144 (p) REVERT: A 185 GLU cc_start: 0.7145 (pm20) cc_final: 0.5974 (mp0) REVERT: A 204 LEU cc_start: 0.7168 (mp) cc_final: 0.6766 (mt) REVERT: A 299 LEU cc_start: 0.7753 (mm) cc_final: 0.7515 (tp) REVERT: A 314 THR cc_start: 0.6811 (t) cc_final: 0.6589 (t) REVERT: A 543 TRP cc_start: 0.7556 (m-10) cc_final: 0.7354 (m-10) REVERT: A 564 GLN cc_start: 0.7585 (mp10) cc_final: 0.7131 (tt0) REVERT: A 656 TYR cc_start: 0.7192 (t80) cc_final: 0.6949 (t80) REVERT: A 713 VAL cc_start: 0.6134 (t) cc_final: 0.5811 (t) outliers start: 4 outliers final: 1 residues processed: 271 average time/residue: 0.2921 time to fit residues: 100.2079 Evaluate side-chains 157 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 711 ASN F 857 GLN A 174 GLN A 281 HIS A 385 GLN A 692 GLN A 736 HIS A 770 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.209222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.178336 restraints weight = 22910.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.181668 restraints weight = 15362.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.184471 restraints weight = 11384.011| |-----------------------------------------------------------------------------| r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8979 Z= 0.159 Angle : 0.781 8.401 12123 Z= 0.390 Chirality : 0.048 0.183 1372 Planarity : 0.006 0.078 1581 Dihedral : 9.206 146.793 1256 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.21 % Allowed : 6.29 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.22), residues: 1092 helix: -3.88 (0.18), residues: 343 sheet: -1.97 (0.60), residues: 68 loop : -2.68 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 543 HIS 0.007 0.001 HIS A 568 PHE 0.019 0.002 PHE A 623 TYR 0.010 0.001 TYR A 653 ARG 0.010 0.001 ARG F 196 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 112) hydrogen bonds : angle 7.45380 ( 336) covalent geometry : bond 0.00353 ( 8979) covalent geometry : angle 0.78083 (12123) *********************** 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 203 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 0.988 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: 0.7237 (mtm-85) cc_final: 0.6893 (mtp180) REVERT: F 401 ILE cc_start: 0.8494 (mt) cc_final: 0.8125 (tp) REVERT: F 546 ILE cc_start: 0.5705 (mt) cc_final: 0.5496 (mt) REVERT: F 629 MET cc_start: 0.6233 (pmm) cc_final: 0.5989 (pmm) REVERT: F 712 THR cc_start: 0.5856 (m) cc_final: 0.5573 (p) REVERT: A 179 PRO cc_start: 0.6039 (Cg_exo) cc_final: 0.5834 (Cg_endo) REVERT: A 310 CYS cc_start: 0.6526 (t) cc_final: 0.6108 (p) REVERT: A 353 LEU cc_start: 0.8368 (tp) cc_final: 0.8049 (tp) REVERT: A 634 MET cc_start: 0.7345 (mmm) cc_final: 0.6935 (mmp) REVERT: A 645 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7809 (tpp80) REVERT: A 646 LEU cc_start: 0.7786 (pt) cc_final: 0.7466 (mt) REVERT: A 709 PHE cc_start: 0.8109 (m-80) cc_final: 0.7902 (m-80) outliers start: 2 outliers final: 1 residues processed: 203 average time/residue: 0.2901 time to fit residues: 75.8879 Evaluate side-chains 140 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 50 optimal weight: 0.0870 chunk 79 optimal weight: 0.0870 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.5336 ------------------------------------------------------------------------------- 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 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 A 711 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.203090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.173096 restraints weight = 24064.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.176484 restraints weight = 16601.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.178888 restraints weight = 12211.634| |-----------------------------------------------------------------------------| r_work (final): 0.4456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.5326 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= 0.119 Angle : 0.701 7.257 12123 Z= 0.346 Chirality : 0.046 0.173 1372 Planarity : 0.004 0.050 1581 Dihedral : 8.546 141.417 1256 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.23), residues: 1092 helix: -3.35 (0.21), residues: 360 sheet: -1.77 (0.60), residues: 78 loop : -2.52 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 543 HIS 0.007 0.001 HIS F 770 PHE 0.012 0.001 PHE A 276 TYR 0.007 0.001 TYR A 808 ARG 0.008 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 112) hydrogen bonds : angle 6.64742 ( 336) covalent geometry : bond 0.00269 ( 8979) covalent geometry : angle 0.70114 (12123) *********************** 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 168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.939 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: F 188 ARG cc_start: 0.7107 (mtm-85) cc_final: 0.6814 (mtp180) REVERT: F 399 SER cc_start: 0.8430 (t) cc_final: 0.8063 (p) REVERT: F 401 ILE cc_start: 0.8385 (mt) cc_final: 0.8073 (mm) REVERT: F 622 MET cc_start: 0.3689 (tpt) cc_final: 0.2835 (mmm) REVERT: F 712 THR cc_start: 0.5931 (m) cc_final: 0.5687 (p) REVERT: F 716 MET cc_start: 0.6462 (ptm) cc_final: 0.6002 (ppp) REVERT: A 265 ASP cc_start: 0.8042 (p0) cc_final: 0.7813 (p0) REVERT: A 310 CYS cc_start: 0.6073 (t) cc_final: 0.5774 (p) REVERT: A 533 ASP cc_start: 0.7435 (p0) cc_final: 0.7004 (p0) REVERT: A 713 VAL cc_start: 0.7184 (t) cc_final: 0.5891 (t) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2364 time to fit residues: 53.2342 Evaluate side-chains 140 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 4 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 F 778 GLN F 857 GLN ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.192711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.160257 restraints weight = 23793.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.163583 restraints weight = 16035.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.165959 restraints weight = 11918.569| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.7413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 8979 Z= 0.259 Angle : 0.911 10.656 12123 Z= 0.453 Chirality : 0.053 0.199 1372 Planarity : 0.007 0.065 1581 Dihedral : 9.497 144.623 1256 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 0.21 % Allowed : 7.14 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.22), residues: 1092 helix: -3.29 (0.20), residues: 386 sheet: -2.14 (0.61), residues: 68 loop : -2.31 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 543 HIS 0.010 0.002 HIS A 281 PHE 0.016 0.003 PHE A 603 TYR 0.022 0.002 TYR A 808 ARG 0.007 0.001 ARG F 781 Details of bonding type rmsd hydrogen bonds : bond 0.04541 ( 112) hydrogen bonds : angle 6.48017 ( 336) covalent geometry : bond 0.00582 ( 8979) covalent geometry : angle 0.91106 (12123) *********************** 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 182 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 186 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8523 (mp0) REVERT: F 199 LYS cc_start: 0.8729 (ptmt) cc_final: 0.8454 (ptmt) REVERT: F 634 MET cc_start: 0.6543 (tpt) cc_final: 0.6331 (tpp) REVERT: F 716 MET cc_start: 0.7431 (ptm) cc_final: 0.7108 (ppp) REVERT: A 353 LEU cc_start: 0.8420 (tp) cc_final: 0.8149 (tp) REVERT: A 578 ASP cc_start: 0.7793 (m-30) cc_final: 0.7463 (m-30) REVERT: A 595 ASN cc_start: 0.8135 (t0) cc_final: 0.7895 (t0) REVERT: A 656 TYR cc_start: 0.8365 (t80) cc_final: 0.8092 (t80) REVERT: A 664 GLU cc_start: 0.6863 (tm-30) cc_final: 0.6644 (tm-30) outliers start: 2 outliers final: 1 residues processed: 182 average time/residue: 0.2239 time to fit residues: 55.2567 Evaluate side-chains 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 17 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 269 GLN F 309 HIS ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 776 GLN F 857 GLN ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN A 641 HIS A 683 HIS ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.196510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.164729 restraints weight = 23323.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.168112 restraints weight = 15661.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.170484 restraints weight = 11587.444| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.7765 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= 0.139 Angle : 0.732 6.991 12123 Z= 0.363 Chirality : 0.048 0.174 1372 Planarity : 0.004 0.046 1581 Dihedral : 8.839 138.503 1256 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.24), residues: 1092 helix: -3.20 (0.21), residues: 389 sheet: -2.47 (0.56), residues: 80 loop : -1.94 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 543 HIS 0.005 0.001 HIS A 641 PHE 0.013 0.002 PHE F 763 TYR 0.009 0.001 TYR F 783 ARG 0.006 0.000 ARG F 331 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 112) hydrogen bonds : angle 6.29666 ( 336) covalent geometry : bond 0.00320 ( 8979) covalent geometry : angle 0.73205 (12123) *********************** 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 172 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 217 GLU cc_start: 0.8239 (tt0) cc_final: 0.7838 (tt0) REVERT: F 629 MET cc_start: 0.6171 (pmm) cc_final: 0.5815 (pmm) REVERT: A 281 HIS cc_start: 0.7584 (p90) cc_final: 0.7246 (p90) REVERT: A 578 ASP cc_start: 0.7737 (m-30) cc_final: 0.7324 (m-30) REVERT: A 622 MET cc_start: 0.5282 (tpt) cc_final: 0.5044 (tpt) REVERT: A 713 VAL cc_start: 0.7568 (t) cc_final: 0.7109 (t) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2353 time to fit residues: 54.8627 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 : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 7 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 101 optimal weight: 0.2980 chunk 89 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN A 404 GLN A 683 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.198386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.167537 restraints weight = 22904.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.171131 restraints weight = 15162.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.173503 restraints weight = 11058.469| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.8068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8979 Z= 0.118 Angle : 0.705 6.984 12123 Z= 0.348 Chirality : 0.046 0.170 1372 Planarity : 0.005 0.069 1581 Dihedral : 8.465 135.449 1256 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.24), residues: 1092 helix: -2.86 (0.23), residues: 374 sheet: -2.32 (0.57), residues: 79 loop : -1.90 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 543 HIS 0.008 0.001 HIS A 281 PHE 0.025 0.002 PHE F 749 TYR 0.008 0.001 TYR F 808 ARG 0.019 0.000 ARG F 750 Details of bonding type rmsd hydrogen bonds : bond 0.02792 ( 112) hydrogen bonds : angle 6.03077 ( 336) covalent geometry : bond 0.00264 ( 8979) covalent geometry : angle 0.70479 (12123) *********************** 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 161 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 167 ASP cc_start: 0.7114 (t0) cc_final: 0.6858 (t0) REVERT: F 217 GLU cc_start: 0.8180 (tt0) cc_final: 0.7758 (tt0) REVERT: F 401 ILE cc_start: 0.8444 (mt) cc_final: 0.8219 (mm) REVERT: F 629 MET cc_start: 0.5966 (pmm) cc_final: 0.5660 (pmm) REVERT: F 698 ARG cc_start: 0.2181 (mmt180) cc_final: 0.1907 (mmt-90) REVERT: A 188 ARG cc_start: 0.8073 (mmt-90) cc_final: 0.7786 (mmp80) REVERT: A 533 ASP cc_start: 0.7617 (p0) cc_final: 0.7284 (p0) REVERT: A 578 ASP cc_start: 0.7650 (m-30) cc_final: 0.7325 (m-30) REVERT: A 595 ASN cc_start: 0.7975 (t0) cc_final: 0.7524 (t0) REVERT: A 622 MET cc_start: 0.5166 (tpt) cc_final: 0.4943 (tpt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2771 time to fit residues: 60.2526 Evaluate side-chains 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 34 optimal weight: 7.9990 chunk 35 optimal weight: 0.0170 chunk 50 optimal weight: 0.0770 chunk 27 optimal weight: 9.9990 chunk 101 optimal weight: 0.4980 chunk 53 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 573 GLN ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN A 683 HIS A 747 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.193375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.162654 restraints weight = 23821.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.166106 restraints weight = 15839.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.168328 restraints weight = 11674.523| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.8333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8979 Z= 0.121 Angle : 0.704 7.329 12123 Z= 0.347 Chirality : 0.047 0.173 1372 Planarity : 0.004 0.057 1581 Dihedral : 8.328 139.561 1256 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.25), residues: 1092 helix: -2.78 (0.23), residues: 376 sheet: -2.07 (0.64), residues: 66 loop : -1.76 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 543 HIS 0.006 0.001 HIS A 360 PHE 0.034 0.002 PHE F 749 TYR 0.007 0.001 TYR F 783 ARG 0.004 0.000 ARG F 528 Details of bonding type rmsd hydrogen bonds : bond 0.02574 ( 112) hydrogen bonds : angle 6.00194 ( 336) covalent geometry : bond 0.00273 ( 8979) covalent geometry : angle 0.70442 (12123) *********************** 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 148 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 217 GLU cc_start: 0.8256 (tt0) cc_final: 0.7857 (tt0) REVERT: F 401 ILE cc_start: 0.8446 (mt) cc_final: 0.8231 (mm) REVERT: F 629 MET cc_start: 0.5841 (pmm) cc_final: 0.5605 (pmm) REVERT: F 668 ARG cc_start: 0.3085 (tpt90) cc_final: 0.2627 (mmm160) REVERT: F 698 ARG cc_start: 0.2467 (mmt180) cc_final: 0.2205 (mmt-90) REVERT: A 533 ASP cc_start: 0.7321 (p0) cc_final: 0.7014 (p0) REVERT: A 535 GLU cc_start: 0.7338 (mp0) cc_final: 0.6926 (mt-10) REVERT: A 578 ASP cc_start: 0.7679 (m-30) cc_final: 0.7383 (m-30) REVERT: A 595 ASN cc_start: 0.8146 (t0) cc_final: 0.7740 (t0) REVERT: A 622 MET cc_start: 0.5087 (tpt) cc_final: 0.4861 (tpt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2743 time to fit residues: 55.3056 Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 52 optimal weight: 0.4980 chunk 101 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 0.0020 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.0994 ------------------------------------------------------------------------------- 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 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.188723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.156930 restraints weight = 23816.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.160275 restraints weight = 15763.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.162529 restraints weight = 11586.588| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.9277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8979 Z= 0.214 Angle : 0.839 7.976 12123 Z= 0.421 Chirality : 0.051 0.192 1372 Planarity : 0.006 0.066 1581 Dihedral : 8.976 142.462 1256 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.24), residues: 1092 helix: -2.93 (0.22), residues: 396 sheet: -2.19 (0.57), residues: 81 loop : -1.87 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 543 HIS 0.006 0.001 HIS A 281 PHE 0.026 0.003 PHE A 601 TYR 0.028 0.002 TYR A 653 ARG 0.006 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 112) hydrogen bonds : angle 6.19474 ( 336) covalent geometry : bond 0.00485 ( 8979) covalent geometry : angle 0.83860 (12123) *********************** 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 147 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.203 Fit side-chains revert: symmetry clash REVERT: F 185 GLU cc_start: 0.7942 (pm20) cc_final: 0.7600 (mt-10) REVERT: F 217 GLU cc_start: 0.8445 (tt0) cc_final: 0.8138 (tt0) REVERT: F 393 LEU cc_start: 0.8121 (mp) cc_final: 0.7843 (tt) REVERT: F 401 ILE cc_start: 0.8566 (mt) cc_final: 0.8236 (mm) REVERT: A 188 ARG cc_start: 0.8222 (mmt-90) cc_final: 0.7974 (mmp80) REVERT: A 533 ASP cc_start: 0.7407 (p0) cc_final: 0.7093 (p0) REVERT: A 535 GLU cc_start: 0.7399 (mp0) cc_final: 0.6923 (mt-10) REVERT: A 578 ASP cc_start: 0.7782 (m-30) cc_final: 0.7504 (m-30) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2730 time to fit residues: 56.4372 Evaluate side-chains 120 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 103 optimal weight: 0.0470 chunk 84 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.188684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.158973 restraints weight = 24207.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.162145 restraints weight = 16085.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.164498 restraints weight = 11810.538| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.9422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8979 Z= 0.126 Angle : 0.740 9.127 12123 Z= 0.364 Chirality : 0.047 0.173 1372 Planarity : 0.004 0.042 1581 Dihedral : 8.252 138.237 1256 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.24), residues: 1092 helix: -2.67 (0.24), residues: 384 sheet: -2.13 (0.58), residues: 77 loop : -1.80 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 543 HIS 0.004 0.001 HIS A 360 PHE 0.014 0.002 PHE A 603 TYR 0.018 0.001 TYR F 319 ARG 0.005 0.000 ARG F 331 Details of bonding type rmsd hydrogen bonds : bond 0.02663 ( 112) hydrogen bonds : angle 5.90522 ( 336) covalent geometry : bond 0.00294 ( 8979) covalent geometry : angle 0.74025 (12123) *********************** 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 151 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 185 GLU cc_start: 0.7916 (pm20) cc_final: 0.7528 (mt-10) REVERT: F 217 GLU cc_start: 0.8408 (tt0) cc_final: 0.8032 (tt0) REVERT: F 391 ILE cc_start: 0.6724 (pt) cc_final: 0.6491 (tp) REVERT: F 393 LEU cc_start: 0.8089 (mp) cc_final: 0.7771 (tt) REVERT: F 401 ILE cc_start: 0.8451 (mt) cc_final: 0.8108 (mm) REVERT: F 562 MET cc_start: 0.5395 (tmm) cc_final: 0.3977 (mmm) REVERT: F 598 ILE cc_start: 0.7691 (mm) cc_final: 0.7350 (mp) REVERT: F 698 ARG cc_start: 0.2517 (mmt180) cc_final: 0.2293 (mmt-90) REVERT: A 533 ASP cc_start: 0.7215 (p0) cc_final: 0.6930 (p0) REVERT: A 535 GLU cc_start: 0.7400 (mp0) cc_final: 0.6925 (mt-10) REVERT: A 578 ASP cc_start: 0.7651 (m-30) cc_final: 0.7416 (m-30) REVERT: A 716 MET cc_start: 0.8327 (mtp) cc_final: 0.8116 (mtm) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2257 time to fit residues: 46.9230 Evaluate side-chains 122 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 71 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 0.0050 chunk 92 optimal weight: 0.0170 chunk 27 optimal weight: 0.9990 chunk 101 optimal weight: 0.0060 chunk 65 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 61 optimal weight: 0.0970 overall best weight: 0.1646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 361 HIS ** F 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN ** A 824 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 = 0.4648 r_free = 0.4648 target = 0.192242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.162821 restraints weight = 23939.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.165897 restraints weight = 15808.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.168294 restraints weight = 11640.374| |-----------------------------------------------------------------------------| r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.9529 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= 0.114 Angle : 0.724 10.420 12123 Z= 0.349 Chirality : 0.046 0.233 1372 Planarity : 0.004 0.042 1581 Dihedral : 7.540 138.011 1256 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.25), residues: 1092 helix: -2.48 (0.24), residues: 386 sheet: -2.12 (0.56), residues: 82 loop : -1.60 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 543 HIS 0.004 0.001 HIS F 770 PHE 0.011 0.001 PHE F 763 TYR 0.013 0.001 TYR F 319 ARG 0.005 0.000 ARG F 331 Details of bonding type rmsd hydrogen bonds : bond 0.02472 ( 112) hydrogen bonds : angle 5.68673 ( 336) covalent geometry : bond 0.00255 ( 8979) covalent geometry : angle 0.72436 (12123) ********************** 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 159 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 217 GLU cc_start: 0.8186 (tt0) cc_final: 0.7668 (tt0) REVERT: F 598 ILE cc_start: 0.7468 (mm) cc_final: 0.7205 (mp) REVERT: F 629 MET cc_start: 0.5823 (pmm) cc_final: 0.5347 (pmm) REVERT: A 177 LEU cc_start: 0.8197 (mt) cc_final: 0.7892 (mt) REVERT: A 533 ASP cc_start: 0.7061 (p0) cc_final: 0.6848 (p0) REVERT: A 535 GLU cc_start: 0.7495 (mp0) cc_final: 0.6946 (mt-10) REVERT: A 578 ASP cc_start: 0.7806 (m-30) cc_final: 0.7534 (m-30) REVERT: A 602 LEU cc_start: 0.8216 (mt) cc_final: 0.7700 (mt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2617 time to fit residues: 57.1984 Evaluate side-chains 127 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 26 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 55 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 195 GLN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN ** A 824 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 = 0.4637 r_free = 0.4637 target = 0.190880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.161337 restraints weight = 24082.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.164409 restraints weight = 16092.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.166651 restraints weight = 11836.150| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.9753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8979 Z= 0.121 Angle : 0.739 10.462 12123 Z= 0.360 Chirality : 0.047 0.206 1372 Planarity : 0.004 0.041 1581 Dihedral : 7.306 135.069 1256 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.25), residues: 1092 helix: -2.32 (0.25), residues: 376 sheet: -2.05 (0.56), residues: 82 loop : -1.59 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 543 HIS 0.004 0.001 HIS A 360 PHE 0.012 0.001 PHE A 337 TYR 0.012 0.001 TYR F 319 ARG 0.006 0.000 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.02521 ( 112) hydrogen bonds : angle 5.69480 ( 336) covalent geometry : bond 0.00277 ( 8979) covalent geometry : angle 0.73921 (12123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3364.73 seconds wall clock time: 61 minutes 12.48 seconds (3672.48 seconds total)