Starting phenix.real_space_refine on Thu Feb 13 13:49:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6og2_20050/02_2025/6og2_20050.cif Found real_map, /net/cci-nas-00/data/ceres_data/6og2_20050/02_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_20050/02_2025/6og2_20050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6og2_20050/02_2025/6og2_20050.map" model { file = "/net/cci-nas-00/data/ceres_data/6og2_20050/02_2025/6og2_20050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6og2_20050/02_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-5592/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: 5.40, per 1000 atoms: 0.61 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: 2.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.87 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: 1.93 Time building geometry restraints manager: 2.33 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.630 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.390 ------------------------------------------------------------------------------- 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= 0.366 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 *********************** 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 : 0.918 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: 0.3076 time to fit residues: 105.0309 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 : 1.210 ------------------------------------------------------------------------------- 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: 0.8980 chunk 98 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4799 r_free = 0.4799 target = 0.209176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.178254 restraints weight = 22984.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.182008 restraints weight = 15229.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.184791 restraints weight = 10987.938| |-----------------------------------------------------------------------------| r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5977 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8979 Z= 0.233 Angle : 0.780 8.070 12123 Z= 0.390 Chirality : 0.048 0.178 1372 Planarity : 0.006 0.072 1581 Dihedral : 9.254 146.800 1256 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.21 % Allowed : 6.08 % Favored : 93.71 % 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: -4.49 (0.22), residues: 1092 helix: -3.86 (0.19), residues: 343 sheet: -2.11 (0.59), residues: 70 loop : -2.70 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 543 HIS 0.007 0.001 HIS A 360 PHE 0.021 0.002 PHE A 623 TYR 0.010 0.001 TYR A 653 ARG 0.012 0.001 ARG F 196 *********************** 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 201 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 199 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 188 ARG cc_start: 0.7197 (mtm-85) cc_final: 0.6823 (mtp180) REVERT: F 399 SER cc_start: 0.8063 (t) cc_final: 0.7687 (p) REVERT: F 401 ILE cc_start: 0.8542 (mt) cc_final: 0.8161 (tp) REVERT: F 629 MET cc_start: 0.6301 (pmm) cc_final: 0.6034 (pmm) REVERT: F 712 THR cc_start: 0.5901 (m) cc_final: 0.5603 (p) REVERT: A 179 PRO cc_start: 0.6000 (Cg_exo) cc_final: 0.5717 (Cg_endo) REVERT: A 275 LEU cc_start: 0.8270 (tt) cc_final: 0.8069 (tt) REVERT: A 310 CYS cc_start: 0.6520 (t) cc_final: 0.6153 (p) REVERT: A 353 LEU cc_start: 0.8347 (tp) cc_final: 0.8036 (tp) REVERT: A 634 MET cc_start: 0.7353 (mmm) cc_final: 0.6880 (mmp) REVERT: A 646 LEU cc_start: 0.7794 (pt) cc_final: 0.7398 (mt) REVERT: A 676 LEU cc_start: 0.7893 (mp) cc_final: 0.7656 (mp) REVERT: A 709 PHE cc_start: 0.8094 (m-80) cc_final: 0.7877 (m-80) REVERT: A 712 THR cc_start: 0.5591 (p) cc_final: 0.5384 (p) outliers start: 2 outliers final: 1 residues processed: 201 average time/residue: 0.2788 time to fit residues: 72.2866 Evaluate side-chains 135 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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: 0.0060 chunk 21 optimal weight: 5.9990 chunk 86 optimal weight: 0.0870 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 79 optimal weight: 0.0270 chunk 91 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.3834 ------------------------------------------------------------------------------- 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 269 GLN A 595 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 = 0.4766 r_free = 0.4766 target = 0.203086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.175309 restraints weight = 24395.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.178285 restraints weight = 17142.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.180183 restraints weight = 12995.964| |-----------------------------------------------------------------------------| r_work (final): 0.4512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.5280 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= 0.179 Angle : 0.703 7.343 12123 Z= 0.347 Chirality : 0.046 0.181 1372 Planarity : 0.005 0.050 1581 Dihedral : 8.559 140.872 1256 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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: -4.14 (0.22), residues: 1092 helix: -3.39 (0.21), residues: 360 sheet: -1.78 (0.57), residues: 84 loop : -2.57 (0.23), residues: 648 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 0.010 0.001 PHE A 623 TYR 0.012 0.001 TYR F 319 ARG 0.007 0.000 ARG A 183 *********************** 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 169 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 188 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.7016 (mtp180) REVERT: F 399 SER cc_start: 0.8413 (t) cc_final: 0.8046 (p) REVERT: F 401 ILE cc_start: 0.8420 (mt) cc_final: 0.8125 (mm) REVERT: F 621 PHE cc_start: 0.5142 (t80) cc_final: 0.4724 (t80) REVERT: F 712 THR cc_start: 0.5956 (m) cc_final: 0.5719 (p) REVERT: F 716 MET cc_start: 0.6382 (ptm) cc_final: 0.5827 (ppp) REVERT: A 177 LEU cc_start: 0.8294 (mt) cc_final: 0.7949 (mt) REVERT: A 179 PRO cc_start: 0.6226 (Cg_exo) cc_final: 0.5754 (Cg_endo) REVERT: A 265 ASP cc_start: 0.8121 (p0) cc_final: 0.7903 (p0) REVERT: A 310 CYS cc_start: 0.6200 (t) cc_final: 0.5779 (p) REVERT: A 353 LEU cc_start: 0.8463 (tp) cc_final: 0.8237 (tp) REVERT: A 533 ASP cc_start: 0.7586 (p0) cc_final: 0.7195 (p0) REVERT: A 664 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6818 (tm-30) REVERT: A 712 THR cc_start: 0.6032 (p) cc_final: 0.5815 (p) REVERT: A 713 VAL cc_start: 0.7067 (t) cc_final: 0.6349 (t) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2370 time to fit residues: 53.6931 Evaluate side-chains 136 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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: 5.9990 chunk 69 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 24 optimal weight: 0.0970 chunk 45 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 12 optimal weight: 0.0470 chunk 17 optimal weight: 0.4980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 309 HIS ** F 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.209836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.178503 restraints weight = 23725.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.181984 restraints weight = 16143.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.184649 restraints weight = 11889.457| |-----------------------------------------------------------------------------| r_work (final): 0.4481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6033 moved from start: 0.5840 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= 0.174 Angle : 0.679 7.212 12123 Z= 0.331 Chirality : 0.045 0.175 1372 Planarity : 0.004 0.047 1581 Dihedral : 8.282 138.769 1256 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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: -3.70 (0.23), residues: 1092 helix: -2.96 (0.23), residues: 359 sheet: -1.43 (0.62), residues: 74 loop : -2.36 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 543 HIS 0.005 0.001 HIS A 747 PHE 0.011 0.001 PHE F 763 TYR 0.012 0.001 TYR F 319 ARG 0.009 0.000 ARG A 528 *********************** 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 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.925 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: 0.7245 (mtm-85) cc_final: 0.6939 (mtp180) REVERT: F 399 SER cc_start: 0.8486 (t) cc_final: 0.8140 (p) REVERT: F 401 ILE cc_start: 0.8343 (mt) cc_final: 0.7984 (mm) REVERT: F 629 MET cc_start: 0.6679 (pmm) cc_final: 0.6334 (pmm) REVERT: F 716 MET cc_start: 0.6569 (ptm) cc_final: 0.6176 (ppp) REVERT: A 179 PRO cc_start: 0.6519 (Cg_exo) cc_final: 0.5817 (Cg_endo) REVERT: A 315 THR cc_start: 0.7752 (p) cc_final: 0.7513 (p) REVERT: A 533 ASP cc_start: 0.7248 (p0) cc_final: 0.6920 (p0) REVERT: A 664 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6723 (tm-30) REVERT: A 713 VAL cc_start: 0.7043 (t) cc_final: 0.5951 (t) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2417 time to fit residues: 53.0228 Evaluate side-chains 126 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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: 0.7980 chunk 24 optimal weight: 10.0000 chunk 93 optimal weight: 0.0370 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 857 GLN A 404 GLN A 641 HIS A 711 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.201352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.170204 restraints weight = 23687.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.173572 restraints weight = 16241.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.176115 restraints weight = 12080.346| |-----------------------------------------------------------------------------| r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.6377 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= 0.179 Angle : 0.669 7.012 12123 Z= 0.330 Chirality : 0.045 0.168 1372 Planarity : 0.004 0.042 1581 Dihedral : 8.133 134.703 1256 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.11 % Allowed : 2.88 % Favored : 97.01 % 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: -3.54 (0.24), residues: 1092 helix: -2.91 (0.23), residues: 372 sheet: -1.69 (0.65), residues: 66 loop : -2.12 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 543 HIS 0.006 0.001 HIS A 641 PHE 0.013 0.001 PHE F 763 TYR 0.013 0.001 TYR F 319 ARG 0.007 0.000 ARG A 645 *********************** 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: 1 poor density : 163 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 167 ASP cc_start: 0.6563 (t0) cc_final: 0.6356 (t0) REVERT: F 188 ARG cc_start: 0.7362 (mtm-85) cc_final: 0.7024 (mtp180) REVERT: F 716 MET cc_start: 0.6803 (ptm) cc_final: 0.6570 (ppp) REVERT: A 185 GLU cc_start: 0.7579 (tp30) cc_final: 0.7377 (tp30) REVERT: A 310 CYS cc_start: 0.6504 (t) cc_final: 0.6073 (p) REVERT: A 315 THR cc_start: 0.8041 (p) cc_final: 0.7758 (p) REVERT: A 533 ASP cc_start: 0.7107 (p0) cc_final: 0.6800 (p0) REVERT: A 595 ASN cc_start: 0.7938 (t0) cc_final: 0.7541 (t0) REVERT: A 653 TYR cc_start: 0.5665 (t80) cc_final: 0.4876 (m-80) REVERT: A 664 GLU cc_start: 0.6914 (tm-30) cc_final: 0.6650 (tm-30) REVERT: A 669 ARG cc_start: 0.6709 (mtp85) cc_final: 0.6285 (mtp180) REVERT: A 713 VAL cc_start: 0.7496 (t) cc_final: 0.6734 (t) REVERT: A 761 VAL cc_start: 0.8002 (m) cc_final: 0.7769 (t) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.2264 time to fit residues: 50.3969 Evaluate side-chains 126 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 9.9990 chunk 36 optimal weight: 0.0030 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 61 optimal weight: 0.1980 chunk 53 optimal weight: 0.0170 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 0.0570 chunk 89 optimal weight: 2.9990 overall best weight: 0.2346 ------------------------------------------------------------------------------- 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 F 769 GLN ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 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 = 0.4781 r_free = 0.4781 target = 0.208404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.176875 restraints weight = 22954.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.180359 restraints weight = 15750.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.182913 restraints weight = 11816.123| |-----------------------------------------------------------------------------| r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8979 Z= 0.159 Angle : 0.659 7.294 12123 Z= 0.323 Chirality : 0.045 0.169 1372 Planarity : 0.004 0.040 1581 Dihedral : 7.906 131.394 1256 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.11 % Allowed : 2.03 % Favored : 97.87 % 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: -3.35 (0.24), residues: 1092 helix: -2.70 (0.24), residues: 362 sheet: -1.73 (0.57), residues: 84 loop : -2.04 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 543 HIS 0.004 0.001 HIS A 747 PHE 0.012 0.001 PHE F 763 TYR 0.013 0.001 TYR F 734 ARG 0.006 0.000 ARG F 236 *********************** 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 160 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 1.000 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: 0.7380 (mtm-85) cc_final: 0.7085 (mtp180) REVERT: F 401 ILE cc_start: 0.8424 (mt) cc_final: 0.8057 (mm) REVERT: F 629 MET cc_start: 0.6906 (pmm) cc_final: 0.6492 (pmm) REVERT: A 315 THR cc_start: 0.7986 (p) cc_final: 0.7713 (p) REVERT: A 533 ASP cc_start: 0.7059 (p0) cc_final: 0.6712 (p0) REVERT: A 595 ASN cc_start: 0.7907 (t0) cc_final: 0.7461 (t0) REVERT: A 653 TYR cc_start: 0.5709 (t80) cc_final: 0.4968 (m-80) REVERT: A 664 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6701 (tm-30) REVERT: A 713 VAL cc_start: 0.7570 (t) cc_final: 0.6736 (t) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.2340 time to fit residues: 50.8840 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 : 1.299 ------------------------------------------------------------------------------- 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: 6.9990 chunk 35 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 79 optimal weight: 0.0030 chunk 97 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 711 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 = 0.4741 r_free = 0.4741 target = 0.204345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.173123 restraints weight = 23860.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.176399 restraints weight = 16381.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.178674 restraints weight = 12320.377| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.7170 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= 0.175 Angle : 0.672 7.421 12123 Z= 0.331 Chirality : 0.046 0.169 1372 Planarity : 0.004 0.037 1581 Dihedral : 7.786 130.978 1256 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.91 % 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: -3.13 (0.24), residues: 1092 helix: -2.63 (0.23), residues: 373 sheet: -1.92 (0.63), residues: 70 loop : -1.75 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 543 HIS 0.005 0.001 HIS F 764 PHE 0.016 0.001 PHE A 276 TYR 0.008 0.001 TYR F 734 ARG 0.005 0.000 ARG A 525 *********************** 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: 1 poor density : 154 time to evaluate : 1.064 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: 0.7500 (mtm-85) cc_final: 0.7208 (mtp180) REVERT: F 629 MET cc_start: 0.6837 (pmm) cc_final: 0.6405 (pmm) REVERT: A 188 ARG cc_start: 0.7804 (mmt-90) cc_final: 0.7431 (mmt-90) REVERT: A 279 GLU cc_start: 0.6391 (tp30) cc_final: 0.6174 (tp30) REVERT: A 533 ASP cc_start: 0.6837 (p0) cc_final: 0.6504 (p0) REVERT: A 595 ASN cc_start: 0.7697 (t0) cc_final: 0.7309 (t0) REVERT: A 664 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6647 (tm-30) REVERT: A 713 VAL cc_start: 0.7434 (t) cc_final: 0.6821 (t) REVERT: A 760 VAL cc_start: 0.6829 (t) cc_final: 0.6588 (m) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.2230 time to fit residues: 46.9377 Evaluate side-chains 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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: 3.9990 chunk 101 optimal weight: 3.9990 chunk 75 optimal weight: 0.0050 chunk 4 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 65 optimal weight: 0.0060 chunk 23 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.0016 ------------------------------------------------------------------------------- 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** F 778 GLN A 221 GLN A 641 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.193637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.164871 restraints weight = 24196.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.167595 restraints weight = 16814.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.169702 restraints weight = 12801.505| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.7637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8979 Z= 0.196 Angle : 0.693 7.527 12123 Z= 0.340 Chirality : 0.046 0.167 1372 Planarity : 0.005 0.076 1581 Dihedral : 7.937 131.081 1256 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: -3.11 (0.24), residues: 1092 helix: -2.61 (0.24), residues: 376 sheet: -2.16 (0.65), residues: 63 loop : -1.71 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 543 HIS 0.009 0.001 HIS F 770 PHE 0.013 0.001 PHE F 763 TYR 0.009 0.001 TYR F 783 ARG 0.008 0.000 ARG A 550 *********************** 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 163 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.063 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: 0.7532 (mtm-85) cc_final: 0.7267 (mtp180) REVERT: F 298 MET cc_start: 0.3882 (pmm) cc_final: 0.3545 (pmm) REVERT: F 629 MET cc_start: 0.6683 (pmm) cc_final: 0.6275 (pmm) REVERT: A 279 GLU cc_start: 0.6442 (tp30) cc_final: 0.6239 (tp30) REVERT: A 353 LEU cc_start: 0.8259 (tp) cc_final: 0.8011 (tp) REVERT: A 533 ASP cc_start: 0.7066 (p0) cc_final: 0.6740 (p0) REVERT: A 578 ASP cc_start: 0.7633 (m-30) cc_final: 0.7321 (m-30) REVERT: A 595 ASN cc_start: 0.7893 (t0) cc_final: 0.7605 (t0) REVERT: A 653 TYR cc_start: 0.6035 (t80) cc_final: 0.4735 (m-80) REVERT: A 664 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6851 (tm-30) REVERT: A 760 VAL cc_start: 0.7372 (t) cc_final: 0.7158 (m) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2296 time to fit residues: 50.6400 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 : 0.967 ------------------------------------------------------------------------------- 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: 0.6980 chunk 104 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 0.0370 chunk 90 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- 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 385 GLN ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 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 = 0.4697 r_free = 0.4697 target = 0.199833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.168219 restraints weight = 23740.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.171706 restraints weight = 16061.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.174270 restraints weight = 11812.369| |-----------------------------------------------------------------------------| r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.8070 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= 0.193 Angle : 0.711 7.779 12123 Z= 0.348 Chirality : 0.046 0.165 1372 Planarity : 0.004 0.063 1581 Dihedral : 7.934 130.608 1256 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -3.07 (0.24), residues: 1092 helix: -2.56 (0.24), residues: 379 sheet: -2.38 (0.61), residues: 68 loop : -1.65 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 543 HIS 0.009 0.001 HIS F 770 PHE 0.012 0.001 PHE F 763 TYR 0.009 0.001 TYR F 783 ARG 0.008 0.001 ARG F 236 *********************** 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 166 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.920 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: 0.7612 (mtm-85) cc_final: 0.7342 (mtp180) REVERT: F 217 GLU cc_start: 0.8441 (tt0) cc_final: 0.8006 (tt0) REVERT: F 401 ILE cc_start: 0.8467 (mt) cc_final: 0.8234 (mt) REVERT: F 629 MET cc_start: 0.6453 (pmm) cc_final: 0.6005 (pmm) REVERT: A 177 LEU cc_start: 0.8289 (mm) cc_final: 0.7983 (mt) REVERT: A 188 ARG cc_start: 0.8005 (mmt-90) cc_final: 0.7397 (tpt170) REVERT: A 273 VAL cc_start: 0.9368 (m) cc_final: 0.9158 (t) REVERT: A 281 HIS cc_start: 0.6764 (p90) cc_final: 0.6413 (p90) REVERT: A 533 ASP cc_start: 0.6952 (p0) cc_final: 0.6602 (p0) REVERT: A 578 ASP cc_start: 0.7683 (m-30) cc_final: 0.7408 (m-30) REVERT: A 664 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6784 (tm-30) REVERT: A 669 ARG cc_start: 0.7332 (mtp85) cc_final: 0.6939 (mtp180) REVERT: A 713 VAL cc_start: 0.7583 (t) cc_final: 0.7202 (t) REVERT: A 760 VAL cc_start: 0.7524 (t) cc_final: 0.7308 (m) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2397 time to fit residues: 53.8480 Evaluate side-chains 129 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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: 0.8980 chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- 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 201 ASN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.187477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.155020 restraints weight = 23717.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.158388 restraints weight = 15981.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.160679 restraints weight = 11891.896| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.8865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8979 Z= 0.283 Angle : 0.802 8.990 12123 Z= 0.401 Chirality : 0.049 0.178 1372 Planarity : 0.006 0.083 1581 Dihedral : 8.494 134.990 1256 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer: Outliers : 0.11 % Allowed : 0.75 % Favored : 99.15 % 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: -3.07 (0.24), residues: 1092 helix: -2.50 (0.25), residues: 378 sheet: -2.57 (0.60), residues: 63 loop : -1.69 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 543 HIS 0.009 0.001 HIS F 770 PHE 0.015 0.002 PHE A 603 TYR 0.012 0.001 TYR F 783 ARG 0.007 0.001 ARG A 528 ********************** 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 : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 199 LYS cc_start: 0.8578 (ptmt) cc_final: 0.8345 (ptmt) REVERT: F 217 GLU cc_start: 0.8327 (tt0) cc_final: 0.7944 (tt0) REVERT: F 393 LEU cc_start: 0.8095 (mp) cc_final: 0.7823 (tt) REVERT: F 562 MET cc_start: 0.5424 (tmm) cc_final: 0.3959 (mmm) REVERT: F 770 HIS cc_start: 0.8206 (t70) cc_final: 0.7851 (t-90) REVERT: A 177 LEU cc_start: 0.8341 (mm) cc_final: 0.8068 (mt) REVERT: A 188 ARG cc_start: 0.8118 (mmt-90) cc_final: 0.7823 (tpt170) REVERT: A 277 ILE cc_start: 0.7673 (mt) cc_final: 0.7408 (mt) REVERT: A 533 ASP cc_start: 0.7148 (p0) cc_final: 0.6844 (p0) REVERT: A 656 TYR cc_start: 0.8477 (t80) cc_final: 0.7992 (t80) REVERT: A 664 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6800 (tm-30) REVERT: A 713 VAL cc_start: 0.7799 (t) cc_final: 0.7223 (t) outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.2399 time to fit residues: 50.8387 Evaluate side-chains 131 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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: 0.1980 chunk 82 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4655 r_free = 0.4655 target = 0.195786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.164385 restraints weight = 23844.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.167737 restraints weight = 16214.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.170059 restraints weight = 11975.951| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.9097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8979 Z= 0.196 Angle : 0.725 8.366 12123 Z= 0.357 Chirality : 0.047 0.172 1372 Planarity : 0.004 0.047 1581 Dihedral : 8.235 132.077 1256 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -2.88 (0.25), residues: 1092 helix: -2.36 (0.25), residues: 384 sheet: -2.34 (0.61), residues: 63 loop : -1.56 (0.25), residues: 645 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 0.015 0.002 PHE A 603 TYR 0.008 0.001 TYR F 783 ARG 0.006 0.001 ARG F 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3058.02 seconds wall clock time: 55 minutes 16.65 seconds (3316.65 seconds total)