Starting phenix.real_space_refine on Sat Mar 7 05:06:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ny1_12644/03_2026/7ny1_12644.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ny1_12644/03_2026/7ny1_12644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ny1_12644/03_2026/7ny1_12644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ny1_12644/03_2026/7ny1_12644.map" model { file = "/net/cci-nas-00/data/ceres_data/7ny1_12644/03_2026/7ny1_12644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ny1_12644/03_2026/7ny1_12644.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 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: 7 Type Number sf(0) Gaussians K 6 8.98 5 P 12 5.49 5 Mg 6 5.21 5 S 138 5.16 5 C 24780 2.51 5 N 6360 2.21 5 O 7128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 216 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38430 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 829, 6376 Classifications: {'peptide': 829} Link IDs: {'PTRANS': 31, 'TRANS': 797} Chain breaks: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 7.57, per 1000 atoms: 0.20 Number of scatterers: 38430 At special positions: 0 Unit cell: (186.651, 168.237, 125.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 6 19.00 S 138 16.00 P 12 15.00 Mg 6 11.99 O 7128 8.00 N 6360 7.00 C 24780 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: 3.43 Conformation dependent library (CDL) restraints added in 1.7 seconds 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9084 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 24 sheets defined 52.8% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.754A pdb=" N THR A 82 " --> pdb=" O MET A 79 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP A 83 " --> pdb=" O LEU A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 83' Processing helix chain 'A' and resid 113 through 119 removed outlier: 3.602A pdb=" N LEU A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 142 through 175 removed outlier: 3.857A pdb=" N ASP A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 315 Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.619A pdb=" N VAL A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 356 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 402 through 411 removed outlier: 4.379A pdb=" N LEU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 429 removed outlier: 3.792A pdb=" N LYS A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 485 removed outlier: 3.635A pdb=" N LEU A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 508 removed outlier: 3.518A pdb=" N GLN A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 550 removed outlier: 3.850A pdb=" N THR A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 573 Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 593 through 603 removed outlier: 3.822A pdb=" N ASP A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 625 removed outlier: 3.519A pdb=" N LYS A 615 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A 616 " --> pdb=" O PRO A 612 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 625 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 645 Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 670 through 714 removed outlier: 3.967A pdb=" N ILE A 674 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 708 " --> pdb=" O ILE A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 729 Processing helix chain 'A' and resid 751 through 781 removed outlier: 3.686A pdb=" N MET A 777 " --> pdb=" O THR A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 807 Processing helix chain 'A' and resid 808 through 813 Processing helix chain 'A' and resid 824 through 845 Processing helix chain 'A' and resid 853 through 878 removed outlier: 3.661A pdb=" N VAL A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 919 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.754A pdb=" N THR B 82 " --> pdb=" O MET B 79 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP B 83 " --> pdb=" O LEU B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'B' and resid 113 through 119 removed outlier: 3.602A pdb=" N LEU B 117 " --> pdb=" O PHE B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 134 Processing helix chain 'B' and resid 142 through 175 removed outlier: 3.857A pdb=" N ASP B 170 " --> pdb=" O GLY B 166 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 315 Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.620A pdb=" N VAL B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 356 Processing helix chain 'B' and resid 364 through 372 Processing helix chain 'B' and resid 402 through 411 removed outlier: 4.379A pdb=" N LEU B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 429 removed outlier: 3.792A pdb=" N LYS B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE B 426 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 485 removed outlier: 3.635A pdb=" N LEU B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 508 removed outlier: 3.517A pdb=" N GLN B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA B 497 " --> pdb=" O GLU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 550 removed outlier: 3.850A pdb=" N THR B 549 " --> pdb=" O CYS B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 573 Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 593 through 603 removed outlier: 3.822A pdb=" N ASP B 599 " --> pdb=" O SER B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 625 removed outlier: 3.519A pdb=" N LYS B 615 " --> pdb=" O PHE B 611 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR B 616 " --> pdb=" O PRO B 612 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 625 " --> pdb=" O ILE B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 645 Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 670 through 714 removed outlier: 3.967A pdb=" N ILE B 674 " --> pdb=" O GLY B 670 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU B 708 " --> pdb=" O ILE B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 751 through 781 removed outlier: 3.686A pdb=" N MET B 777 " --> pdb=" O THR B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 807 Processing helix chain 'B' and resid 808 through 813 Processing helix chain 'B' and resid 824 through 845 Processing helix chain 'B' and resid 853 through 878 removed outlier: 3.660A pdb=" N VAL B 858 " --> pdb=" O ILE B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 919 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.754A pdb=" N THR C 82 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP C 83 " --> pdb=" O LEU C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 83' Processing helix chain 'C' and resid 113 through 119 removed outlier: 3.602A pdb=" N LEU C 117 " --> pdb=" O PHE C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 Processing helix chain 'C' and resid 142 through 175 removed outlier: 3.857A pdb=" N ASP C 170 " --> pdb=" O GLY C 166 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 315 Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.620A pdb=" N VAL C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 356 Processing helix chain 'C' and resid 364 through 372 Processing helix chain 'C' and resid 402 through 411 removed outlier: 4.379A pdb=" N LEU C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 411 " --> pdb=" O THR C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 429 removed outlier: 3.792A pdb=" N LYS C 424 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE C 426 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 485 removed outlier: 3.635A pdb=" N LEU C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 508 removed outlier: 3.518A pdb=" N GLN C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA C 497 " --> pdb=" O GLU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 550 removed outlier: 3.850A pdb=" N THR C 549 " --> pdb=" O CYS C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 573 Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 593 through 603 removed outlier: 3.823A pdb=" N ASP C 599 " --> pdb=" O SER C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 625 removed outlier: 3.519A pdb=" N LYS C 615 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR C 616 " --> pdb=" O PRO C 612 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 625 " --> pdb=" O ILE C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 645 Processing helix chain 'C' and resid 655 through 662 Processing helix chain 'C' and resid 670 through 714 removed outlier: 3.967A pdb=" N ILE C 674 " --> pdb=" O GLY C 670 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU C 708 " --> pdb=" O ILE C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 729 Processing helix chain 'C' and resid 751 through 781 removed outlier: 3.686A pdb=" N MET C 777 " --> pdb=" O THR C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 807 Processing helix chain 'C' and resid 808 through 813 Processing helix chain 'C' and resid 824 through 845 Processing helix chain 'C' and resid 853 through 878 removed outlier: 3.661A pdb=" N VAL C 858 " --> pdb=" O ILE C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 919 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.754A pdb=" N THR D 82 " --> pdb=" O MET D 79 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP D 83 " --> pdb=" O LEU D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 79 through 83' Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.602A pdb=" N LEU D 117 " --> pdb=" O PHE D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 134 Processing helix chain 'D' and resid 142 through 175 removed outlier: 3.857A pdb=" N ASP D 170 " --> pdb=" O GLY D 166 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 315 Processing helix chain 'D' and resid 318 through 334 removed outlier: 3.619A pdb=" N VAL D 334 " --> pdb=" O THR D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 356 Processing helix chain 'D' and resid 364 through 372 Processing helix chain 'D' and resid 402 through 411 removed outlier: 4.379A pdb=" N LEU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 411 " --> pdb=" O THR D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 429 removed outlier: 3.792A pdb=" N LYS D 424 " --> pdb=" O ASP D 420 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE D 426 " --> pdb=" O ILE D 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 485 removed outlier: 3.635A pdb=" N LEU D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 508 removed outlier: 3.518A pdb=" N GLN D 496 " --> pdb=" O GLU D 492 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA D 497 " --> pdb=" O GLU D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 550 removed outlier: 3.850A pdb=" N THR D 549 " --> pdb=" O CYS D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 573 Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 593 through 603 removed outlier: 3.822A pdb=" N ASP D 599 " --> pdb=" O SER D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 625 removed outlier: 3.519A pdb=" N LYS D 615 " --> pdb=" O PHE D 611 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR D 616 " --> pdb=" O PRO D 612 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D 625 " --> pdb=" O ILE D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 645 Processing helix chain 'D' and resid 655 through 662 Processing helix chain 'D' and resid 670 through 714 removed outlier: 3.967A pdb=" N ILE D 674 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU D 708 " --> pdb=" O ILE D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 729 Processing helix chain 'D' and resid 751 through 781 removed outlier: 3.686A pdb=" N MET D 777 " --> pdb=" O THR D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 807 Processing helix chain 'D' and resid 808 through 813 Processing helix chain 'D' and resid 824 through 845 Processing helix chain 'D' and resid 853 through 878 removed outlier: 3.661A pdb=" N VAL D 858 " --> pdb=" O ILE D 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 919 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.754A pdb=" N THR E 82 " --> pdb=" O MET E 79 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP E 83 " --> pdb=" O LEU E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing helix chain 'E' and resid 113 through 119 removed outlier: 3.602A pdb=" N LEU E 117 " --> pdb=" O PHE E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 Processing helix chain 'E' and resid 142 through 175 removed outlier: 3.857A pdb=" N ASP E 170 " --> pdb=" O GLY E 166 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 315 Processing helix chain 'E' and resid 318 through 334 removed outlier: 3.620A pdb=" N VAL E 334 " --> pdb=" O THR E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 356 Processing helix chain 'E' and resid 364 through 372 Processing helix chain 'E' and resid 402 through 411 removed outlier: 4.379A pdb=" N LEU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA E 411 " --> pdb=" O THR E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 429 removed outlier: 3.792A pdb=" N LYS E 424 " --> pdb=" O ASP E 420 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA E 425 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE E 426 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU E 427 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 485 removed outlier: 3.635A pdb=" N LEU E 481 " --> pdb=" O PRO E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 508 removed outlier: 3.517A pdb=" N GLN E 496 " --> pdb=" O GLU E 492 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA E 497 " --> pdb=" O GLU E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 550 removed outlier: 3.850A pdb=" N THR E 549 " --> pdb=" O CYS E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 573 Processing helix chain 'E' and resid 581 through 585 Processing helix chain 'E' and resid 593 through 603 removed outlier: 3.822A pdb=" N ASP E 599 " --> pdb=" O SER E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 625 removed outlier: 3.519A pdb=" N LYS E 615 " --> pdb=" O PHE E 611 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR E 616 " --> pdb=" O PRO E 612 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG E 625 " --> pdb=" O ILE E 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 645 Processing helix chain 'E' and resid 655 through 662 Processing helix chain 'E' and resid 670 through 714 removed outlier: 3.967A pdb=" N ILE E 674 " --> pdb=" O GLY E 670 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU E 708 " --> pdb=" O ILE E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 718 through 729 Processing helix chain 'E' and resid 751 through 781 removed outlier: 3.686A pdb=" N MET E 777 " --> pdb=" O THR E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 792 through 807 Processing helix chain 'E' and resid 808 through 813 Processing helix chain 'E' and resid 824 through 845 Processing helix chain 'E' and resid 853 through 878 removed outlier: 3.660A pdb=" N VAL E 858 " --> pdb=" O ILE E 854 " (cutoff:3.500A) Processing helix chain 'E' and resid 896 through 919 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.754A pdb=" N THR F 82 " --> pdb=" O MET F 79 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP F 83 " --> pdb=" O LEU F 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 79 through 83' Processing helix chain 'F' and resid 113 through 119 removed outlier: 3.602A pdb=" N LEU F 117 " --> pdb=" O PHE F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 134 Processing helix chain 'F' and resid 142 through 175 removed outlier: 3.857A pdb=" N ASP F 170 " --> pdb=" O GLY F 166 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 315 Processing helix chain 'F' and resid 318 through 334 removed outlier: 3.620A pdb=" N VAL F 334 " --> pdb=" O THR F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 356 Processing helix chain 'F' and resid 364 through 372 Processing helix chain 'F' and resid 402 through 411 removed outlier: 4.379A pdb=" N LEU F 406 " --> pdb=" O GLU F 402 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA F 411 " --> pdb=" O THR F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 429 removed outlier: 3.792A pdb=" N LYS F 424 " --> pdb=" O ASP F 420 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA F 425 " --> pdb=" O ALA F 421 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE F 426 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU F 427 " --> pdb=" O ASP F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 485 removed outlier: 3.635A pdb=" N LEU F 481 " --> pdb=" O PRO F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 508 removed outlier: 3.518A pdb=" N GLN F 496 " --> pdb=" O GLU F 492 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA F 497 " --> pdb=" O GLU F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 550 removed outlier: 3.850A pdb=" N THR F 549 " --> pdb=" O CYS F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 573 Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 593 through 603 removed outlier: 3.823A pdb=" N ASP F 599 " --> pdb=" O SER F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 625 removed outlier: 3.519A pdb=" N LYS F 615 " --> pdb=" O PHE F 611 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR F 616 " --> pdb=" O PRO F 612 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG F 625 " --> pdb=" O ILE F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 645 Processing helix chain 'F' and resid 655 through 662 Processing helix chain 'F' and resid 670 through 714 removed outlier: 3.967A pdb=" N ILE F 674 " --> pdb=" O GLY F 670 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU F 708 " --> pdb=" O ILE F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 729 Processing helix chain 'F' and resid 751 through 781 removed outlier: 3.686A pdb=" N MET F 777 " --> pdb=" O THR F 773 " (cutoff:3.500A) Processing helix chain 'F' and resid 792 through 807 Processing helix chain 'F' and resid 808 through 813 Processing helix chain 'F' and resid 824 through 845 Processing helix chain 'F' and resid 853 through 878 removed outlier: 3.661A pdb=" N VAL F 858 " --> pdb=" O ILE F 854 " (cutoff:3.500A) Processing helix chain 'F' and resid 896 through 919 Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 205 removed outlier: 3.632A pdb=" N VAL A 204 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 256 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 226 removed outlier: 6.518A pdb=" N GLN A 224 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 250 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 358 through 360 removed outlier: 6.833A pdb=" N VAL A 629 " --> pdb=" O THR A 647 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE A 649 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N MET A 631 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE A 374 " --> pdb=" O ALA A 630 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR A 632 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS A 376 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A 375 " --> pdb=" O LYS A 555 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU A 557 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER A 377 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR A 579 " --> pdb=" O ALA A 608 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 389 through 390 removed outlier: 6.401A pdb=" N ILE A 526 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ARG A 517 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY A 528 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU A 463 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 445 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 203 through 205 removed outlier: 3.632A pdb=" N VAL B 204 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B 256 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 224 through 226 removed outlier: 6.518A pdb=" N GLN B 224 " --> pdb=" O LYS B 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 250 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 358 through 360 removed outlier: 6.833A pdb=" N VAL B 629 " --> pdb=" O THR B 647 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE B 649 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N MET B 631 " --> pdb=" O ILE B 649 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 374 " --> pdb=" O ALA B 630 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N THR B 632 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS B 376 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 375 " --> pdb=" O LYS B 555 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU B 557 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER B 377 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR B 579 " --> pdb=" O ALA B 608 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 389 through 390 removed outlier: 6.401A pdb=" N ILE B 526 " --> pdb=" O ARG B 517 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ARG B 517 " --> pdb=" O ILE B 526 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY B 528 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU B 463 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL B 445 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 203 through 205 removed outlier: 3.632A pdb=" N VAL C 204 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA C 256 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 224 through 226 removed outlier: 6.518A pdb=" N GLN C 224 " --> pdb=" O LYS C 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA C 250 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 358 through 360 removed outlier: 6.833A pdb=" N VAL C 629 " --> pdb=" O THR C 647 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE C 649 " --> pdb=" O VAL C 629 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N MET C 631 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE C 374 " --> pdb=" O ALA C 630 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N THR C 632 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS C 376 " --> pdb=" O THR C 632 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU C 375 " --> pdb=" O LYS C 555 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU C 557 " --> pdb=" O LEU C 375 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER C 377 " --> pdb=" O LEU C 557 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR C 579 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 389 through 390 removed outlier: 6.401A pdb=" N ILE C 526 " --> pdb=" O ARG C 517 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ARG C 517 " --> pdb=" O ILE C 526 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY C 528 " --> pdb=" O VAL C 515 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU C 463 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL C 445 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 203 through 205 removed outlier: 3.632A pdb=" N VAL D 204 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA D 256 " --> pdb=" O VAL D 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 224 through 226 removed outlier: 6.518A pdb=" N GLN D 224 " --> pdb=" O LYS D 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA D 250 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 358 through 360 removed outlier: 6.833A pdb=" N VAL D 629 " --> pdb=" O THR D 647 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE D 649 " --> pdb=" O VAL D 629 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N MET D 631 " --> pdb=" O ILE D 649 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE D 374 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR D 632 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS D 376 " --> pdb=" O THR D 632 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU D 375 " --> pdb=" O LYS D 555 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU D 557 " --> pdb=" O LEU D 375 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER D 377 " --> pdb=" O LEU D 557 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR D 579 " --> pdb=" O ALA D 608 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 389 through 390 removed outlier: 6.401A pdb=" N ILE D 526 " --> pdb=" O ARG D 517 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ARG D 517 " --> pdb=" O ILE D 526 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY D 528 " --> pdb=" O VAL D 515 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU D 463 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL D 445 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 203 through 205 removed outlier: 3.632A pdb=" N VAL E 204 " --> pdb=" O ALA E 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA E 256 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 224 through 226 removed outlier: 6.518A pdb=" N GLN E 224 " --> pdb=" O LYS E 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA E 250 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 358 through 360 removed outlier: 6.833A pdb=" N VAL E 629 " --> pdb=" O THR E 647 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE E 649 " --> pdb=" O VAL E 629 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N MET E 631 " --> pdb=" O ILE E 649 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE E 374 " --> pdb=" O ALA E 630 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N THR E 632 " --> pdb=" O ILE E 374 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS E 376 " --> pdb=" O THR E 632 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU E 375 " --> pdb=" O LYS E 555 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU E 557 " --> pdb=" O LEU E 375 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER E 377 " --> pdb=" O LEU E 557 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR E 579 " --> pdb=" O ALA E 608 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 389 through 390 removed outlier: 6.401A pdb=" N ILE E 526 " --> pdb=" O ARG E 517 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ARG E 517 " --> pdb=" O ILE E 526 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY E 528 " --> pdb=" O VAL E 515 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU E 463 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL E 445 " --> pdb=" O GLU E 463 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 203 through 205 removed outlier: 3.632A pdb=" N VAL F 204 " --> pdb=" O ALA F 256 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA F 256 " --> pdb=" O VAL F 204 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 224 through 226 removed outlier: 6.518A pdb=" N GLN F 224 " --> pdb=" O LYS F 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA F 250 " --> pdb=" O ASP F 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 358 through 360 removed outlier: 6.833A pdb=" N VAL F 629 " --> pdb=" O THR F 647 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE F 649 " --> pdb=" O VAL F 629 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N MET F 631 " --> pdb=" O ILE F 649 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE F 374 " --> pdb=" O ALA F 630 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N THR F 632 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS F 376 " --> pdb=" O THR F 632 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU F 375 " --> pdb=" O LYS F 555 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU F 557 " --> pdb=" O LEU F 375 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER F 377 " --> pdb=" O LEU F 557 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR F 579 " --> pdb=" O ALA F 608 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 389 through 390 removed outlier: 6.401A pdb=" N ILE F 526 " --> pdb=" O ARG F 517 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ARG F 517 " --> pdb=" O ILE F 526 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY F 528 " --> pdb=" O VAL F 515 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU F 463 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL F 445 " --> pdb=" O GLU F 463 " (cutoff:3.500A) 2046 hydrogen bonds defined for protein. 6066 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: 9.54 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9036 1.33 - 1.45: 8426 1.45 - 1.58: 21496 1.58 - 1.70: 0 1.70 - 1.83: 240 Bond restraints: 39198 Sorted by residual: bond pdb=" O5' ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sigma weight residual 1.610 1.826 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O5' ADP C1001 " pdb=" PA ADP C1001 " ideal model delta sigma weight residual 1.610 1.826 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O5' ADP E1001 " pdb=" PA ADP E1001 " ideal model delta sigma weight residual 1.610 1.826 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O5' ADP B1001 " pdb=" PA ADP B1001 " ideal model delta sigma weight residual 1.610 1.826 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sigma weight residual 1.610 1.826 -0.216 2.00e-02 2.50e+03 1.17e+02 ... (remaining 39193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 52992 3.96 - 7.92: 198 7.92 - 11.88: 30 11.88 - 15.85: 30 15.85 - 19.81: 6 Bond angle restraints: 53256 Sorted by residual: angle pdb=" O1A ADP C1001 " pdb=" PA ADP C1001 " pdb=" O5' ADP C1001 " ideal model delta sigma weight residual 108.20 88.39 19.81 3.00e+00 1.11e-01 4.36e+01 angle pdb=" O1A ADP F1001 " pdb=" PA ADP F1001 " pdb=" O5' ADP F1001 " ideal model delta sigma weight residual 108.20 88.39 19.81 3.00e+00 1.11e-01 4.36e+01 angle pdb=" O1A ADP D1001 " pdb=" PA ADP D1001 " pdb=" O5' ADP D1001 " ideal model delta sigma weight residual 108.20 88.40 19.80 3.00e+00 1.11e-01 4.36e+01 angle pdb=" O1A ADP A1001 " pdb=" PA ADP A1001 " pdb=" O5' ADP A1001 " ideal model delta sigma weight residual 108.20 88.40 19.80 3.00e+00 1.11e-01 4.36e+01 angle pdb=" O1A ADP E1001 " pdb=" PA ADP E1001 " pdb=" O5' ADP E1001 " ideal model delta sigma weight residual 108.20 88.40 19.80 3.00e+00 1.11e-01 4.36e+01 ... (remaining 53251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.30: 22464 30.30 - 60.60: 654 60.60 - 90.90: 24 90.90 - 121.20: 0 121.20 - 151.50: 12 Dihedral angle restraints: 23154 sinusoidal: 8988 harmonic: 14166 Sorted by residual: dihedral pdb=" O2A ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PA ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 91.50 -151.50 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O2A ADP D1001 " pdb=" O3A ADP D1001 " pdb=" PA ADP D1001 " pdb=" PB ADP D1001 " ideal model delta sinusoidal sigma weight residual -60.00 91.50 -151.50 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O2A ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PA ADP F1001 " pdb=" PB ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 91.50 -151.50 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 23151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 4111 0.038 - 0.076: 1586 0.076 - 0.114: 437 0.114 - 0.152: 76 0.152 - 0.190: 24 Chirality restraints: 6234 Sorted by residual: chirality pdb=" C2' ADP E1001 " pdb=" C1' ADP E1001 " pdb=" C3' ADP E1001 " pdb=" O2' ADP E1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" C2' ADP B1001 " pdb=" C1' ADP B1001 " pdb=" C3' ADP B1001 " pdb=" O2' ADP B1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" C2' ADP F1001 " pdb=" C1' ADP F1001 " pdb=" C3' ADP F1001 " pdb=" O2' ADP F1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.02e-01 ... (remaining 6231 not shown) Planarity restraints: 6708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 709 " -0.030 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP D 709 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP D 709 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 709 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 709 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 709 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 709 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 709 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 709 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 709 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 709 " 0.030 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP A 709 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A 709 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 709 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 709 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 709 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 709 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 709 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 709 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 709 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 709 " -0.030 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP E 709 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP E 709 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP E 709 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 709 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 709 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 709 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 709 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 709 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 709 " -0.003 2.00e-02 2.50e+03 ... (remaining 6705 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.84: 12754 2.84 - 3.42: 43378 3.42 - 3.99: 69368 3.99 - 4.57: 100796 4.57 - 5.14: 143868 Nonbonded interactions: 370164 Sorted by model distance: nonbonded pdb=" CB SER B 892 " pdb=" CD1 LEU C 902 " model vdw 2.268 3.860 nonbonded pdb=" CB SER E 892 " pdb=" CD1 LEU F 902 " model vdw 2.268 3.860 nonbonded pdb=" CB SER C 892 " pdb=" CD1 LEU D 902 " model vdw 2.268 3.860 nonbonded pdb=" CD1 LEU A 902 " pdb=" CB SER F 892 " model vdw 2.268 3.860 nonbonded pdb=" CB SER D 892 " pdb=" CD1 LEU E 902 " model vdw 2.268 3.860 ... (remaining 370159 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.490 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: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 36.190 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 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 0.216 39198 Z= 0.291 Angle : 0.816 19.808 53256 Z= 0.391 Chirality : 0.044 0.190 6234 Planarity : 0.005 0.082 6708 Dihedral : 14.198 151.503 14070 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.12), residues: 4938 helix: 0.88 (0.10), residues: 2544 sheet: -1.48 (0.28), residues: 318 loop : -2.07 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 859 TYR 0.016 0.002 TYR E 691 PHE 0.012 0.001 PHE C 841 TRP 0.063 0.003 TRP D 709 HIS 0.007 0.001 HIS B 701 Details of bonding type rmsd covalent geometry : bond 0.00618 (39198) covalent geometry : angle 0.81590 (53256) hydrogen bonds : bond 0.17215 ( 2046) hydrogen bonds : angle 6.19504 ( 6066) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 983 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8122 (m-80) cc_final: 0.7825 (m-80) REVERT: A 252 LYS cc_start: 0.7080 (tptt) cc_final: 0.6764 (tptt) REVERT: A 303 PHE cc_start: 0.7289 (t80) cc_final: 0.6895 (t80) REVERT: A 317 ASN cc_start: 0.7889 (m-40) cc_final: 0.7683 (m-40) REVERT: A 385 LYS cc_start: 0.7865 (mtpp) cc_final: 0.7632 (mtpp) REVERT: A 474 LYS cc_start: 0.7849 (ttpt) cc_final: 0.7520 (ttpt) REVERT: A 567 GLU cc_start: 0.7319 (tp30) cc_final: 0.6822 (tp30) REVERT: A 569 SER cc_start: 0.8091 (m) cc_final: 0.7539 (p) REVERT: A 627 TYR cc_start: 0.8035 (m-80) cc_final: 0.7708 (m-80) REVERT: A 759 SER cc_start: 0.8300 (m) cc_final: 0.7897 (p) REVERT: A 844 TRP cc_start: 0.7956 (m-90) cc_final: 0.7697 (m-10) REVERT: A 898 LYS cc_start: 0.8052 (mmmm) cc_final: 0.7641 (mmmm) REVERT: A 901 SER cc_start: 0.8341 (t) cc_final: 0.7590 (p) REVERT: A 904 ASP cc_start: 0.7485 (t0) cc_final: 0.7193 (t0) REVERT: A 910 GLN cc_start: 0.7846 (tp-100) cc_final: 0.7562 (mt0) REVERT: B 171 GLU cc_start: 0.6783 (tp30) cc_final: 0.6549 (tp30) REVERT: B 317 ASN cc_start: 0.7905 (m-40) cc_final: 0.7674 (m-40) REVERT: B 332 ILE cc_start: 0.7822 (pt) cc_final: 0.7600 (pt) REVERT: B 369 LEU cc_start: 0.8190 (tp) cc_final: 0.7984 (tt) REVERT: B 385 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7754 (mtpp) REVERT: B 474 LYS cc_start: 0.7939 (ttpt) cc_final: 0.7545 (ttpt) REVERT: B 498 TYR cc_start: 0.6825 (t80) cc_final: 0.6265 (t80) REVERT: B 539 ASP cc_start: 0.7029 (p0) cc_final: 0.6788 (p0) REVERT: B 548 LYS cc_start: 0.7693 (mtpp) cc_final: 0.7332 (mtpp) REVERT: B 567 GLU cc_start: 0.7295 (tp30) cc_final: 0.6780 (tp30) REVERT: B 569 SER cc_start: 0.8150 (m) cc_final: 0.7913 (m) REVERT: B 582 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7389 (mm-30) REVERT: B 627 TYR cc_start: 0.7886 (m-80) cc_final: 0.7638 (m-80) REVERT: B 656 ASP cc_start: 0.7293 (m-30) cc_final: 0.6890 (m-30) REVERT: B 749 LYS cc_start: 0.8171 (ptpt) cc_final: 0.7968 (ptpt) REVERT: B 898 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7614 (mmmm) REVERT: B 901 SER cc_start: 0.8544 (t) cc_final: 0.8025 (p) REVERT: B 902 LEU cc_start: 0.8239 (tp) cc_final: 0.7940 (tp) REVERT: B 904 ASP cc_start: 0.7573 (t0) cc_final: 0.7278 (t0) REVERT: B 910 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7556 (mt0) REVERT: C 120 PHE cc_start: 0.7910 (m-80) cc_final: 0.7657 (m-80) REVERT: C 301 VAL cc_start: 0.8431 (t) cc_final: 0.7831 (m) REVERT: C 303 PHE cc_start: 0.7587 (t80) cc_final: 0.7258 (t80) REVERT: C 314 TYR cc_start: 0.7894 (m-80) cc_final: 0.7624 (m-80) REVERT: C 315 ARG cc_start: 0.7739 (mtt90) cc_final: 0.7525 (mtt90) REVERT: C 474 LYS cc_start: 0.7827 (ttpt) cc_final: 0.7541 (ttpt) REVERT: C 481 LEU cc_start: 0.7293 (mm) cc_final: 0.7030 (mp) REVERT: C 539 ASP cc_start: 0.7034 (p0) cc_final: 0.6737 (p0) REVERT: C 548 LYS cc_start: 0.7777 (mtpp) cc_final: 0.7462 (mtpp) REVERT: C 569 SER cc_start: 0.8124 (m) cc_final: 0.7844 (m) REVERT: C 593 PRO cc_start: 0.8145 (Cg_exo) cc_final: 0.7914 (Cg_endo) REVERT: C 627 TYR cc_start: 0.7897 (m-80) cc_final: 0.7550 (m-80) REVERT: C 656 ASP cc_start: 0.7217 (m-30) cc_final: 0.6752 (m-30) REVERT: C 775 THR cc_start: 0.8344 (m) cc_final: 0.8142 (p) REVERT: C 844 TRP cc_start: 0.8079 (m-90) cc_final: 0.7841 (m-10) REVERT: C 865 PHE cc_start: 0.8160 (t80) cc_final: 0.7915 (t80) REVERT: C 898 LYS cc_start: 0.7920 (mmmm) cc_final: 0.7538 (mmmm) REVERT: C 901 SER cc_start: 0.8483 (t) cc_final: 0.7990 (p) REVERT: C 904 ASP cc_start: 0.7564 (t0) cc_final: 0.7305 (t0) REVERT: C 910 GLN cc_start: 0.7763 (tp-100) cc_final: 0.7491 (mt0) REVERT: D 303 PHE cc_start: 0.7503 (t80) cc_final: 0.7192 (t80) REVERT: D 385 LYS cc_start: 0.7861 (mtpp) cc_final: 0.7569 (mtpp) REVERT: D 474 LYS cc_start: 0.7832 (ttpt) cc_final: 0.7472 (ttpt) REVERT: D 481 LEU cc_start: 0.7206 (mm) cc_final: 0.6937 (mp) REVERT: D 498 TYR cc_start: 0.6990 (t80) cc_final: 0.6337 (t80) REVERT: D 539 ASP cc_start: 0.7188 (p0) cc_final: 0.6956 (p0) REVERT: D 566 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.7143 (mtp85) REVERT: D 567 GLU cc_start: 0.7230 (tp30) cc_final: 0.6662 (tp30) REVERT: D 569 SER cc_start: 0.8102 (m) cc_final: 0.7551 (p) REVERT: D 582 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7328 (mm-30) REVERT: D 656 ASP cc_start: 0.7256 (m-30) cc_final: 0.6784 (m-30) REVERT: D 833 LEU cc_start: 0.8679 (tt) cc_final: 0.8471 (tp) REVERT: D 844 TRP cc_start: 0.8167 (m-90) cc_final: 0.7929 (m-10) REVERT: D 898 LYS cc_start: 0.8115 (mmmm) cc_final: 0.7716 (mmmm) REVERT: D 901 SER cc_start: 0.8326 (t) cc_final: 0.7865 (p) REVERT: D 903 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6983 (mt-10) REVERT: D 904 ASP cc_start: 0.7520 (t0) cc_final: 0.7229 (t0) REVERT: D 910 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7632 (mt0) REVERT: E 164 GLN cc_start: 0.7008 (tt0) cc_final: 0.6776 (tt0) REVERT: E 171 GLU cc_start: 0.6962 (tp30) cc_final: 0.6670 (tp30) REVERT: E 176 LEU cc_start: 0.8360 (tp) cc_final: 0.7989 (tt) REVERT: E 300 LEU cc_start: 0.8437 (mt) cc_final: 0.8111 (mm) REVERT: E 303 PHE cc_start: 0.7468 (t80) cc_final: 0.7196 (t80) REVERT: E 312 SER cc_start: 0.8160 (m) cc_final: 0.7959 (p) REVERT: E 385 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7846 (mtpp) REVERT: E 474 LYS cc_start: 0.7503 (ttpt) cc_final: 0.7006 (ttpt) REVERT: E 481 LEU cc_start: 0.7226 (mm) cc_final: 0.7013 (mp) REVERT: E 498 TYR cc_start: 0.6943 (t80) cc_final: 0.6379 (t80) REVERT: E 539 ASP cc_start: 0.7174 (p0) cc_final: 0.6959 (p0) REVERT: E 542 LYS cc_start: 0.7967 (pttp) cc_final: 0.7729 (pttp) REVERT: E 548 LYS cc_start: 0.7726 (mtpp) cc_final: 0.7356 (mtpp) REVERT: E 570 ARG cc_start: 0.7184 (ttm170) cc_final: 0.6904 (ttm170) REVERT: E 602 GLU cc_start: 0.6906 (tt0) cc_final: 0.6496 (tt0) REVERT: E 627 TYR cc_start: 0.7996 (m-80) cc_final: 0.7773 (m-80) REVERT: E 656 ASP cc_start: 0.7284 (m-30) cc_final: 0.6771 (m-30) REVERT: E 738 TYR cc_start: 0.6443 (m-80) cc_final: 0.6239 (m-80) REVERT: E 775 THR cc_start: 0.8322 (m) cc_final: 0.8081 (p) REVERT: E 898 LYS cc_start: 0.8017 (mmmm) cc_final: 0.7645 (mmmm) REVERT: E 901 SER cc_start: 0.8397 (t) cc_final: 0.7928 (p) REVERT: E 902 LEU cc_start: 0.8152 (tp) cc_final: 0.7882 (tp) REVERT: E 904 ASP cc_start: 0.7476 (t0) cc_final: 0.7271 (t0) REVERT: F 164 GLN cc_start: 0.6901 (tt0) cc_final: 0.6669 (tt0) REVERT: F 252 LYS cc_start: 0.6937 (tptt) cc_final: 0.6570 (tptt) REVERT: F 301 VAL cc_start: 0.8416 (t) cc_final: 0.7813 (m) REVERT: F 303 PHE cc_start: 0.7503 (t80) cc_final: 0.7211 (t80) REVERT: F 359 ILE cc_start: 0.8150 (mp) cc_final: 0.7934 (mm) REVERT: F 361 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7550 (tp-100) REVERT: F 474 LYS cc_start: 0.7657 (ttpt) cc_final: 0.7219 (ttpt) REVERT: F 569 SER cc_start: 0.8172 (m) cc_final: 0.7916 (m) REVERT: F 683 GLN cc_start: 0.7935 (mt0) cc_final: 0.7711 (mt0) REVERT: F 759 SER cc_start: 0.8103 (m) cc_final: 0.7801 (p) REVERT: F 775 THR cc_start: 0.8332 (m) cc_final: 0.8124 (p) REVERT: F 800 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7664 (tm-30) REVERT: F 806 ASN cc_start: 0.8140 (m-40) cc_final: 0.7939 (m-40) REVERT: F 833 LEU cc_start: 0.8560 (tt) cc_final: 0.8267 (tt) REVERT: F 844 TRP cc_start: 0.8104 (m-90) cc_final: 0.7848 (m-10) REVERT: F 898 LYS cc_start: 0.7985 (mmmm) cc_final: 0.7626 (mmmm) REVERT: F 901 SER cc_start: 0.8427 (t) cc_final: 0.7949 (p) REVERT: F 902 LEU cc_start: 0.7941 (tp) cc_final: 0.7739 (tt) outliers start: 0 outliers final: 0 residues processed: 983 average time/residue: 0.2322 time to fit residues: 376.3331 Evaluate side-chains 853 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 853 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 0.6980 chunk 197 optimal weight: 0.0010 chunk 388 optimal weight: 0.9980 chunk 455 optimal weight: 0.4980 chunk 215 optimal weight: 0.0040 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.0070 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 0.9990 overall best weight: 0.2416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN A 683 GLN A 815 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 ASN B 683 GLN B 815 ASN C 571 GLN C 637 ASN C 714 ASN D 164 GLN D 637 ASN D 683 GLN D 815 ASN E 577 ASN E 637 ASN E 780 GLN E 815 ASN E 915 GLN F 637 ASN F 815 ASN F 915 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.184727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140070 restraints weight = 53825.099| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.44 r_work: 0.3518 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39198 Z= 0.128 Angle : 0.638 10.397 53256 Z= 0.322 Chirality : 0.042 0.147 6234 Planarity : 0.005 0.074 6708 Dihedral : 8.271 143.175 5328 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.10 % Allowed : 9.82 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.12), residues: 4938 helix: 1.34 (0.10), residues: 2562 sheet: -1.35 (0.27), residues: 336 loop : -2.35 (0.12), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 253 TYR 0.024 0.002 TYR D 541 PHE 0.021 0.001 PHE C 600 TRP 0.030 0.002 TRP B 709 HIS 0.007 0.001 HIS E 701 Details of bonding type rmsd covalent geometry : bond 0.00270 (39198) covalent geometry : angle 0.63774 (53256) hydrogen bonds : bond 0.04241 ( 2046) hydrogen bonds : angle 4.73488 ( 6066) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 924 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8067 (m-80) cc_final: 0.7757 (m-80) REVERT: A 174 LYS cc_start: 0.7784 (tttp) cc_final: 0.7510 (tttp) REVERT: A 303 PHE cc_start: 0.8329 (t80) cc_final: 0.7905 (t80) REVERT: A 385 LYS cc_start: 0.8150 (mtpp) cc_final: 0.7888 (mtpp) REVERT: A 474 LYS cc_start: 0.7713 (ttpt) cc_final: 0.7353 (ttpt) REVERT: A 539 ASP cc_start: 0.7897 (p0) cc_final: 0.7641 (p0) REVERT: A 567 GLU cc_start: 0.8333 (tp30) cc_final: 0.7771 (tp30) REVERT: A 569 SER cc_start: 0.8555 (m) cc_final: 0.8049 (p) REVERT: A 627 TYR cc_start: 0.8372 (m-80) cc_final: 0.8069 (m-80) REVERT: A 751 ASN cc_start: 0.8460 (t0) cc_final: 0.8189 (t0) REVERT: A 759 SER cc_start: 0.8639 (m) cc_final: 0.8209 (p) REVERT: A 844 TRP cc_start: 0.8109 (m-90) cc_final: 0.7814 (m-10) REVERT: A 898 LYS cc_start: 0.8164 (mmmm) cc_final: 0.7746 (mmmm) REVERT: A 901 SER cc_start: 0.8646 (t) cc_final: 0.7945 (p) REVERT: A 904 ASP cc_start: 0.8028 (t0) cc_final: 0.7766 (t0) REVERT: A 905 PHE cc_start: 0.8677 (t80) cc_final: 0.8457 (t80) REVERT: B 116 PHE cc_start: 0.7818 (t80) cc_final: 0.7467 (t80) REVERT: B 120 PHE cc_start: 0.8129 (m-80) cc_final: 0.7586 (m-80) REVERT: B 171 GLU cc_start: 0.7467 (tp30) cc_final: 0.6974 (tp30) REVERT: B 174 LYS cc_start: 0.7897 (tttp) cc_final: 0.7656 (tttp) REVERT: B 252 LYS cc_start: 0.7338 (tptt) cc_final: 0.7030 (tptt) REVERT: B 385 LYS cc_start: 0.8255 (mtpp) cc_final: 0.7983 (mtpp) REVERT: B 474 LYS cc_start: 0.7981 (ttpt) cc_final: 0.7601 (ttpt) REVERT: B 567 GLU cc_start: 0.8320 (tp30) cc_final: 0.7738 (tp30) REVERT: B 579 TYR cc_start: 0.8321 (m-10) cc_final: 0.8047 (m-80) REVERT: B 582 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8004 (mm-30) REVERT: B 599 ASP cc_start: 0.8552 (t0) cc_final: 0.8269 (t0) REVERT: B 656 ASP cc_start: 0.8220 (m-30) cc_final: 0.7985 (m-30) REVERT: B 751 ASN cc_start: 0.8421 (t0) cc_final: 0.8138 (t0) REVERT: B 754 LYS cc_start: 0.8691 (tttt) cc_final: 0.8459 (tttm) REVERT: B 837 LEU cc_start: 0.8574 (mt) cc_final: 0.8349 (mt) REVERT: B 898 LYS cc_start: 0.8114 (mmmm) cc_final: 0.7726 (mmmm) REVERT: B 901 SER cc_start: 0.8723 (t) cc_final: 0.8248 (p) REVERT: B 904 ASP cc_start: 0.8028 (t0) cc_final: 0.7688 (t0) REVERT: B 910 GLN cc_start: 0.8421 (tp-100) cc_final: 0.8217 (mt0) REVERT: C 120 PHE cc_start: 0.7749 (m-80) cc_final: 0.7477 (m-80) REVERT: C 171 GLU cc_start: 0.7390 (tp30) cc_final: 0.6820 (tp30) REVERT: C 301 VAL cc_start: 0.8419 (t) cc_final: 0.7589 (m) REVERT: C 303 PHE cc_start: 0.8422 (t80) cc_final: 0.8093 (t80) REVERT: C 314 TYR cc_start: 0.8463 (m-80) cc_final: 0.7999 (m-80) REVERT: C 474 LYS cc_start: 0.7751 (ttpt) cc_final: 0.7405 (ttpt) REVERT: C 542 LYS cc_start: 0.8437 (pttp) cc_final: 0.8170 (pttp) REVERT: C 567 GLU cc_start: 0.8216 (tp30) cc_final: 0.7779 (tp30) REVERT: C 569 SER cc_start: 0.8595 (m) cc_final: 0.8349 (m) REVERT: C 620 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8219 (tm-30) REVERT: C 714 ASN cc_start: 0.8729 (t0) cc_final: 0.8460 (t0) REVERT: C 751 ASN cc_start: 0.8319 (t0) cc_final: 0.8010 (t0) REVERT: C 826 GLN cc_start: 0.8365 (mp10) cc_final: 0.8059 (mp10) REVERT: C 844 TRP cc_start: 0.8294 (m-90) cc_final: 0.7934 (m-10) REVERT: C 865 PHE cc_start: 0.8590 (t80) cc_final: 0.8327 (t80) REVERT: C 898 LYS cc_start: 0.7974 (mmmm) cc_final: 0.7608 (mmmm) REVERT: C 901 SER cc_start: 0.8721 (t) cc_final: 0.8278 (p) REVERT: C 904 ASP cc_start: 0.8001 (t0) cc_final: 0.7665 (t0) REVERT: C 910 GLN cc_start: 0.8476 (tp-100) cc_final: 0.8234 (mt0) REVERT: D 171 GLU cc_start: 0.7513 (tp30) cc_final: 0.6877 (tp30) REVERT: D 174 LYS cc_start: 0.7614 (tttp) cc_final: 0.7313 (tttp) REVERT: D 209 ILE cc_start: 0.8062 (mm) cc_final: 0.7744 (tp) REVERT: D 303 PHE cc_start: 0.8337 (t80) cc_final: 0.7989 (t80) REVERT: D 385 LYS cc_start: 0.8067 (mtpp) cc_final: 0.7845 (mtpp) REVERT: D 474 LYS cc_start: 0.7818 (ttpt) cc_final: 0.7312 (ttpt) REVERT: D 539 ASP cc_start: 0.7893 (p0) cc_final: 0.7602 (p0) REVERT: D 567 GLU cc_start: 0.8269 (tp30) cc_final: 0.7700 (tp30) REVERT: D 569 SER cc_start: 0.8543 (m) cc_final: 0.8059 (p) REVERT: D 582 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8026 (mm-30) REVERT: D 602 GLU cc_start: 0.8082 (tt0) cc_final: 0.7791 (tt0) REVERT: D 627 TYR cc_start: 0.8331 (m-80) cc_final: 0.8108 (m-80) REVERT: D 656 ASP cc_start: 0.7934 (m-30) cc_final: 0.7577 (m-30) REVERT: D 679 LYS cc_start: 0.8618 (mtmm) cc_final: 0.8389 (mtpp) REVERT: D 833 LEU cc_start: 0.8683 (tt) cc_final: 0.8431 (tp) REVERT: D 844 TRP cc_start: 0.8304 (m-90) cc_final: 0.8000 (m-10) REVERT: D 898 LYS cc_start: 0.8246 (mmmm) cc_final: 0.7948 (mmmm) REVERT: D 901 SER cc_start: 0.8642 (t) cc_final: 0.8225 (p) REVERT: D 903 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7446 (mt-10) REVERT: D 904 ASP cc_start: 0.8001 (t0) cc_final: 0.7751 (t0) REVERT: D 911 ARG cc_start: 0.8287 (mtt90) cc_final: 0.8047 (mtt180) REVERT: D 915 GLN cc_start: 0.8463 (tt0) cc_final: 0.7897 (mt0) REVERT: E 171 GLU cc_start: 0.7601 (tp30) cc_final: 0.7086 (tp30) REVERT: E 252 LYS cc_start: 0.7129 (tptt) cc_final: 0.6677 (tptt) REVERT: E 300 LEU cc_start: 0.8559 (mt) cc_final: 0.8254 (mm) REVERT: E 303 PHE cc_start: 0.8292 (t80) cc_final: 0.8046 (t80) REVERT: E 312 SER cc_start: 0.8689 (m) cc_final: 0.8247 (p) REVERT: E 481 LEU cc_start: 0.7045 (mm) cc_final: 0.6802 (mp) REVERT: E 498 TYR cc_start: 0.6770 (t80) cc_final: 0.6318 (t80) REVERT: E 542 LYS cc_start: 0.8348 (pttp) cc_final: 0.8081 (pttp) REVERT: E 569 SER cc_start: 0.8575 (m) cc_final: 0.8351 (m) REVERT: E 570 ARG cc_start: 0.8091 (ttm170) cc_final: 0.7857 (ttm170) REVERT: E 579 TYR cc_start: 0.8419 (m-10) cc_final: 0.8171 (m-80) REVERT: E 582 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7868 (mm-30) REVERT: E 595 SER cc_start: 0.8531 (p) cc_final: 0.8323 (p) REVERT: E 656 ASP cc_start: 0.8157 (m-30) cc_final: 0.7917 (m-30) REVERT: E 751 ASN cc_start: 0.8190 (t0) cc_final: 0.7880 (t0) REVERT: E 898 LYS cc_start: 0.8178 (mmmm) cc_final: 0.7797 (mmmm) REVERT: E 901 SER cc_start: 0.8642 (t) cc_final: 0.8246 (p) REVERT: E 904 ASP cc_start: 0.8014 (t0) cc_final: 0.7755 (t0) REVERT: F 303 PHE cc_start: 0.8408 (t80) cc_final: 0.8156 (t80) REVERT: F 314 TYR cc_start: 0.8535 (m-80) cc_final: 0.8291 (m-80) REVERT: F 474 LYS cc_start: 0.7495 (ttpt) cc_final: 0.6920 (ttpt) REVERT: F 751 ASN cc_start: 0.8313 (t0) cc_final: 0.8026 (t0) REVERT: F 833 LEU cc_start: 0.8611 (tt) cc_final: 0.8355 (tt) REVERT: F 844 TRP cc_start: 0.8267 (m-90) cc_final: 0.7898 (m-10) REVERT: F 898 LYS cc_start: 0.8051 (mmmm) cc_final: 0.7692 (mmmm) REVERT: F 901 SER cc_start: 0.8615 (t) cc_final: 0.8240 (p) outliers start: 45 outliers final: 28 residues processed: 933 average time/residue: 0.2348 time to fit residues: 355.9553 Evaluate side-chains 881 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 853 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 548 LYS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 681 SER Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 681 SER Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 703 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 134 optimal weight: 2.9990 chunk 312 optimal weight: 1.9990 chunk 347 optimal weight: 0.9990 chunk 322 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 282 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 425 optimal weight: 0.8980 chunk 280 optimal weight: 0.0570 chunk 337 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN A 683 GLN A 815 ASN B 637 ASN ** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 815 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 GLN C 637 ASN C 916 HIS D 637 ASN D 683 GLN E 637 ASN ** E 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 815 ASN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 637 ASN F 789 ASN F 806 ASN F 815 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.181823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136846 restraints weight = 53774.690| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.48 r_work: 0.3469 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39198 Z= 0.156 Angle : 0.613 7.861 53256 Z= 0.309 Chirality : 0.043 0.163 6234 Planarity : 0.004 0.060 6708 Dihedral : 7.842 136.619 5328 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.05 % Allowed : 13.74 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.12), residues: 4938 helix: 1.47 (0.10), residues: 2580 sheet: -1.71 (0.26), residues: 348 loop : -2.31 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 625 TYR 0.020 0.002 TYR D 541 PHE 0.017 0.001 PHE B 868 TRP 0.029 0.002 TRP A 709 HIS 0.007 0.001 HIS C 916 Details of bonding type rmsd covalent geometry : bond 0.00345 (39198) covalent geometry : angle 0.61349 (53256) hydrogen bonds : bond 0.04288 ( 2046) hydrogen bonds : angle 4.54474 ( 6066) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 911 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 PHE cc_start: 0.7527 (t80) cc_final: 0.7325 (t80) REVERT: A 120 PHE cc_start: 0.8169 (m-80) cc_final: 0.7797 (m-80) REVERT: A 174 LYS cc_start: 0.7884 (tttp) cc_final: 0.7619 (tttp) REVERT: A 202 LEU cc_start: 0.6865 (mt) cc_final: 0.6621 (mp) REVERT: A 385 LYS cc_start: 0.8277 (mtpp) cc_final: 0.8008 (mtpp) REVERT: A 474 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7532 (ttpt) REVERT: A 539 ASP cc_start: 0.7912 (p0) cc_final: 0.7610 (p0) REVERT: A 567 GLU cc_start: 0.8272 (tp30) cc_final: 0.7745 (tp30) REVERT: A 569 SER cc_start: 0.8607 (m) cc_final: 0.8090 (p) REVERT: A 605 ASP cc_start: 0.7761 (m-30) cc_final: 0.7551 (t0) REVERT: A 624 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8362 (mt0) REVERT: A 720 GLU cc_start: 0.8008 (mp0) cc_final: 0.7622 (mp0) REVERT: A 751 ASN cc_start: 0.8430 (t0) cc_final: 0.8155 (t0) REVERT: A 759 SER cc_start: 0.8562 (m) cc_final: 0.8179 (p) REVERT: A 805 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7417 (mt-10) REVERT: A 844 TRP cc_start: 0.8357 (m-90) cc_final: 0.8036 (m-10) REVERT: A 898 LYS cc_start: 0.8102 (mmmm) cc_final: 0.7674 (mmmm) REVERT: A 901 SER cc_start: 0.8700 (t) cc_final: 0.8104 (p) REVERT: A 904 ASP cc_start: 0.8050 (t0) cc_final: 0.7775 (t0) REVERT: A 905 PHE cc_start: 0.8677 (t80) cc_final: 0.8416 (t80) REVERT: B 116 PHE cc_start: 0.7820 (t80) cc_final: 0.7517 (t80) REVERT: B 120 PHE cc_start: 0.8187 (m-80) cc_final: 0.7713 (m-80) REVERT: B 171 GLU cc_start: 0.7442 (tp30) cc_final: 0.7021 (tp30) REVERT: B 174 LYS cc_start: 0.8031 (tttp) cc_final: 0.7775 (tttp) REVERT: B 252 LYS cc_start: 0.7510 (tptt) cc_final: 0.7195 (tptt) REVERT: B 346 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7963 (mmm) REVERT: B 385 LYS cc_start: 0.8417 (mtpp) cc_final: 0.7962 (mtpp) REVERT: B 387 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7270 (pttm) REVERT: B 474 LYS cc_start: 0.8048 (ttpt) cc_final: 0.7572 (ttpt) REVERT: B 498 TYR cc_start: 0.6818 (t80) cc_final: 0.6415 (t80) REVERT: B 567 GLU cc_start: 0.8280 (tp30) cc_final: 0.7748 (tp30) REVERT: B 582 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7964 (mm-30) REVERT: B 583 ARG cc_start: 0.8803 (mtp-110) cc_final: 0.8297 (mtp-110) REVERT: B 599 ASP cc_start: 0.8472 (t0) cc_final: 0.8216 (t0) REVERT: B 656 ASP cc_start: 0.8246 (m-30) cc_final: 0.8000 (m-30) REVERT: B 751 ASN cc_start: 0.8484 (t0) cc_final: 0.8181 (t0) REVERT: B 754 LYS cc_start: 0.8633 (tttt) cc_final: 0.8395 (tttm) REVERT: B 844 TRP cc_start: 0.8414 (m-90) cc_final: 0.7976 (m-10) REVERT: B 848 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7684 (mm-30) REVERT: B 898 LYS cc_start: 0.8064 (mmmm) cc_final: 0.7806 (mmmm) REVERT: B 904 ASP cc_start: 0.8068 (t0) cc_final: 0.7737 (t0) REVERT: C 120 PHE cc_start: 0.7787 (m-80) cc_final: 0.7443 (m-80) REVERT: C 171 GLU cc_start: 0.7448 (tp30) cc_final: 0.6907 (tp30) REVERT: C 174 LYS cc_start: 0.7733 (tttp) cc_final: 0.7384 (tttp) REVERT: C 303 PHE cc_start: 0.8330 (t80) cc_final: 0.8059 (t80) REVERT: C 314 TYR cc_start: 0.8532 (m-80) cc_final: 0.8229 (m-80) REVERT: C 380 THR cc_start: 0.8447 (t) cc_final: 0.8096 (p) REVERT: C 474 LYS cc_start: 0.7878 (ttpt) cc_final: 0.7490 (ttpt) REVERT: C 542 LYS cc_start: 0.8321 (pttp) cc_final: 0.8060 (pttp) REVERT: C 567 GLU cc_start: 0.8242 (tp30) cc_final: 0.8004 (tp30) REVERT: C 570 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7944 (ttm110) REVERT: C 751 ASN cc_start: 0.8426 (t0) cc_final: 0.8068 (t0) REVERT: C 865 PHE cc_start: 0.8587 (t80) cc_final: 0.8318 (t80) REVERT: C 898 LYS cc_start: 0.7966 (mmmm) cc_final: 0.7614 (mmmm) REVERT: C 901 SER cc_start: 0.8776 (t) cc_final: 0.8261 (p) REVERT: C 904 ASP cc_start: 0.8054 (t0) cc_final: 0.7726 (t0) REVERT: C 905 PHE cc_start: 0.8483 (t80) cc_final: 0.8106 (t80) REVERT: C 910 GLN cc_start: 0.8515 (tp-100) cc_final: 0.8284 (mt0) REVERT: C 916 HIS cc_start: 0.8218 (m-70) cc_final: 0.7957 (m170) REVERT: D 144 PHE cc_start: 0.7618 (t80) cc_final: 0.7346 (t80) REVERT: D 171 GLU cc_start: 0.7408 (tp30) cc_final: 0.6880 (tp30) REVERT: D 174 LYS cc_start: 0.7769 (tttp) cc_final: 0.7518 (tttp) REVERT: D 303 PHE cc_start: 0.8332 (t80) cc_final: 0.7984 (t80) REVERT: D 474 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7486 (ttpt) REVERT: D 539 ASP cc_start: 0.7964 (p0) cc_final: 0.7730 (p0) REVERT: D 548 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8022 (mtpp) REVERT: D 558 THR cc_start: 0.8401 (m) cc_final: 0.8090 (t) REVERT: D 567 GLU cc_start: 0.8268 (tp30) cc_final: 0.7742 (tp30) REVERT: D 569 SER cc_start: 0.8642 (m) cc_final: 0.8174 (p) REVERT: D 615 LYS cc_start: 0.8616 (mtpp) cc_final: 0.7898 (mtmt) REVERT: D 656 ASP cc_start: 0.7973 (m-30) cc_final: 0.7728 (m-30) REVERT: D 679 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8370 (mtpp) REVERT: D 833 LEU cc_start: 0.8647 (tt) cc_final: 0.8400 (tp) REVERT: D 898 LYS cc_start: 0.8320 (mmmm) cc_final: 0.7888 (mmmm) REVERT: D 901 SER cc_start: 0.8645 (t) cc_final: 0.8212 (p) REVERT: D 904 ASP cc_start: 0.8029 (t0) cc_final: 0.7754 (t0) REVERT: E 171 GLU cc_start: 0.7627 (tp30) cc_final: 0.7171 (tp30) REVERT: E 252 LYS cc_start: 0.7459 (tptt) cc_final: 0.6987 (tptt) REVERT: E 300 LEU cc_start: 0.8617 (mt) cc_final: 0.8347 (mm) REVERT: E 303 PHE cc_start: 0.8216 (t80) cc_final: 0.7911 (t80) REVERT: E 346 MET cc_start: 0.8308 (mmm) cc_final: 0.8108 (mmm) REVERT: E 357 LYS cc_start: 0.8234 (mmmm) cc_final: 0.8009 (mmmm) REVERT: E 498 TYR cc_start: 0.6747 (t80) cc_final: 0.6385 (t80) REVERT: E 542 LYS cc_start: 0.8230 (pttp) cc_final: 0.8015 (pttp) REVERT: E 558 THR cc_start: 0.8333 (m) cc_final: 0.8021 (t) REVERT: E 566 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7969 (ttm-80) REVERT: E 569 SER cc_start: 0.8522 (m) cc_final: 0.8285 (m) REVERT: E 570 ARG cc_start: 0.8022 (ttm170) cc_final: 0.7790 (ttm170) REVERT: E 751 ASN cc_start: 0.8359 (t0) cc_final: 0.8058 (t0) REVERT: E 783 ASN cc_start: 0.8828 (p0) cc_final: 0.8421 (p0) REVERT: E 848 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7648 (mm-30) REVERT: E 878 LEU cc_start: 0.8590 (mp) cc_final: 0.8326 (mt) REVERT: E 898 LYS cc_start: 0.8093 (mmmm) cc_final: 0.7736 (mmmm) REVERT: E 901 SER cc_start: 0.8725 (t) cc_final: 0.8276 (p) REVERT: E 903 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7548 (mt-10) REVERT: E 904 ASP cc_start: 0.7981 (t0) cc_final: 0.7716 (t0) REVERT: F 120 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: F 171 GLU cc_start: 0.7341 (tp30) cc_final: 0.6824 (tp30) REVERT: F 174 LYS cc_start: 0.7506 (tttp) cc_final: 0.7179 (tttp) REVERT: F 209 ILE cc_start: 0.8271 (mm) cc_final: 0.7884 (tp) REVERT: F 299 ILE cc_start: 0.8853 (mm) cc_final: 0.8647 (mt) REVERT: F 369 LEU cc_start: 0.8499 (tp) cc_final: 0.8296 (tp) REVERT: F 385 LYS cc_start: 0.8456 (mtpp) cc_final: 0.8205 (mtpp) REVERT: F 474 LYS cc_start: 0.7633 (ttpt) cc_final: 0.7082 (ttpt) REVERT: F 510 PHE cc_start: 0.7338 (m-80) cc_final: 0.7097 (m-80) REVERT: F 567 GLU cc_start: 0.8364 (tp30) cc_final: 0.7847 (tp30) REVERT: F 569 SER cc_start: 0.8676 (m) cc_final: 0.8374 (p) REVERT: F 599 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8207 (m-30) REVERT: F 638 ASP cc_start: 0.7888 (p0) cc_final: 0.7627 (p0) REVERT: F 848 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7586 (mm-30) REVERT: F 898 LYS cc_start: 0.8082 (mmmm) cc_final: 0.7715 (mmmm) REVERT: F 901 SER cc_start: 0.8713 (t) cc_final: 0.8270 (p) REVERT: F 910 GLN cc_start: 0.8508 (mt0) cc_final: 0.8295 (mt0) outliers start: 84 outliers final: 51 residues processed: 943 average time/residue: 0.2299 time to fit residues: 355.9851 Evaluate side-chains 912 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 856 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 703 GLU Chi-restraints excluded: chain C residue 749 LYS Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 850 SER Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain D residue 548 LYS Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain D residue 902 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 681 SER Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 703 GLU Chi-restraints excluded: chain E residue 821 SER Chi-restraints excluded: chain E residue 833 LEU Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 599 ASP Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 703 GLU Chi-restraints excluded: chain F residue 850 SER Chi-restraints excluded: chain F residue 871 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 14 optimal weight: 0.0980 chunk 300 optimal weight: 0.6980 chunk 177 optimal weight: 5.9990 chunk 388 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 472 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 346 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 348 optimal weight: 5.9990 chunk 479 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN A 815 ASN A 910 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 ASN ** B 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 815 ASN B 910 GLN C 111 ASN C 637 ASN C 806 ASN C 916 HIS ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 571 GLN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 571 GLN E 714 ASN F 111 ASN F 815 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.186889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142415 restraints weight = 53026.244| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.42 r_work: 0.3493 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39198 Z= 0.149 Angle : 0.599 8.023 53256 Z= 0.299 Chirality : 0.042 0.161 6234 Planarity : 0.004 0.065 6708 Dihedral : 7.535 126.492 5328 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.05 % Allowed : 16.06 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.12), residues: 4938 helix: 1.57 (0.10), residues: 2610 sheet: -1.76 (0.26), residues: 348 loop : -2.32 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 715 TYR 0.020 0.002 TYR D 694 PHE 0.015 0.001 PHE B 868 TRP 0.022 0.001 TRP E 846 HIS 0.007 0.001 HIS E 701 Details of bonding type rmsd covalent geometry : bond 0.00333 (39198) covalent geometry : angle 0.59892 (53256) hydrogen bonds : bond 0.03938 ( 2046) hydrogen bonds : angle 4.42475 ( 6066) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 895 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8117 (m-80) cc_final: 0.7753 (m-80) REVERT: A 171 GLU cc_start: 0.7348 (tp30) cc_final: 0.6834 (tp30) REVERT: A 174 LYS cc_start: 0.7942 (tttp) cc_final: 0.7690 (tttp) REVERT: A 385 LYS cc_start: 0.8325 (mtpp) cc_final: 0.7996 (mtpp) REVERT: A 387 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7595 (pttm) REVERT: A 474 LYS cc_start: 0.7872 (ttpt) cc_final: 0.7576 (ttpt) REVERT: A 567 GLU cc_start: 0.8265 (tp30) cc_final: 0.7742 (tp30) REVERT: A 569 SER cc_start: 0.8535 (m) cc_final: 0.8036 (p) REVERT: A 624 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8347 (mt0) REVERT: A 720 GLU cc_start: 0.7978 (mp0) cc_final: 0.7572 (mp0) REVERT: A 722 VAL cc_start: 0.8377 (OUTLIER) cc_final: 0.8152 (t) REVERT: A 746 THR cc_start: 0.8234 (p) cc_final: 0.7933 (t) REVERT: A 759 SER cc_start: 0.8559 (m) cc_final: 0.8161 (p) REVERT: A 844 TRP cc_start: 0.8417 (m-90) cc_final: 0.8032 (m-10) REVERT: A 848 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7593 (mm-30) REVERT: A 898 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7661 (mmmm) REVERT: A 901 SER cc_start: 0.8597 (t) cc_final: 0.7924 (p) REVERT: A 904 ASP cc_start: 0.8062 (t0) cc_final: 0.7805 (t0) REVERT: B 116 PHE cc_start: 0.7852 (t80) cc_final: 0.7523 (t80) REVERT: B 120 PHE cc_start: 0.8198 (m-80) cc_final: 0.7712 (m-80) REVERT: B 171 GLU cc_start: 0.7558 (tp30) cc_final: 0.7179 (tp30) REVERT: B 174 LYS cc_start: 0.8070 (tttp) cc_final: 0.7831 (tttp) REVERT: B 252 LYS cc_start: 0.7580 (tptt) cc_final: 0.7150 (tptt) REVERT: B 385 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8034 (mtpp) REVERT: B 387 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7325 (pttm) REVERT: B 474 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7615 (ttpt) REVERT: B 498 TYR cc_start: 0.6864 (t80) cc_final: 0.6570 (t80) REVERT: B 567 GLU cc_start: 0.8280 (tp30) cc_final: 0.7748 (tp30) REVERT: B 582 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8013 (mm-30) REVERT: B 599 ASP cc_start: 0.8461 (t0) cc_final: 0.8230 (t0) REVERT: B 605 ASP cc_start: 0.7736 (m-30) cc_final: 0.7509 (t0) REVERT: B 624 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8332 (mt0) REVERT: B 656 ASP cc_start: 0.8275 (m-30) cc_final: 0.8027 (m-30) REVERT: B 722 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.8116 (t) REVERT: B 751 ASN cc_start: 0.8469 (t0) cc_final: 0.8101 (t0) REVERT: B 754 LYS cc_start: 0.8653 (tttt) cc_final: 0.8395 (tttm) REVERT: B 793 MET cc_start: 0.8649 (mtp) cc_final: 0.8431 (mtm) REVERT: B 843 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8551 (mt) REVERT: B 844 TRP cc_start: 0.8464 (m-90) cc_final: 0.8027 (m-10) REVERT: B 848 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7747 (mm-30) REVERT: B 898 LYS cc_start: 0.8029 (mmmm) cc_final: 0.7774 (mmmm) REVERT: B 899 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7898 (mm-40) REVERT: B 903 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7406 (mt-10) REVERT: B 904 ASP cc_start: 0.8066 (t0) cc_final: 0.7748 (t0) REVERT: B 911 ARG cc_start: 0.8677 (mtt90) cc_final: 0.8454 (mtt180) REVERT: C 116 PHE cc_start: 0.7508 (t80) cc_final: 0.7018 (t80) REVERT: C 120 PHE cc_start: 0.7744 (m-80) cc_final: 0.7229 (m-80) REVERT: C 162 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6759 (mt-10) REVERT: C 171 GLU cc_start: 0.7408 (tp30) cc_final: 0.6925 (tp30) REVERT: C 174 LYS cc_start: 0.7726 (tttp) cc_final: 0.7367 (tttp) REVERT: C 303 PHE cc_start: 0.8326 (t80) cc_final: 0.8116 (t80) REVERT: C 314 TYR cc_start: 0.8485 (m-80) cc_final: 0.8167 (m-80) REVERT: C 380 THR cc_start: 0.8502 (t) cc_final: 0.8141 (p) REVERT: C 474 LYS cc_start: 0.7987 (ttpt) cc_final: 0.7716 (ttpt) REVERT: C 542 LYS cc_start: 0.8309 (pttp) cc_final: 0.8058 (pttp) REVERT: C 567 GLU cc_start: 0.8231 (tp30) cc_final: 0.7908 (tp30) REVERT: C 569 SER cc_start: 0.8602 (m) cc_final: 0.8243 (p) REVERT: C 570 ARG cc_start: 0.8282 (ttm110) cc_final: 0.7988 (ttm110) REVERT: C 624 GLN cc_start: 0.8717 (mm110) cc_final: 0.8409 (mt0) REVERT: C 751 ASN cc_start: 0.8423 (t0) cc_final: 0.8093 (t0) REVERT: C 775 THR cc_start: 0.8620 (m) cc_final: 0.8206 (p) REVERT: C 898 LYS cc_start: 0.7960 (mmmm) cc_final: 0.7731 (mmmm) REVERT: C 904 ASP cc_start: 0.8031 (t0) cc_final: 0.7698 (t0) REVERT: D 144 PHE cc_start: 0.7662 (t80) cc_final: 0.7351 (t80) REVERT: D 171 GLU cc_start: 0.7381 (tp30) cc_final: 0.6929 (tp30) REVERT: D 174 LYS cc_start: 0.7794 (tttp) cc_final: 0.7511 (tttp) REVERT: D 303 PHE cc_start: 0.8325 (t80) cc_final: 0.8000 (t80) REVERT: D 474 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7570 (ttpt) REVERT: D 539 ASP cc_start: 0.7902 (p0) cc_final: 0.7691 (p0) REVERT: D 548 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8247 (mtpp) REVERT: D 558 THR cc_start: 0.8565 (m) cc_final: 0.8278 (t) REVERT: D 567 GLU cc_start: 0.8322 (tp30) cc_final: 0.7803 (tp30) REVERT: D 569 SER cc_start: 0.8581 (m) cc_final: 0.8117 (p) REVERT: D 595 SER cc_start: 0.8848 (p) cc_final: 0.8562 (p) REVERT: D 605 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7384 (t0) REVERT: D 615 LYS cc_start: 0.8587 (mtpp) cc_final: 0.7809 (mtmt) REVERT: D 625 ARG cc_start: 0.8638 (mmt180) cc_final: 0.8337 (mmt180) REVERT: D 656 ASP cc_start: 0.8061 (m-30) cc_final: 0.7769 (m-30) REVERT: D 730 ASP cc_start: 0.7911 (t0) cc_final: 0.7588 (t0) REVERT: D 795 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7283 (mm-30) REVERT: D 833 LEU cc_start: 0.8529 (tt) cc_final: 0.8295 (tp) REVERT: D 848 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7637 (mm-30) REVERT: D 898 LYS cc_start: 0.8331 (mmmm) cc_final: 0.7874 (mmmm) REVERT: D 901 SER cc_start: 0.8670 (t) cc_final: 0.8175 (p) REVERT: D 904 ASP cc_start: 0.8067 (t0) cc_final: 0.7781 (t0) REVERT: D 915 GLN cc_start: 0.8649 (tt0) cc_final: 0.8172 (mt0) REVERT: E 171 GLU cc_start: 0.7688 (tp30) cc_final: 0.7277 (tp30) REVERT: E 252 LYS cc_start: 0.7504 (tptt) cc_final: 0.6977 (tttt) REVERT: E 300 LEU cc_start: 0.8554 (mt) cc_final: 0.8301 (mm) REVERT: E 498 TYR cc_start: 0.6899 (t80) cc_final: 0.6584 (t80) REVERT: E 542 LYS cc_start: 0.8220 (pttp) cc_final: 0.8011 (pttp) REVERT: E 558 THR cc_start: 0.8497 (m) cc_final: 0.8221 (t) REVERT: E 569 SER cc_start: 0.8637 (m) cc_final: 0.8429 (m) REVERT: E 570 ARG cc_start: 0.8187 (ttm170) cc_final: 0.7966 (ttm170) REVERT: E 582 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7951 (mm-30) REVERT: E 638 ASP cc_start: 0.7774 (p0) cc_final: 0.7541 (p0) REVERT: E 751 ASN cc_start: 0.8383 (t0) cc_final: 0.8098 (t0) REVERT: E 775 THR cc_start: 0.8564 (m) cc_final: 0.8152 (p) REVERT: E 783 ASN cc_start: 0.8868 (p0) cc_final: 0.8483 (p0) REVERT: E 805 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7544 (mt-10) REVERT: E 843 ILE cc_start: 0.8960 (mm) cc_final: 0.8655 (mt) REVERT: E 848 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7733 (mm-30) REVERT: E 878 LEU cc_start: 0.8511 (mp) cc_final: 0.8225 (mp) REVERT: E 898 LYS cc_start: 0.8079 (mmmm) cc_final: 0.7691 (mmmm) REVERT: E 901 SER cc_start: 0.8667 (t) cc_final: 0.8198 (p) REVERT: E 904 ASP cc_start: 0.8024 (t0) cc_final: 0.7724 (t0) REVERT: E 907 VAL cc_start: 0.8548 (t) cc_final: 0.8310 (p) REVERT: F 171 GLU cc_start: 0.7322 (tp30) cc_final: 0.6849 (tp30) REVERT: F 174 LYS cc_start: 0.7553 (tttp) cc_final: 0.7250 (tttp) REVERT: F 385 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8136 (mtpp) REVERT: F 387 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7467 (pttm) REVERT: F 474 LYS cc_start: 0.7738 (ttpt) cc_final: 0.7271 (ttpt) REVERT: F 567 GLU cc_start: 0.8379 (tp30) cc_final: 0.7876 (tp30) REVERT: F 569 SER cc_start: 0.8715 (m) cc_final: 0.8395 (p) REVERT: F 620 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8169 (tm-30) REVERT: F 624 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8316 (mt0) REVERT: F 775 THR cc_start: 0.8532 (m) cc_final: 0.8143 (p) REVERT: F 848 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7719 (mm-30) REVERT: F 898 LYS cc_start: 0.8095 (mmmm) cc_final: 0.7698 (mmmm) REVERT: F 901 SER cc_start: 0.8736 (t) cc_final: 0.8263 (p) REVERT: F 904 ASP cc_start: 0.7941 (t0) cc_final: 0.7721 (t0) REVERT: F 910 GLN cc_start: 0.8479 (mt0) cc_final: 0.8260 (mt0) outliers start: 84 outliers final: 50 residues processed: 931 average time/residue: 0.2400 time to fit residues: 365.5366 Evaluate side-chains 926 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 868 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 681 SER Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 703 GLU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 548 LYS Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 533 MET Chi-restraints excluded: chain E residue 681 SER Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 714 ASN Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 599 ASP Chi-restraints excluded: chain F residue 655 SER Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 703 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 261 optimal weight: 10.0000 chunk 462 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 484 optimal weight: 2.9990 chunk 367 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 341 optimal weight: 0.0570 chunk 364 optimal weight: 20.0000 chunk 389 optimal weight: 1.9990 chunk 98 optimal weight: 30.0000 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN A 740 ASN A 910 GLN B 111 ASN B 291 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 ASN B 683 GLN ** B 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 815 ASN B 910 GLN C 637 ASN C 916 HIS ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN E 291 ASN E 317 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.183920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.139239 restraints weight = 52571.803| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.50 r_work: 0.3492 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39198 Z= 0.130 Angle : 0.589 11.421 53256 Z= 0.292 Chirality : 0.042 0.154 6234 Planarity : 0.004 0.068 6708 Dihedral : 7.343 122.951 5328 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.17 % Allowed : 17.47 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.12), residues: 4938 helix: 1.66 (0.10), residues: 2610 sheet: -1.81 (0.26), residues: 348 loop : -2.28 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 583 TYR 0.036 0.002 TYR D 541 PHE 0.014 0.001 PHE B 505 TRP 0.016 0.001 TRP E 846 HIS 0.007 0.001 HIS E 701 Details of bonding type rmsd covalent geometry : bond 0.00289 (39198) covalent geometry : angle 0.58881 (53256) hydrogen bonds : bond 0.03750 ( 2046) hydrogen bonds : angle 4.33869 ( 6066) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 883 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.5739 (mmp) cc_final: 0.5359 (mmp) REVERT: A 120 PHE cc_start: 0.8152 (m-80) cc_final: 0.7778 (m-80) REVERT: A 171 GLU cc_start: 0.7326 (tp30) cc_final: 0.6820 (tp30) REVERT: A 174 LYS cc_start: 0.7990 (tttp) cc_final: 0.7748 (tttp) REVERT: A 385 LYS cc_start: 0.8365 (mtpp) cc_final: 0.8022 (mtpp) REVERT: A 387 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7588 (pttm) REVERT: A 474 LYS cc_start: 0.7873 (ttpt) cc_final: 0.7572 (ttpt) REVERT: A 567 GLU cc_start: 0.8294 (tp30) cc_final: 0.7795 (tp30) REVERT: A 569 SER cc_start: 0.8582 (m) cc_final: 0.8038 (p) REVERT: A 599 ASP cc_start: 0.8441 (m-30) cc_final: 0.8183 (m-30) REVERT: A 624 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8286 (mt0) REVERT: A 627 TYR cc_start: 0.7983 (m-80) cc_final: 0.7732 (m-10) REVERT: A 720 GLU cc_start: 0.8017 (mp0) cc_final: 0.7599 (mp0) REVERT: A 746 THR cc_start: 0.8213 (p) cc_final: 0.7919 (t) REVERT: A 759 SER cc_start: 0.8552 (m) cc_final: 0.8157 (p) REVERT: A 898 LYS cc_start: 0.8085 (mmmm) cc_final: 0.7630 (mmmm) REVERT: A 901 SER cc_start: 0.8612 (t) cc_final: 0.7947 (p) REVERT: A 904 ASP cc_start: 0.8075 (t0) cc_final: 0.7828 (t0) REVERT: B 116 PHE cc_start: 0.7816 (t80) cc_final: 0.7491 (t80) REVERT: B 120 PHE cc_start: 0.8235 (m-80) cc_final: 0.7759 (m-80) REVERT: B 171 GLU cc_start: 0.7552 (tp30) cc_final: 0.7191 (tp30) REVERT: B 174 LYS cc_start: 0.8096 (tttp) cc_final: 0.7854 (tttp) REVERT: B 252 LYS cc_start: 0.7618 (tptt) cc_final: 0.7174 (tptt) REVERT: B 346 MET cc_start: 0.8282 (mmm) cc_final: 0.7640 (mmm) REVERT: B 385 LYS cc_start: 0.8480 (mtpp) cc_final: 0.8230 (mtpp) REVERT: B 387 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7513 (pttm) REVERT: B 474 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7613 (ttpt) REVERT: B 498 TYR cc_start: 0.6880 (t80) cc_final: 0.6596 (t80) REVERT: B 504 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7389 (pt0) REVERT: B 567 GLU cc_start: 0.8323 (tp30) cc_final: 0.7804 (tp30) REVERT: B 582 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8030 (mm-30) REVERT: B 605 ASP cc_start: 0.7697 (m-30) cc_final: 0.7460 (t0) REVERT: B 624 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8405 (mt0) REVERT: B 656 ASP cc_start: 0.8305 (m-30) cc_final: 0.8043 (m-30) REVERT: B 663 ASP cc_start: 0.7764 (m-30) cc_final: 0.7484 (m-30) REVERT: B 793 MET cc_start: 0.8642 (mtp) cc_final: 0.8409 (mtm) REVERT: B 843 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8622 (mt) REVERT: B 844 TRP cc_start: 0.8431 (m-90) cc_final: 0.8013 (m-10) REVERT: B 848 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7755 (mm-30) REVERT: B 898 LYS cc_start: 0.8011 (mmmm) cc_final: 0.7757 (mmmm) REVERT: B 903 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7478 (mt-10) REVERT: B 904 ASP cc_start: 0.8098 (t0) cc_final: 0.7793 (t0) REVERT: B 911 ARG cc_start: 0.8691 (mtt90) cc_final: 0.8479 (mtt180) REVERT: C 116 PHE cc_start: 0.7559 (t80) cc_final: 0.7074 (t80) REVERT: C 120 PHE cc_start: 0.7784 (m-80) cc_final: 0.7281 (m-80) REVERT: C 162 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6857 (mm-30) REVERT: C 171 GLU cc_start: 0.7337 (tp30) cc_final: 0.6877 (tp30) REVERT: C 174 LYS cc_start: 0.7815 (tttp) cc_final: 0.7463 (tttp) REVERT: C 314 TYR cc_start: 0.8457 (m-80) cc_final: 0.8118 (m-80) REVERT: C 380 THR cc_start: 0.8537 (t) cc_final: 0.8212 (p) REVERT: C 474 LYS cc_start: 0.7956 (ttpt) cc_final: 0.7650 (ttpt) REVERT: C 567 GLU cc_start: 0.8222 (tp30) cc_final: 0.7910 (tp30) REVERT: C 569 SER cc_start: 0.8656 (m) cc_final: 0.8299 (p) REVERT: C 570 ARG cc_start: 0.8281 (ttm110) cc_final: 0.7946 (ttm110) REVERT: C 582 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7959 (mm-30) REVERT: C 624 GLN cc_start: 0.8658 (mm110) cc_final: 0.8373 (mt0) REVERT: C 775 THR cc_start: 0.8598 (m) cc_final: 0.8133 (p) REVERT: C 826 GLN cc_start: 0.8213 (mp10) cc_final: 0.7982 (mp10) REVERT: C 865 PHE cc_start: 0.8509 (t80) cc_final: 0.8219 (t80) REVERT: C 904 ASP cc_start: 0.8013 (t0) cc_final: 0.7687 (t0) REVERT: C 905 PHE cc_start: 0.8474 (t80) cc_final: 0.8169 (t80) REVERT: D 144 PHE cc_start: 0.7648 (t80) cc_final: 0.7371 (t80) REVERT: D 171 GLU cc_start: 0.7332 (tp30) cc_final: 0.6864 (tp30) REVERT: D 174 LYS cc_start: 0.7823 (tttp) cc_final: 0.7575 (tttp) REVERT: D 235 LEU cc_start: 0.3767 (OUTLIER) cc_final: 0.3564 (mm) REVERT: D 303 PHE cc_start: 0.8322 (t80) cc_final: 0.8004 (t80) REVERT: D 474 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7668 (ttpt) REVERT: D 558 THR cc_start: 0.8622 (m) cc_final: 0.8355 (t) REVERT: D 567 GLU cc_start: 0.8340 (tp30) cc_final: 0.7855 (tp30) REVERT: D 569 SER cc_start: 0.8638 (m) cc_final: 0.8151 (p) REVERT: D 574 LEU cc_start: 0.8501 (tp) cc_final: 0.8063 (tp) REVERT: D 595 SER cc_start: 0.8854 (p) cc_final: 0.8610 (p) REVERT: D 605 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7368 (t0) REVERT: D 615 LYS cc_start: 0.8559 (mtpp) cc_final: 0.7730 (mtmt) REVERT: D 656 ASP cc_start: 0.8033 (m-30) cc_final: 0.7752 (m-30) REVERT: D 730 ASP cc_start: 0.7946 (t0) cc_final: 0.7634 (t0) REVERT: D 795 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7335 (mm-30) REVERT: D 877 ILE cc_start: 0.8467 (mt) cc_final: 0.8255 (mt) REVERT: D 898 LYS cc_start: 0.8328 (mmmm) cc_final: 0.7840 (mmmm) REVERT: D 901 SER cc_start: 0.8641 (t) cc_final: 0.8157 (p) REVERT: D 904 ASP cc_start: 0.8062 (t0) cc_final: 0.7821 (t0) REVERT: E 171 GLU cc_start: 0.7674 (tp30) cc_final: 0.7287 (tp30) REVERT: E 252 LYS cc_start: 0.7538 (tptt) cc_final: 0.7289 (tptt) REVERT: E 355 LYS cc_start: 0.8397 (ttmt) cc_final: 0.8181 (ttmt) REVERT: E 386 ASN cc_start: 0.8070 (t0) cc_final: 0.7835 (t0) REVERT: E 474 LYS cc_start: 0.7462 (ttpt) cc_final: 0.6920 (ttpt) REVERT: E 498 TYR cc_start: 0.6931 (t80) cc_final: 0.6614 (t80) REVERT: E 558 THR cc_start: 0.8507 (m) cc_final: 0.8229 (t) REVERT: E 582 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7939 (mm-30) REVERT: E 775 THR cc_start: 0.8537 (m) cc_final: 0.8105 (p) REVERT: E 843 ILE cc_start: 0.8948 (mm) cc_final: 0.8674 (mt) REVERT: E 878 LEU cc_start: 0.8487 (mp) cc_final: 0.8270 (mt) REVERT: E 898 LYS cc_start: 0.8063 (mmmm) cc_final: 0.7800 (mmmm) REVERT: E 904 ASP cc_start: 0.8014 (t0) cc_final: 0.7666 (t0) REVERT: E 907 VAL cc_start: 0.8654 (t) cc_final: 0.8353 (p) REVERT: F 171 GLU cc_start: 0.7318 (tp30) cc_final: 0.6863 (tp30) REVERT: F 174 LYS cc_start: 0.7623 (tttp) cc_final: 0.7328 (tttp) REVERT: F 209 ILE cc_start: 0.8369 (mm) cc_final: 0.7964 (tp) REVERT: F 385 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8159 (mtpp) REVERT: F 387 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7419 (pttm) REVERT: F 474 LYS cc_start: 0.7667 (ttpt) cc_final: 0.7232 (ttpt) REVERT: F 567 GLU cc_start: 0.8344 (tp30) cc_final: 0.7876 (tp30) REVERT: F 569 SER cc_start: 0.8722 (m) cc_final: 0.8429 (p) REVERT: F 582 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7785 (mm-30) REVERT: F 624 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8287 (mt0) REVERT: F 775 THR cc_start: 0.8524 (m) cc_final: 0.8143 (p) REVERT: F 826 GLN cc_start: 0.8215 (mp10) cc_final: 0.8003 (mp10) REVERT: F 848 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7697 (mm-30) REVERT: F 898 LYS cc_start: 0.8108 (mmmm) cc_final: 0.7725 (mmmm) REVERT: F 901 SER cc_start: 0.8723 (t) cc_final: 0.8233 (p) REVERT: F 904 ASP cc_start: 0.7950 (t0) cc_final: 0.7726 (t0) REVERT: F 910 GLN cc_start: 0.8518 (mt0) cc_final: 0.8310 (mt0) outliers start: 89 outliers final: 60 residues processed: 927 average time/residue: 0.2383 time to fit residues: 361.5226 Evaluate side-chains 925 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 859 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 681 SER Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 703 GLU Chi-restraints excluded: chain C residue 740 ASN Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 681 SER Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain E residue 703 GLU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 748 VAL Chi-restraints excluded: chain E residue 749 LYS Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 596 GLU Chi-restraints excluded: chain F residue 599 ASP Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 681 SER Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 703 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 56 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 396 optimal weight: 0.7980 chunk 258 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 7 optimal weight: 0.0170 chunk 335 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 488 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 637 ASN A 910 GLN B 95 GLN B 637 ASN B 899 GLN C 95 GLN C 637 ASN D 95 GLN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 GLN E 95 GLN F 95 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.187748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.143320 restraints weight = 52806.316| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.40 r_work: 0.3478 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 39198 Z= 0.167 Angle : 0.596 8.709 53256 Z= 0.297 Chirality : 0.043 0.184 6234 Planarity : 0.004 0.061 6708 Dihedral : 7.202 119.437 5328 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.56 % Allowed : 17.76 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.12), residues: 4938 helix: 1.63 (0.10), residues: 2610 sheet: -1.90 (0.26), residues: 354 loop : -2.32 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 583 TYR 0.030 0.002 TYR A 541 PHE 0.017 0.001 PHE B 868 TRP 0.021 0.001 TRP A 846 HIS 0.007 0.001 HIS E 701 Details of bonding type rmsd covalent geometry : bond 0.00373 (39198) covalent geometry : angle 0.59633 (53256) hydrogen bonds : bond 0.04001 ( 2046) hydrogen bonds : angle 4.36469 ( 6066) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 874 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.5710 (mmp) cc_final: 0.5292 (mmp) REVERT: A 120 PHE cc_start: 0.8088 (m-80) cc_final: 0.7704 (m-80) REVERT: A 171 GLU cc_start: 0.7315 (tp30) cc_final: 0.6810 (tp30) REVERT: A 174 LYS cc_start: 0.8022 (tttp) cc_final: 0.7789 (tttp) REVERT: A 385 LYS cc_start: 0.8347 (mtpp) cc_final: 0.7937 (mtpp) REVERT: A 387 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7576 (pttm) REVERT: A 474 LYS cc_start: 0.7833 (ttpt) cc_final: 0.7470 (ttpt) REVERT: A 567 GLU cc_start: 0.8293 (tp30) cc_final: 0.7812 (tp30) REVERT: A 569 SER cc_start: 0.8575 (m) cc_final: 0.8075 (p) REVERT: A 595 SER cc_start: 0.8955 (p) cc_final: 0.8348 (p) REVERT: A 599 ASP cc_start: 0.8458 (m-30) cc_final: 0.8255 (m-30) REVERT: A 602 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7990 (tm-30) REVERT: A 605 ASP cc_start: 0.7651 (m-30) cc_final: 0.7386 (t0) REVERT: A 624 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8254 (mt0) REVERT: A 720 GLU cc_start: 0.8013 (mp0) cc_final: 0.7572 (mp0) REVERT: A 722 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.8134 (t) REVERT: A 759 SER cc_start: 0.8538 (m) cc_final: 0.8147 (p) REVERT: A 898 LYS cc_start: 0.8093 (mmmm) cc_final: 0.7626 (mmmm) REVERT: A 901 SER cc_start: 0.8588 (t) cc_final: 0.7921 (p) REVERT: A 904 ASP cc_start: 0.8010 (t0) cc_final: 0.7780 (t0) REVERT: B 116 PHE cc_start: 0.7765 (t80) cc_final: 0.7516 (t80) REVERT: B 120 PHE cc_start: 0.8145 (m-80) cc_final: 0.7691 (m-80) REVERT: B 171 GLU cc_start: 0.7582 (tp30) cc_final: 0.7202 (tp30) REVERT: B 174 LYS cc_start: 0.8139 (tttp) cc_final: 0.7910 (tttp) REVERT: B 252 LYS cc_start: 0.7652 (tptt) cc_final: 0.7158 (tptt) REVERT: B 346 MET cc_start: 0.8287 (mmm) cc_final: 0.7888 (mmm) REVERT: B 385 LYS cc_start: 0.8470 (mtpp) cc_final: 0.8116 (mtpp) REVERT: B 474 LYS cc_start: 0.8095 (ttpt) cc_final: 0.7574 (ttpt) REVERT: B 498 TYR cc_start: 0.6941 (t80) cc_final: 0.6713 (t80) REVERT: B 504 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7332 (pt0) REVERT: B 567 GLU cc_start: 0.8339 (tp30) cc_final: 0.7823 (tp30) REVERT: B 582 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8006 (mm-30) REVERT: B 624 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8396 (mt0) REVERT: B 656 ASP cc_start: 0.8295 (m-30) cc_final: 0.8018 (m-30) REVERT: B 663 ASP cc_start: 0.7725 (m-30) cc_final: 0.7460 (m-30) REVERT: B 793 MET cc_start: 0.8624 (mtp) cc_final: 0.8399 (mtm) REVERT: B 843 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8616 (mt) REVERT: B 844 TRP cc_start: 0.8483 (m-90) cc_final: 0.8060 (m-10) REVERT: B 848 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7771 (mm-30) REVERT: B 898 LYS cc_start: 0.8029 (mmmm) cc_final: 0.7680 (mmmm) REVERT: B 903 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7539 (mt-10) REVERT: B 904 ASP cc_start: 0.8030 (t0) cc_final: 0.7737 (t0) REVERT: B 911 ARG cc_start: 0.8743 (mtt90) cc_final: 0.8515 (mtt180) REVERT: C 116 PHE cc_start: 0.7606 (t80) cc_final: 0.7053 (t80) REVERT: C 120 PHE cc_start: 0.7734 (m-80) cc_final: 0.7197 (m-80) REVERT: C 162 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7004 (mm-30) REVERT: C 171 GLU cc_start: 0.7335 (tp30) cc_final: 0.6890 (tp30) REVERT: C 174 LYS cc_start: 0.7854 (tttp) cc_final: 0.7505 (tttp) REVERT: C 314 TYR cc_start: 0.8515 (m-80) cc_final: 0.8200 (m-80) REVERT: C 380 THR cc_start: 0.8569 (t) cc_final: 0.8203 (p) REVERT: C 387 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7630 (pttm) REVERT: C 457 LYS cc_start: 0.7546 (ttmm) cc_final: 0.7220 (mttm) REVERT: C 474 LYS cc_start: 0.7932 (ttpt) cc_final: 0.7612 (ttpt) REVERT: C 567 GLU cc_start: 0.8255 (tp30) cc_final: 0.7928 (tp30) REVERT: C 569 SER cc_start: 0.8605 (m) cc_final: 0.8281 (p) REVERT: C 570 ARG cc_start: 0.8305 (ttm110) cc_final: 0.7994 (ttm110) REVERT: C 624 GLN cc_start: 0.8628 (mm110) cc_final: 0.8344 (mt0) REVERT: C 638 ASP cc_start: 0.7756 (p0) cc_final: 0.7446 (p0) REVERT: C 775 THR cc_start: 0.8614 (m) cc_final: 0.8161 (p) REVERT: C 795 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7749 (mm-30) REVERT: C 826 GLN cc_start: 0.8183 (mp10) cc_final: 0.7958 (mp10) REVERT: C 865 PHE cc_start: 0.8557 (t80) cc_final: 0.8257 (t80) REVERT: C 904 ASP cc_start: 0.8045 (t0) cc_final: 0.7732 (t0) REVERT: D 171 GLU cc_start: 0.7287 (tp30) cc_final: 0.6833 (tp30) REVERT: D 174 LYS cc_start: 0.7897 (tttp) cc_final: 0.7594 (tttp) REVERT: D 235 LEU cc_start: 0.3781 (OUTLIER) cc_final: 0.3580 (mm) REVERT: D 303 PHE cc_start: 0.8304 (t80) cc_final: 0.7998 (t80) REVERT: D 474 LYS cc_start: 0.7954 (ttpt) cc_final: 0.7628 (ttpt) REVERT: D 558 THR cc_start: 0.8634 (m) cc_final: 0.8374 (t) REVERT: D 567 GLU cc_start: 0.8351 (tp30) cc_final: 0.7905 (tp30) REVERT: D 569 SER cc_start: 0.8657 (m) cc_final: 0.8223 (p) REVERT: D 574 LEU cc_start: 0.8516 (tp) cc_final: 0.8014 (tp) REVERT: D 595 SER cc_start: 0.8879 (p) cc_final: 0.8628 (p) REVERT: D 615 LYS cc_start: 0.8652 (mtpp) cc_final: 0.7900 (mtmt) REVERT: D 624 GLN cc_start: 0.8543 (mt0) cc_final: 0.8281 (mt0) REVERT: D 656 ASP cc_start: 0.8067 (m-30) cc_final: 0.7761 (m-30) REVERT: D 730 ASP cc_start: 0.7940 (t0) cc_final: 0.7552 (t0) REVERT: D 746 THR cc_start: 0.8032 (p) cc_final: 0.7719 (t) REVERT: D 795 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7382 (mm-30) REVERT: D 898 LYS cc_start: 0.8285 (mmmm) cc_final: 0.7799 (mmmm) REVERT: D 901 SER cc_start: 0.8681 (t) cc_final: 0.8182 (p) REVERT: D 904 ASP cc_start: 0.8022 (t0) cc_final: 0.7770 (t0) REVERT: E 168 ILE cc_start: 0.8320 (tp) cc_final: 0.7963 (tp) REVERT: E 171 GLU cc_start: 0.7705 (tp30) cc_final: 0.7317 (tp30) REVERT: E 355 LYS cc_start: 0.8394 (ttmt) cc_final: 0.8188 (ttmt) REVERT: E 474 LYS cc_start: 0.7449 (ttpt) cc_final: 0.6873 (ttpt) REVERT: E 498 TYR cc_start: 0.6920 (t80) cc_final: 0.6647 (t80) REVERT: E 541 TYR cc_start: 0.7817 (t80) cc_final: 0.7592 (t80) REVERT: E 558 THR cc_start: 0.8547 (m) cc_final: 0.8270 (t) REVERT: E 582 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7935 (mm-30) REVERT: E 638 ASP cc_start: 0.7803 (p0) cc_final: 0.7470 (p0) REVERT: E 775 THR cc_start: 0.8525 (m) cc_final: 0.8082 (p) REVERT: E 843 ILE cc_start: 0.8920 (mm) cc_final: 0.8675 (mt) REVERT: E 878 LEU cc_start: 0.8551 (mp) cc_final: 0.8233 (mp) REVERT: E 898 LYS cc_start: 0.8054 (mmmm) cc_final: 0.7786 (mmmm) REVERT: E 904 ASP cc_start: 0.7955 (t0) cc_final: 0.7608 (t0) REVERT: E 907 VAL cc_start: 0.8686 (t) cc_final: 0.8402 (p) REVERT: F 162 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7094 (mm-30) REVERT: F 171 GLU cc_start: 0.7264 (tp30) cc_final: 0.6832 (tp30) REVERT: F 174 LYS cc_start: 0.7696 (tttp) cc_final: 0.7385 (tttp) REVERT: F 235 LEU cc_start: 0.3240 (OUTLIER) cc_final: 0.3038 (mm) REVERT: F 356 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7807 (ttmm) REVERT: F 385 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8125 (mtpp) REVERT: F 387 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7413 (pttm) REVERT: F 474 LYS cc_start: 0.7624 (ttpt) cc_final: 0.7134 (ttpt) REVERT: F 567 GLU cc_start: 0.8352 (tp30) cc_final: 0.7880 (tp30) REVERT: F 569 SER cc_start: 0.8698 (m) cc_final: 0.8415 (p) REVERT: F 624 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8301 (mt0) REVERT: F 638 ASP cc_start: 0.7827 (p0) cc_final: 0.7506 (p0) REVERT: F 695 ARG cc_start: 0.8582 (tpp-160) cc_final: 0.8298 (tpt170) REVERT: F 775 THR cc_start: 0.8522 (m) cc_final: 0.8128 (p) REVERT: F 826 GLN cc_start: 0.8185 (mp10) cc_final: 0.7961 (mp10) REVERT: F 848 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7686 (mm-30) REVERT: F 898 LYS cc_start: 0.8063 (mmmm) cc_final: 0.7775 (mmmm) REVERT: F 904 ASP cc_start: 0.7924 (t0) cc_final: 0.7707 (t0) REVERT: F 910 GLN cc_start: 0.8531 (mt0) cc_final: 0.8319 (mt0) outliers start: 105 outliers final: 70 residues processed: 924 average time/residue: 0.2360 time to fit residues: 357.0906 Evaluate side-chains 947 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 869 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 659 ARG Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 681 SER Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 703 GLU Chi-restraints excluded: chain C residue 740 ASN Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 688 MET Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 701 HIS Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain D residue 871 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 361 GLN Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 681 SER Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain E residue 703 GLU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 748 VAL Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 596 GLU Chi-restraints excluded: chain F residue 599 ASP Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 681 SER Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 703 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 29 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 240 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 chunk 476 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 206 optimal weight: 1.9990 chunk 38 optimal weight: 30.0000 chunk 76 optimal weight: 0.6980 chunk 172 optimal weight: 7.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN A 740 ASN A 910 GLN B 899 GLN C 538 HIS C 637 ASN D 826 GLN E 571 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.183031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.138463 restraints weight = 53153.966| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.44 r_work: 0.3480 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39198 Z= 0.154 Angle : 0.594 12.035 53256 Z= 0.294 Chirality : 0.042 0.168 6234 Planarity : 0.004 0.057 6708 Dihedral : 7.072 118.245 5328 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.56 % Allowed : 18.59 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.12), residues: 4938 helix: 1.65 (0.10), residues: 2610 sheet: -1.88 (0.26), residues: 354 loop : -2.30 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 715 TYR 0.034 0.002 TYR A 541 PHE 0.015 0.001 PHE B 868 TRP 0.019 0.001 TRP A 846 HIS 0.007 0.001 HIS E 701 Details of bonding type rmsd covalent geometry : bond 0.00346 (39198) covalent geometry : angle 0.59410 (53256) hydrogen bonds : bond 0.03857 ( 2046) hydrogen bonds : angle 4.33267 ( 6066) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 865 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.5636 (mmp) cc_final: 0.5219 (mmp) REVERT: A 120 PHE cc_start: 0.8121 (m-80) cc_final: 0.7707 (m-80) REVERT: A 171 GLU cc_start: 0.7296 (tp30) cc_final: 0.6791 (tp30) REVERT: A 174 LYS cc_start: 0.8060 (tttp) cc_final: 0.7810 (tttp) REVERT: A 363 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8469 (mp) REVERT: A 385 LYS cc_start: 0.8374 (mtpp) cc_final: 0.7931 (mtpp) REVERT: A 387 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7543 (pttm) REVERT: A 474 LYS cc_start: 0.7859 (ttpt) cc_final: 0.7464 (ttpt) REVERT: A 567 GLU cc_start: 0.8306 (tp30) cc_final: 0.7834 (tp30) REVERT: A 569 SER cc_start: 0.8570 (m) cc_final: 0.8076 (p) REVERT: A 574 LEU cc_start: 0.8546 (tp) cc_final: 0.7923 (tp) REVERT: A 595 SER cc_start: 0.8939 (p) cc_final: 0.8357 (p) REVERT: A 599 ASP cc_start: 0.8450 (m-30) cc_final: 0.8171 (m-30) REVERT: A 605 ASP cc_start: 0.7616 (m-30) cc_final: 0.7354 (t0) REVERT: A 624 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8228 (mt0) REVERT: A 720 GLU cc_start: 0.8036 (mp0) cc_final: 0.7565 (mp0) REVERT: A 759 SER cc_start: 0.8536 (m) cc_final: 0.8155 (p) REVERT: A 844 TRP cc_start: 0.8452 (m-90) cc_final: 0.8146 (m-10) REVERT: A 898 LYS cc_start: 0.8072 (mmmm) cc_final: 0.7602 (mmmm) REVERT: A 901 SER cc_start: 0.8578 (t) cc_final: 0.7923 (p) REVERT: A 904 ASP cc_start: 0.8031 (t0) cc_final: 0.7829 (t0) REVERT: B 116 PHE cc_start: 0.7758 (t80) cc_final: 0.7466 (t80) REVERT: B 120 PHE cc_start: 0.8188 (m-80) cc_final: 0.7731 (m-80) REVERT: B 171 GLU cc_start: 0.7590 (tp30) cc_final: 0.7214 (tp30) REVERT: B 174 LYS cc_start: 0.8100 (tttp) cc_final: 0.7876 (tttp) REVERT: B 252 LYS cc_start: 0.7656 (tptt) cc_final: 0.7239 (tptt) REVERT: B 346 MET cc_start: 0.8293 (mmm) cc_final: 0.7884 (mmp) REVERT: B 474 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7569 (ttpt) REVERT: B 498 TYR cc_start: 0.7097 (t80) cc_final: 0.6878 (t80) REVERT: B 504 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7287 (tm-30) REVERT: B 567 GLU cc_start: 0.8349 (tp30) cc_final: 0.7835 (tp30) REVERT: B 582 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7999 (mm-30) REVERT: B 599 ASP cc_start: 0.8348 (t0) cc_final: 0.8025 (t0) REVERT: B 605 ASP cc_start: 0.7702 (m-30) cc_final: 0.7493 (t0) REVERT: B 624 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8391 (mt0) REVERT: B 638 ASP cc_start: 0.7955 (p0) cc_final: 0.7752 (p0) REVERT: B 656 ASP cc_start: 0.8308 (m-30) cc_final: 0.8005 (m-30) REVERT: B 793 MET cc_start: 0.8598 (mtp) cc_final: 0.8376 (mtm) REVERT: B 843 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8636 (mt) REVERT: B 844 TRP cc_start: 0.8469 (m-90) cc_final: 0.8038 (m-10) REVERT: B 848 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7763 (mm-30) REVERT: B 898 LYS cc_start: 0.8037 (mmmm) cc_final: 0.7691 (mmmm) REVERT: B 903 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7528 (mt-10) REVERT: B 904 ASP cc_start: 0.8065 (t0) cc_final: 0.7777 (t0) REVERT: B 917 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7381 (tm-30) REVERT: C 116 PHE cc_start: 0.7617 (t80) cc_final: 0.7394 (t80) REVERT: C 120 PHE cc_start: 0.7749 (m-80) cc_final: 0.7337 (m-10) REVERT: C 162 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7001 (mm-30) REVERT: C 171 GLU cc_start: 0.7340 (tp30) cc_final: 0.6913 (tp30) REVERT: C 174 LYS cc_start: 0.7875 (tttp) cc_final: 0.7538 (tttp) REVERT: C 314 TYR cc_start: 0.8522 (m-80) cc_final: 0.8174 (m-80) REVERT: C 380 THR cc_start: 0.8584 (t) cc_final: 0.8216 (p) REVERT: C 387 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7644 (pttm) REVERT: C 457 LYS cc_start: 0.7553 (ttmm) cc_final: 0.7226 (mttm) REVERT: C 474 LYS cc_start: 0.7964 (ttpt) cc_final: 0.7610 (ttpt) REVERT: C 567 GLU cc_start: 0.8245 (tp30) cc_final: 0.7931 (tp30) REVERT: C 569 SER cc_start: 0.8614 (m) cc_final: 0.8293 (p) REVERT: C 570 ARG cc_start: 0.8313 (ttm110) cc_final: 0.8020 (ttm110) REVERT: C 624 GLN cc_start: 0.8615 (mm110) cc_final: 0.8317 (mt0) REVERT: C 638 ASP cc_start: 0.7712 (p0) cc_final: 0.7405 (p0) REVERT: C 691 TYR cc_start: 0.8564 (t80) cc_final: 0.8090 (t80) REVERT: C 695 ARG cc_start: 0.8522 (tpp-160) cc_final: 0.8213 (mmm160) REVERT: C 775 THR cc_start: 0.8634 (m) cc_final: 0.8179 (p) REVERT: C 804 THR cc_start: 0.8361 (p) cc_final: 0.8150 (p) REVERT: C 904 ASP cc_start: 0.8057 (t0) cc_final: 0.7740 (t0) REVERT: D 171 GLU cc_start: 0.7298 (tp30) cc_final: 0.6868 (tp30) REVERT: D 174 LYS cc_start: 0.7932 (tttp) cc_final: 0.7620 (tttp) REVERT: D 303 PHE cc_start: 0.8310 (t80) cc_final: 0.7995 (t80) REVERT: D 474 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7656 (ttpt) REVERT: D 558 THR cc_start: 0.8664 (m) cc_final: 0.8407 (t) REVERT: D 567 GLU cc_start: 0.8362 (tp30) cc_final: 0.7922 (tp30) REVERT: D 569 SER cc_start: 0.8730 (m) cc_final: 0.8274 (p) REVERT: D 595 SER cc_start: 0.8857 (p) cc_final: 0.8602 (p) REVERT: D 605 ASP cc_start: 0.7769 (t0) cc_final: 0.7359 (t0) REVERT: D 615 LYS cc_start: 0.8667 (mtpp) cc_final: 0.7793 (mttt) REVERT: D 624 GLN cc_start: 0.8558 (mt0) cc_final: 0.8253 (mt0) REVERT: D 730 ASP cc_start: 0.7939 (t0) cc_final: 0.7543 (t0) REVERT: D 795 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7302 (mm-30) REVERT: D 877 ILE cc_start: 0.8468 (mt) cc_final: 0.8261 (mt) REVERT: D 898 LYS cc_start: 0.8245 (mmmm) cc_final: 0.7747 (mmmm) REVERT: D 901 SER cc_start: 0.8665 (t) cc_final: 0.8166 (p) REVERT: D 904 ASP cc_start: 0.8047 (t0) cc_final: 0.7834 (t0) REVERT: E 168 ILE cc_start: 0.8296 (tp) cc_final: 0.7942 (tp) REVERT: E 171 GLU cc_start: 0.7707 (tp30) cc_final: 0.7338 (tp30) REVERT: E 299 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8500 (mt) REVERT: E 355 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8212 (ttmt) REVERT: E 474 LYS cc_start: 0.7490 (ttpt) cc_final: 0.6882 (ttpt) REVERT: E 498 TYR cc_start: 0.7009 (t80) cc_final: 0.6733 (t80) REVERT: E 541 TYR cc_start: 0.7803 (t80) cc_final: 0.7595 (t80) REVERT: E 558 THR cc_start: 0.8567 (m) cc_final: 0.8305 (t) REVERT: E 582 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7889 (mm-30) REVERT: E 775 THR cc_start: 0.8516 (m) cc_final: 0.8067 (p) REVERT: E 843 ILE cc_start: 0.8903 (mm) cc_final: 0.8666 (mt) REVERT: E 898 LYS cc_start: 0.8008 (mmmm) cc_final: 0.7751 (mmmm) REVERT: E 904 ASP cc_start: 0.7983 (t0) cc_final: 0.7630 (t0) REVERT: E 907 VAL cc_start: 0.8659 (t) cc_final: 0.8386 (p) REVERT: E 911 ARG cc_start: 0.8819 (mtm-85) cc_final: 0.8594 (mtt180) REVERT: F 120 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: F 162 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7148 (mm-30) REVERT: F 171 GLU cc_start: 0.7292 (tp30) cc_final: 0.6858 (tp30) REVERT: F 174 LYS cc_start: 0.7712 (tttp) cc_final: 0.7391 (tttp) REVERT: F 209 ILE cc_start: 0.8431 (mm) cc_final: 0.8028 (tp) REVERT: F 235 LEU cc_start: 0.3295 (OUTLIER) cc_final: 0.3091 (mm) REVERT: F 385 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8125 (mtpp) REVERT: F 387 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7495 (pttm) REVERT: F 474 LYS cc_start: 0.7672 (ttpt) cc_final: 0.7165 (ttpt) REVERT: F 504 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7473 (tm-30) REVERT: F 567 GLU cc_start: 0.8339 (tp30) cc_final: 0.7892 (tp30) REVERT: F 569 SER cc_start: 0.8715 (m) cc_final: 0.8411 (p) REVERT: F 624 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8290 (mt0) REVERT: F 638 ASP cc_start: 0.7860 (p0) cc_final: 0.7520 (p0) REVERT: F 695 ARG cc_start: 0.8560 (tpp-160) cc_final: 0.8261 (tpt170) REVERT: F 720 GLU cc_start: 0.8236 (mp0) cc_final: 0.8034 (mp0) REVERT: F 775 THR cc_start: 0.8511 (m) cc_final: 0.8136 (p) REVERT: F 826 GLN cc_start: 0.8205 (mp10) cc_final: 0.7974 (mp10) REVERT: F 898 LYS cc_start: 0.8020 (mmmm) cc_final: 0.7729 (mmmm) REVERT: F 904 ASP cc_start: 0.7924 (t0) cc_final: 0.7709 (t0) REVERT: F 910 GLN cc_start: 0.8542 (mt0) cc_final: 0.8334 (mt0) outliers start: 105 outliers final: 73 residues processed: 920 average time/residue: 0.2280 time to fit residues: 347.7876 Evaluate side-chains 935 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 854 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 659 ARG Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 681 SER Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 703 GLU Chi-restraints excluded: chain C residue 740 ASN Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 701 HIS Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 361 GLN Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 659 ARG Chi-restraints excluded: chain E residue 681 SER Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain E residue 703 GLU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 748 VAL Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 596 GLU Chi-restraints excluded: chain F residue 599 ASP Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 655 SER Chi-restraints excluded: chain F residue 681 SER Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 703 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 8 optimal weight: 0.9990 chunk 355 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 331 optimal weight: 4.9990 chunk 420 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 430 optimal weight: 6.9990 chunk 155 optimal weight: 0.4980 chunk 100 optimal weight: 10.0000 chunk 316 optimal weight: 2.9990 chunk 466 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 910 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 826 GLN B 899 GLN C 538 HIS C 637 ASN D 826 GLN E 317 ASN E 714 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.183519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.138849 restraints weight = 52747.904| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.45 r_work: 0.3478 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39198 Z= 0.155 Angle : 0.595 9.820 53256 Z= 0.295 Chirality : 0.042 0.190 6234 Planarity : 0.004 0.058 6708 Dihedral : 6.987 117.116 5328 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.58 % Allowed : 18.93 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.12), residues: 4938 helix: 1.64 (0.10), residues: 2610 sheet: -2.05 (0.24), residues: 414 loop : -2.39 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 715 TYR 0.037 0.002 TYR D 541 PHE 0.023 0.001 PHE C 303 TRP 0.018 0.001 TRP A 846 HIS 0.007 0.001 HIS E 701 Details of bonding type rmsd covalent geometry : bond 0.00347 (39198) covalent geometry : angle 0.59464 (53256) hydrogen bonds : bond 0.03866 ( 2046) hydrogen bonds : angle 4.32136 ( 6066) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 864 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.5646 (mmp) cc_final: 0.5217 (mmp) REVERT: A 120 PHE cc_start: 0.8091 (m-80) cc_final: 0.7676 (m-80) REVERT: A 171 GLU cc_start: 0.7278 (tp30) cc_final: 0.6816 (tp30) REVERT: A 179 LYS cc_start: 0.7558 (ptpp) cc_final: 0.6953 (ptpp) REVERT: A 385 LYS cc_start: 0.8339 (mtpp) cc_final: 0.7867 (mtpp) REVERT: A 387 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7493 (pttm) REVERT: A 474 LYS cc_start: 0.7769 (ttpt) cc_final: 0.7379 (ttpt) REVERT: A 567 GLU cc_start: 0.8251 (tp30) cc_final: 0.7803 (tp30) REVERT: A 569 SER cc_start: 0.8566 (m) cc_final: 0.8082 (p) REVERT: A 574 LEU cc_start: 0.8537 (tp) cc_final: 0.7903 (tp) REVERT: A 595 SER cc_start: 0.8937 (p) cc_final: 0.8345 (p) REVERT: A 599 ASP cc_start: 0.8466 (m-30) cc_final: 0.8201 (m-30) REVERT: A 605 ASP cc_start: 0.7682 (m-30) cc_final: 0.7447 (t0) REVERT: A 624 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8191 (mt0) REVERT: A 720 GLU cc_start: 0.7969 (mp0) cc_final: 0.7523 (mp0) REVERT: A 746 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7916 (t) REVERT: A 759 SER cc_start: 0.8549 (m) cc_final: 0.8153 (p) REVERT: A 844 TRP cc_start: 0.8455 (m-90) cc_final: 0.8188 (m-10) REVERT: A 898 LYS cc_start: 0.8077 (mmmm) cc_final: 0.7597 (mmmm) REVERT: A 901 SER cc_start: 0.8575 (t) cc_final: 0.7935 (p) REVERT: A 904 ASP cc_start: 0.8028 (t0) cc_final: 0.7825 (t0) REVERT: B 116 PHE cc_start: 0.7690 (t80) cc_final: 0.7391 (t80) REVERT: B 120 PHE cc_start: 0.8135 (m-80) cc_final: 0.7683 (m-80) REVERT: B 171 GLU cc_start: 0.7558 (tp30) cc_final: 0.7203 (tp30) REVERT: B 174 LYS cc_start: 0.8134 (tttp) cc_final: 0.7925 (tttp) REVERT: B 252 LYS cc_start: 0.7639 (tptt) cc_final: 0.7393 (tptt) REVERT: B 474 LYS cc_start: 0.8022 (ttpt) cc_final: 0.7535 (ttpt) REVERT: B 504 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7217 (tm-30) REVERT: B 533 MET cc_start: 0.5710 (OUTLIER) cc_final: 0.5468 (ttm) REVERT: B 567 GLU cc_start: 0.8307 (tp30) cc_final: 0.7803 (tp30) REVERT: B 582 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7986 (mm-30) REVERT: B 599 ASP cc_start: 0.8368 (t0) cc_final: 0.8017 (t0) REVERT: B 605 ASP cc_start: 0.7700 (m-30) cc_final: 0.7485 (t0) REVERT: B 624 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8353 (mt0) REVERT: B 656 ASP cc_start: 0.8244 (m-30) cc_final: 0.7970 (m-30) REVERT: B 793 MET cc_start: 0.8629 (mtp) cc_final: 0.8403 (mtm) REVERT: B 843 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8638 (mt) REVERT: B 844 TRP cc_start: 0.8487 (m-90) cc_final: 0.8055 (m-10) REVERT: B 848 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7800 (mm-30) REVERT: B 903 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7522 (mt-10) REVERT: B 904 ASP cc_start: 0.8028 (t0) cc_final: 0.7741 (t0) REVERT: B 917 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7373 (tm-30) REVERT: C 116 PHE cc_start: 0.7618 (t80) cc_final: 0.7211 (t80) REVERT: C 120 PHE cc_start: 0.7740 (m-80) cc_final: 0.7183 (m-80) REVERT: C 162 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7007 (mm-30) REVERT: C 171 GLU cc_start: 0.7281 (tp30) cc_final: 0.6882 (tp30) REVERT: C 174 LYS cc_start: 0.7839 (tttp) cc_final: 0.7506 (tttp) REVERT: C 314 TYR cc_start: 0.8541 (m-80) cc_final: 0.8229 (m-80) REVERT: C 380 THR cc_start: 0.8583 (t) cc_final: 0.8270 (p) REVERT: C 387 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7576 (pttm) REVERT: C 403 ASP cc_start: 0.5830 (t70) cc_final: 0.5369 (t0) REVERT: C 423 ASP cc_start: 0.8108 (t70) cc_final: 0.7765 (t70) REVERT: C 457 LYS cc_start: 0.7561 (ttmm) cc_final: 0.7283 (mttm) REVERT: C 474 LYS cc_start: 0.7915 (ttpt) cc_final: 0.7547 (ttpt) REVERT: C 567 GLU cc_start: 0.8235 (tp30) cc_final: 0.7889 (tp30) REVERT: C 570 ARG cc_start: 0.8225 (ttm110) cc_final: 0.8001 (ttm110) REVERT: C 624 GLN cc_start: 0.8588 (mm110) cc_final: 0.8280 (mt0) REVERT: C 638 ASP cc_start: 0.7750 (p0) cc_final: 0.7464 (p0) REVERT: C 775 THR cc_start: 0.8663 (m) cc_final: 0.8200 (p) REVERT: C 804 THR cc_start: 0.8356 (p) cc_final: 0.8152 (p) REVERT: C 826 GLN cc_start: 0.8236 (mp10) cc_final: 0.7989 (mp10) REVERT: C 896 ASN cc_start: 0.7481 (p0) cc_final: 0.7214 (p0) REVERT: C 904 ASP cc_start: 0.8058 (t0) cc_final: 0.7739 (t0) REVERT: C 917 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7345 (tm-30) REVERT: D 171 GLU cc_start: 0.7325 (tp30) cc_final: 0.6902 (tp30) REVERT: D 174 LYS cc_start: 0.7937 (tttp) cc_final: 0.7615 (tttp) REVERT: D 303 PHE cc_start: 0.8278 (t80) cc_final: 0.7979 (t80) REVERT: D 474 LYS cc_start: 0.7983 (ttpt) cc_final: 0.7623 (ttpt) REVERT: D 558 THR cc_start: 0.8689 (m) cc_final: 0.8454 (t) REVERT: D 567 GLU cc_start: 0.8318 (tp30) cc_final: 0.7887 (tp30) REVERT: D 569 SER cc_start: 0.8733 (m) cc_final: 0.8277 (p) REVERT: D 595 SER cc_start: 0.8857 (p) cc_final: 0.8607 (p) REVERT: D 605 ASP cc_start: 0.7747 (t0) cc_final: 0.7259 (t0) REVERT: D 615 LYS cc_start: 0.8678 (mtpp) cc_final: 0.7938 (mtmt) REVERT: D 624 GLN cc_start: 0.8553 (mt0) cc_final: 0.8262 (mt0) REVERT: D 730 ASP cc_start: 0.7924 (t0) cc_final: 0.7526 (t0) REVERT: D 795 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7372 (mm-30) REVERT: D 898 LYS cc_start: 0.8205 (mmmm) cc_final: 0.7820 (mmmm) REVERT: D 904 ASP cc_start: 0.8033 (t0) cc_final: 0.7831 (t0) REVERT: E 168 ILE cc_start: 0.8260 (tp) cc_final: 0.7891 (tp) REVERT: E 171 GLU cc_start: 0.7707 (tp30) cc_final: 0.7347 (tp30) REVERT: E 299 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8492 (mt) REVERT: E 355 LYS cc_start: 0.8402 (ttmt) cc_final: 0.8198 (ttmt) REVERT: E 474 LYS cc_start: 0.7409 (ttpt) cc_final: 0.6819 (ttpt) REVERT: E 498 TYR cc_start: 0.6930 (t80) cc_final: 0.6680 (t80) REVERT: E 541 TYR cc_start: 0.7814 (t80) cc_final: 0.7603 (t80) REVERT: E 558 THR cc_start: 0.8578 (m) cc_final: 0.8290 (t) REVERT: E 582 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7845 (mm-30) REVERT: E 775 THR cc_start: 0.8509 (m) cc_final: 0.8063 (p) REVERT: E 843 ILE cc_start: 0.8870 (mm) cc_final: 0.8634 (mt) REVERT: E 898 LYS cc_start: 0.7983 (mmmm) cc_final: 0.7712 (mmmm) REVERT: E 904 ASP cc_start: 0.7968 (t0) cc_final: 0.7615 (t0) REVERT: E 907 VAL cc_start: 0.8647 (t) cc_final: 0.8359 (p) REVERT: F 120 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7386 (m-80) REVERT: F 162 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7167 (mm-30) REVERT: F 171 GLU cc_start: 0.7288 (tp30) cc_final: 0.6858 (tp30) REVERT: F 174 LYS cc_start: 0.7733 (tttp) cc_final: 0.7405 (tttp) REVERT: F 209 ILE cc_start: 0.8474 (mm) cc_final: 0.8041 (tp) REVERT: F 303 PHE cc_start: 0.8316 (t80) cc_final: 0.8073 (t80) REVERT: F 385 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8068 (mtpp) REVERT: F 387 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7424 (pttm) REVERT: F 474 LYS cc_start: 0.7591 (ttpt) cc_final: 0.7101 (ttpt) REVERT: F 567 GLU cc_start: 0.8328 (tp30) cc_final: 0.7880 (tp30) REVERT: F 569 SER cc_start: 0.8709 (m) cc_final: 0.8409 (p) REVERT: F 638 ASP cc_start: 0.7871 (p0) cc_final: 0.7542 (p0) REVERT: F 695 ARG cc_start: 0.8573 (tpp-160) cc_final: 0.8276 (tpt170) REVERT: F 775 THR cc_start: 0.8509 (m) cc_final: 0.8125 (p) REVERT: F 826 GLN cc_start: 0.8195 (mp10) cc_final: 0.7960 (mp10) REVERT: F 843 ILE cc_start: 0.8861 (mm) cc_final: 0.8645 (mt) REVERT: F 848 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7725 (mm-30) REVERT: F 850 SER cc_start: 0.8525 (t) cc_final: 0.8151 (p) REVERT: F 898 LYS cc_start: 0.8003 (mmmm) cc_final: 0.7712 (mmmm) REVERT: F 904 ASP cc_start: 0.7913 (t0) cc_final: 0.7675 (t0) REVERT: F 910 GLN cc_start: 0.8538 (mt0) cc_final: 0.8331 (mt0) REVERT: F 917 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7367 (tm-30) outliers start: 106 outliers final: 74 residues processed: 915 average time/residue: 0.2255 time to fit residues: 341.7230 Evaluate side-chains 947 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 865 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 659 ARG Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 681 SER Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 703 GLU Chi-restraints excluded: chain C residue 740 ASN Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 701 HIS Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 361 GLN Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 659 ARG Chi-restraints excluded: chain E residue 681 SER Chi-restraints excluded: chain E residue 688 MET Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain E residue 703 GLU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 748 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 596 GLU Chi-restraints excluded: chain F residue 599 ASP Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 681 SER Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 703 GLU Chi-restraints excluded: chain F residue 740 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 189 optimal weight: 0.9990 chunk 243 optimal weight: 0.9990 chunk 351 optimal weight: 0.5980 chunk 231 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 170 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 118 optimal weight: 0.4980 chunk 403 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 ASN A 910 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 826 GLN B 899 GLN C 538 HIS D 111 ASN D 826 GLN E 740 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.183863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139725 restraints weight = 53012.680| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.41 r_work: 0.3497 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39198 Z= 0.128 Angle : 0.586 9.699 53256 Z= 0.288 Chirality : 0.042 0.212 6234 Planarity : 0.004 0.056 6708 Dihedral : 6.864 118.436 5328 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.24 % Allowed : 19.35 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.12), residues: 4938 helix: 1.71 (0.10), residues: 2622 sheet: -1.76 (0.27), residues: 354 loop : -2.29 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 715 TYR 0.031 0.002 TYR D 541 PHE 0.020 0.001 PHE C 303 TRP 0.014 0.001 TRP E 846 HIS 0.007 0.001 HIS E 701 Details of bonding type rmsd covalent geometry : bond 0.00288 (39198) covalent geometry : angle 0.58555 (53256) hydrogen bonds : bond 0.03599 ( 2046) hydrogen bonds : angle 4.26406 ( 6066) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 896 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.5590 (mmp) cc_final: 0.5184 (mmp) REVERT: A 120 PHE cc_start: 0.8095 (m-80) cc_final: 0.7662 (m-80) REVERT: A 171 GLU cc_start: 0.7343 (tp30) cc_final: 0.6896 (tp30) REVERT: A 179 LYS cc_start: 0.7561 (ptpp) cc_final: 0.6962 (ptpp) REVERT: A 235 LEU cc_start: 0.4261 (OUTLIER) cc_final: 0.4000 (mm) REVERT: A 385 LYS cc_start: 0.8330 (mtpp) cc_final: 0.7840 (mtpp) REVERT: A 387 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7436 (pttm) REVERT: A 474 LYS cc_start: 0.7797 (ttpt) cc_final: 0.7414 (ttpt) REVERT: A 567 GLU cc_start: 0.8217 (tp30) cc_final: 0.7780 (tp30) REVERT: A 569 SER cc_start: 0.8587 (m) cc_final: 0.8105 (p) REVERT: A 595 SER cc_start: 0.8902 (p) cc_final: 0.8294 (p) REVERT: A 599 ASP cc_start: 0.8451 (m-30) cc_final: 0.8186 (m-30) REVERT: A 605 ASP cc_start: 0.7625 (m-30) cc_final: 0.7409 (t0) REVERT: A 624 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8143 (mt0) REVERT: A 720 GLU cc_start: 0.7958 (mp0) cc_final: 0.7511 (mp0) REVERT: A 746 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7877 (t) REVERT: A 759 SER cc_start: 0.8540 (m) cc_final: 0.8143 (p) REVERT: A 898 LYS cc_start: 0.8033 (mmmm) cc_final: 0.7557 (mmmm) REVERT: A 901 SER cc_start: 0.8551 (t) cc_final: 0.7894 (p) REVERT: B 116 PHE cc_start: 0.7693 (t80) cc_final: 0.7395 (t80) REVERT: B 120 PHE cc_start: 0.8159 (m-80) cc_final: 0.7708 (m-80) REVERT: B 171 GLU cc_start: 0.7546 (tp30) cc_final: 0.7203 (tp30) REVERT: B 174 LYS cc_start: 0.8170 (tttp) cc_final: 0.7940 (tttp) REVERT: B 252 LYS cc_start: 0.7679 (tptt) cc_final: 0.7433 (tptt) REVERT: B 346 MET cc_start: 0.8252 (mmm) cc_final: 0.7938 (mmm) REVERT: B 355 LYS cc_start: 0.8459 (ttmt) cc_final: 0.8231 (ttmt) REVERT: B 474 LYS cc_start: 0.8030 (ttpt) cc_final: 0.7680 (ttpt) REVERT: B 504 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7226 (tm-30) REVERT: B 533 MET cc_start: 0.5698 (tmm) cc_final: 0.5460 (ttt) REVERT: B 567 GLU cc_start: 0.8300 (tp30) cc_final: 0.7807 (tp30) REVERT: B 582 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7964 (mm-30) REVERT: B 599 ASP cc_start: 0.8331 (t0) cc_final: 0.7989 (t0) REVERT: B 605 ASP cc_start: 0.7692 (m-30) cc_final: 0.7485 (t0) REVERT: B 624 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8352 (mt0) REVERT: B 638 ASP cc_start: 0.7958 (p0) cc_final: 0.7724 (p0) REVERT: B 656 ASP cc_start: 0.8236 (m-30) cc_final: 0.7963 (m-30) REVERT: B 843 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8654 (mt) REVERT: B 844 TRP cc_start: 0.8463 (m-90) cc_final: 0.8072 (m-10) REVERT: B 848 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7750 (mm-30) REVERT: B 903 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7499 (mt-10) REVERT: B 904 ASP cc_start: 0.8042 (t0) cc_final: 0.7739 (t0) REVERT: B 917 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7294 (tm-30) REVERT: C 116 PHE cc_start: 0.7583 (t80) cc_final: 0.7378 (t80) REVERT: C 120 PHE cc_start: 0.7769 (m-80) cc_final: 0.7340 (m-10) REVERT: C 162 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7028 (mm-30) REVERT: C 171 GLU cc_start: 0.7293 (tp30) cc_final: 0.6899 (tp30) REVERT: C 174 LYS cc_start: 0.7855 (tttp) cc_final: 0.7514 (tttp) REVERT: C 314 TYR cc_start: 0.8497 (m-80) cc_final: 0.8171 (m-80) REVERT: C 380 THR cc_start: 0.8558 (t) cc_final: 0.8273 (p) REVERT: C 387 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7589 (pttm) REVERT: C 403 ASP cc_start: 0.5817 (t70) cc_final: 0.5368 (t0) REVERT: C 423 ASP cc_start: 0.8065 (t70) cc_final: 0.7723 (t70) REVERT: C 457 LYS cc_start: 0.7508 (ttmm) cc_final: 0.7283 (mttm) REVERT: C 474 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7604 (ttpt) REVERT: C 567 GLU cc_start: 0.8221 (tp30) cc_final: 0.7874 (tp30) REVERT: C 570 ARG cc_start: 0.8262 (ttm110) cc_final: 0.8044 (ttm110) REVERT: C 624 GLN cc_start: 0.8609 (mm110) cc_final: 0.8300 (mt0) REVERT: C 775 THR cc_start: 0.8640 (m) cc_final: 0.8175 (p) REVERT: C 826 GLN cc_start: 0.8236 (mp10) cc_final: 0.7981 (mp10) REVERT: C 896 ASN cc_start: 0.7373 (p0) cc_final: 0.7057 (p0) REVERT: C 904 ASP cc_start: 0.8086 (t0) cc_final: 0.7744 (t0) REVERT: C 917 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7277 (tm-30) REVERT: D 171 GLU cc_start: 0.7336 (tp30) cc_final: 0.6922 (tp30) REVERT: D 174 LYS cc_start: 0.7966 (tttp) cc_final: 0.7641 (tttp) REVERT: D 303 PHE cc_start: 0.8269 (t80) cc_final: 0.7965 (t80) REVERT: D 379 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8303 (ttpp) REVERT: D 474 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7626 (ttpt) REVERT: D 558 THR cc_start: 0.8675 (m) cc_final: 0.8449 (t) REVERT: D 567 GLU cc_start: 0.8312 (tp30) cc_final: 0.7909 (tp30) REVERT: D 569 SER cc_start: 0.8735 (m) cc_final: 0.8317 (p) REVERT: D 595 SER cc_start: 0.8837 (p) cc_final: 0.8591 (p) REVERT: D 605 ASP cc_start: 0.7701 (t0) cc_final: 0.7170 (t0) REVERT: D 615 LYS cc_start: 0.8659 (mtpp) cc_final: 0.7923 (mtmt) REVERT: D 624 GLN cc_start: 0.8540 (mt0) cc_final: 0.8253 (mt0) REVERT: D 679 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8321 (mtpp) REVERT: D 730 ASP cc_start: 0.7919 (t0) cc_final: 0.7580 (t0) REVERT: D 795 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7357 (mm-30) REVERT: D 898 LYS cc_start: 0.8149 (mmmm) cc_final: 0.7716 (mmmm) REVERT: D 899 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7956 (mm-40) REVERT: D 901 SER cc_start: 0.8619 (t) cc_final: 0.8112 (p) REVERT: D 904 ASP cc_start: 0.8023 (t0) cc_final: 0.7819 (t0) REVERT: D 915 GLN cc_start: 0.8628 (tt0) cc_final: 0.8222 (mt0) REVERT: D 917 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7629 (tm-30) REVERT: E 171 GLU cc_start: 0.7695 (tp30) cc_final: 0.7339 (tp30) REVERT: E 299 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8518 (mt) REVERT: E 355 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8144 (ttmt) REVERT: E 356 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7974 (mttm) REVERT: E 474 LYS cc_start: 0.7408 (ttpt) cc_final: 0.6802 (ttpt) REVERT: E 498 TYR cc_start: 0.6953 (t80) cc_final: 0.6687 (t80) REVERT: E 558 THR cc_start: 0.8534 (m) cc_final: 0.8268 (t) REVERT: E 566 ARG cc_start: 0.8189 (ttm-80) cc_final: 0.7957 (ttm-80) REVERT: E 736 ILE cc_start: 0.8719 (tp) cc_final: 0.8464 (tt) REVERT: E 775 THR cc_start: 0.8491 (m) cc_final: 0.8017 (p) REVERT: E 843 ILE cc_start: 0.8871 (mm) cc_final: 0.8629 (mt) REVERT: E 898 LYS cc_start: 0.7965 (mmmm) cc_final: 0.7731 (mmmm) REVERT: E 899 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7367 (mm-40) REVERT: E 903 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7400 (mt-10) REVERT: E 904 ASP cc_start: 0.7976 (t0) cc_final: 0.7651 (t0) REVERT: E 907 VAL cc_start: 0.8560 (t) cc_final: 0.8294 (p) REVERT: E 917 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7313 (tm-30) REVERT: F 120 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7389 (m-80) REVERT: F 162 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7142 (mm-30) REVERT: F 171 GLU cc_start: 0.7308 (tp30) cc_final: 0.6873 (tp30) REVERT: F 174 LYS cc_start: 0.7684 (tttp) cc_final: 0.7385 (tttp) REVERT: F 209 ILE cc_start: 0.8452 (mm) cc_final: 0.8049 (tp) REVERT: F 303 PHE cc_start: 0.8303 (t80) cc_final: 0.8074 (t80) REVERT: F 385 LYS cc_start: 0.8487 (mtpp) cc_final: 0.8091 (mtpp) REVERT: F 387 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7367 (pttm) REVERT: F 474 LYS cc_start: 0.7624 (ttpt) cc_final: 0.7111 (ttpt) REVERT: F 567 GLU cc_start: 0.8264 (tp30) cc_final: 0.7846 (tp30) REVERT: F 569 SER cc_start: 0.8714 (m) cc_final: 0.8392 (p) REVERT: F 638 ASP cc_start: 0.7864 (p0) cc_final: 0.7548 (p0) REVERT: F 695 ARG cc_start: 0.8537 (tpp-160) cc_final: 0.8233 (tpt170) REVERT: F 696 ILE cc_start: 0.8622 (pt) cc_final: 0.8370 (pt) REVERT: F 775 THR cc_start: 0.8491 (m) cc_final: 0.8107 (p) REVERT: F 826 GLN cc_start: 0.8150 (mp10) cc_final: 0.7914 (mp10) REVERT: F 843 ILE cc_start: 0.8864 (mm) cc_final: 0.8628 (mt) REVERT: F 848 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7676 (mm-30) REVERT: F 865 PHE cc_start: 0.8652 (t80) cc_final: 0.8233 (t80) REVERT: F 898 LYS cc_start: 0.7939 (mmmm) cc_final: 0.7646 (mmmm) REVERT: F 904 ASP cc_start: 0.7926 (t0) cc_final: 0.7699 (t0) REVERT: F 910 GLN cc_start: 0.8524 (mt0) cc_final: 0.8314 (mt0) REVERT: F 917 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7288 (tm-30) outliers start: 92 outliers final: 74 residues processed: 939 average time/residue: 0.2339 time to fit residues: 361.9571 Evaluate side-chains 973 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 891 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 659 ARG Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 681 SER Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 703 GLU Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 688 MET Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 701 HIS Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 361 GLN Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 681 SER Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain E residue 703 GLU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 740 ASN Chi-restraints excluded: chain E residue 748 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 596 GLU Chi-restraints excluded: chain F residue 599 ASP Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 681 SER Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 703 GLU Chi-restraints excluded: chain F residue 758 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 458 optimal weight: 1.9990 chunk 376 optimal weight: 0.9980 chunk 203 optimal weight: 10.0000 chunk 430 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 476 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 416 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 454 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 ASN A 815 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 826 GLN C 899 GLN E 571 GLN E 740 ASN F 624 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.185683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142006 restraints weight = 52734.511| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.49 r_work: 0.3487 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39198 Z= 0.138 Angle : 0.595 9.277 53256 Z= 0.293 Chirality : 0.042 0.230 6234 Planarity : 0.004 0.057 6708 Dihedral : 6.816 120.995 5328 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.05 % Allowed : 19.81 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.12), residues: 4938 helix: 1.67 (0.10), residues: 2622 sheet: -1.74 (0.27), residues: 354 loop : -2.29 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 715 TYR 0.030 0.002 TYR F 541 PHE 0.020 0.001 PHE C 303 TRP 0.014 0.001 TRP D 846 HIS 0.007 0.001 HIS E 701 Details of bonding type rmsd covalent geometry : bond 0.00310 (39198) covalent geometry : angle 0.59486 (53256) hydrogen bonds : bond 0.03677 ( 2046) hydrogen bonds : angle 4.25873 ( 6066) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 882 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.5564 (mmp) cc_final: 0.5170 (mmp) REVERT: A 120 PHE cc_start: 0.8112 (m-80) cc_final: 0.7679 (m-80) REVERT: A 171 GLU cc_start: 0.7377 (tp30) cc_final: 0.6967 (tp30) REVERT: A 179 LYS cc_start: 0.7589 (ptpp) cc_final: 0.6988 (ptpp) REVERT: A 235 LEU cc_start: 0.4337 (OUTLIER) cc_final: 0.4073 (mm) REVERT: A 385 LYS cc_start: 0.8332 (mtpp) cc_final: 0.7849 (mtpp) REVERT: A 387 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7485 (pttm) REVERT: A 474 LYS cc_start: 0.7752 (ttpt) cc_final: 0.7362 (ttpt) REVERT: A 504 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7081 (pt0) REVERT: A 567 GLU cc_start: 0.8211 (tp30) cc_final: 0.7789 (tp30) REVERT: A 569 SER cc_start: 0.8580 (m) cc_final: 0.8115 (p) REVERT: A 595 SER cc_start: 0.8991 (p) cc_final: 0.8748 (p) REVERT: A 605 ASP cc_start: 0.7621 (m-30) cc_final: 0.7401 (t0) REVERT: A 624 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8166 (mt0) REVERT: A 720 GLU cc_start: 0.7957 (mp0) cc_final: 0.7505 (mp0) REVERT: A 746 THR cc_start: 0.8186 (p) cc_final: 0.7884 (t) REVERT: A 759 SER cc_start: 0.8551 (m) cc_final: 0.8154 (p) REVERT: A 898 LYS cc_start: 0.8056 (mmmm) cc_final: 0.7582 (mmmm) REVERT: A 901 SER cc_start: 0.8571 (t) cc_final: 0.7926 (p) REVERT: B 116 PHE cc_start: 0.7672 (t80) cc_final: 0.7389 (t80) REVERT: B 120 PHE cc_start: 0.8114 (m-80) cc_final: 0.7674 (m-80) REVERT: B 171 GLU cc_start: 0.7576 (tp30) cc_final: 0.7235 (tp30) REVERT: B 174 LYS cc_start: 0.8196 (tttp) cc_final: 0.7973 (tttp) REVERT: B 252 LYS cc_start: 0.7664 (tptt) cc_final: 0.7437 (tptt) REVERT: B 355 LYS cc_start: 0.8454 (ttmt) cc_final: 0.8231 (ttmt) REVERT: B 474 LYS cc_start: 0.8002 (ttpt) cc_final: 0.7677 (ttpt) REVERT: B 504 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7263 (tm-30) REVERT: B 567 GLU cc_start: 0.8353 (tp30) cc_final: 0.7869 (tp30) REVERT: B 569 SER cc_start: 0.8618 (m) cc_final: 0.8347 (p) REVERT: B 582 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7963 (mm-30) REVERT: B 599 ASP cc_start: 0.8307 (t0) cc_final: 0.7947 (t0) REVERT: B 605 ASP cc_start: 0.7675 (m-30) cc_final: 0.7466 (t0) REVERT: B 624 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8334 (mt0) REVERT: B 638 ASP cc_start: 0.7982 (p0) cc_final: 0.7621 (p0) REVERT: B 656 ASP cc_start: 0.8244 (m-30) cc_final: 0.7958 (m-30) REVERT: B 843 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8656 (mt) REVERT: B 844 TRP cc_start: 0.8471 (m-90) cc_final: 0.8091 (m-10) REVERT: B 848 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7773 (mm-30) REVERT: B 898 LYS cc_start: 0.8002 (mmmm) cc_final: 0.7686 (mmmm) REVERT: B 903 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7500 (mt-10) REVERT: B 904 ASP cc_start: 0.8041 (t0) cc_final: 0.7745 (t0) REVERT: B 917 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7321 (tm-30) REVERT: C 116 PHE cc_start: 0.7602 (t80) cc_final: 0.7365 (t80) REVERT: C 120 PHE cc_start: 0.7778 (m-80) cc_final: 0.7335 (m-10) REVERT: C 162 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7019 (mm-30) REVERT: C 171 GLU cc_start: 0.7316 (tp30) cc_final: 0.6888 (tp30) REVERT: C 174 LYS cc_start: 0.7867 (tttp) cc_final: 0.7534 (tttp) REVERT: C 314 TYR cc_start: 0.8502 (m-80) cc_final: 0.8170 (m-80) REVERT: C 380 THR cc_start: 0.8585 (t) cc_final: 0.8224 (p) REVERT: C 387 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7448 (pttm) REVERT: C 388 LEU cc_start: 0.7801 (mp) cc_final: 0.7492 (mp) REVERT: C 403 ASP cc_start: 0.5797 (t70) cc_final: 0.5369 (t0) REVERT: C 423 ASP cc_start: 0.8054 (t70) cc_final: 0.7711 (t70) REVERT: C 457 LYS cc_start: 0.7576 (ttmm) cc_final: 0.7341 (mttm) REVERT: C 474 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7535 (ttpt) REVERT: C 567 GLU cc_start: 0.8205 (tp30) cc_final: 0.7849 (tp30) REVERT: C 570 ARG cc_start: 0.8209 (ttm110) cc_final: 0.8007 (ttm110) REVERT: C 624 GLN cc_start: 0.8595 (mm110) cc_final: 0.8305 (mt0) REVERT: C 775 THR cc_start: 0.8665 (m) cc_final: 0.8216 (p) REVERT: C 826 GLN cc_start: 0.8220 (mp10) cc_final: 0.7968 (mp10) REVERT: C 896 ASN cc_start: 0.7404 (p0) cc_final: 0.7086 (p0) REVERT: C 904 ASP cc_start: 0.8092 (t0) cc_final: 0.7750 (t0) REVERT: C 917 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7300 (tm-30) REVERT: D 171 GLU cc_start: 0.7315 (tp30) cc_final: 0.6919 (tp30) REVERT: D 174 LYS cc_start: 0.7975 (tttp) cc_final: 0.7653 (tttp) REVERT: D 303 PHE cc_start: 0.8271 (t80) cc_final: 0.7976 (t80) REVERT: D 379 LYS cc_start: 0.8491 (ttpt) cc_final: 0.8269 (ttpp) REVERT: D 474 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7601 (ttpt) REVERT: D 558 THR cc_start: 0.8665 (m) cc_final: 0.8442 (t) REVERT: D 567 GLU cc_start: 0.8290 (tp30) cc_final: 0.7895 (tp30) REVERT: D 569 SER cc_start: 0.8726 (m) cc_final: 0.8275 (p) REVERT: D 595 SER cc_start: 0.8865 (p) cc_final: 0.8615 (p) REVERT: D 605 ASP cc_start: 0.7777 (t0) cc_final: 0.7249 (t0) REVERT: D 615 LYS cc_start: 0.8673 (mtpp) cc_final: 0.7940 (mtmt) REVERT: D 624 GLN cc_start: 0.8542 (mt0) cc_final: 0.8259 (mt0) REVERT: D 679 LYS cc_start: 0.8525 (mtmm) cc_final: 0.8312 (mtpp) REVERT: D 730 ASP cc_start: 0.7919 (t0) cc_final: 0.7588 (t0) REVERT: D 746 THR cc_start: 0.8021 (p) cc_final: 0.7684 (t) REVERT: D 795 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7364 (mm-30) REVERT: D 898 LYS cc_start: 0.8132 (mmmm) cc_final: 0.7823 (mmmm) REVERT: D 899 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7962 (mm-40) REVERT: D 915 GLN cc_start: 0.8638 (tt0) cc_final: 0.8240 (mt0) REVERT: E 171 GLU cc_start: 0.7712 (tp30) cc_final: 0.7343 (tp30) REVERT: E 299 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8537 (mt) REVERT: E 355 LYS cc_start: 0.8360 (ttmt) cc_final: 0.8151 (ttmt) REVERT: E 387 LYS cc_start: 0.8051 (pttm) cc_final: 0.7723 (pttm) REVERT: E 474 LYS cc_start: 0.7361 (ttpt) cc_final: 0.6782 (ttpt) REVERT: E 498 TYR cc_start: 0.7002 (t80) cc_final: 0.6745 (t80) REVERT: E 558 THR cc_start: 0.8543 (m) cc_final: 0.8274 (t) REVERT: E 736 ILE cc_start: 0.8724 (tp) cc_final: 0.8508 (tt) REVERT: E 775 THR cc_start: 0.8515 (m) cc_final: 0.8055 (p) REVERT: E 843 ILE cc_start: 0.8882 (mm) cc_final: 0.8639 (mt) REVERT: E 848 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7662 (mm-30) REVERT: E 898 LYS cc_start: 0.7962 (mmmm) cc_final: 0.7740 (mmmm) REVERT: E 899 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7396 (mm-40) REVERT: E 903 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7396 (mt-10) REVERT: E 904 ASP cc_start: 0.7966 (t0) cc_final: 0.7654 (t0) REVERT: E 907 VAL cc_start: 0.8596 (t) cc_final: 0.8392 (p) REVERT: E 917 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7348 (tm-30) REVERT: F 119 PHE cc_start: 0.7486 (m-10) cc_final: 0.7254 (m-10) REVERT: F 120 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: F 162 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7168 (mm-30) REVERT: F 171 GLU cc_start: 0.7312 (tp30) cc_final: 0.6875 (tp30) REVERT: F 174 LYS cc_start: 0.7713 (tttp) cc_final: 0.7427 (tttp) REVERT: F 209 ILE cc_start: 0.8454 (mm) cc_final: 0.8037 (tp) REVERT: F 303 PHE cc_start: 0.8307 (t80) cc_final: 0.8076 (t80) REVERT: F 385 LYS cc_start: 0.8506 (mtpp) cc_final: 0.8102 (mtpp) REVERT: F 387 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7392 (pttm) REVERT: F 474 LYS cc_start: 0.7598 (ttpt) cc_final: 0.7138 (ttpt) REVERT: F 567 GLU cc_start: 0.8285 (tp30) cc_final: 0.7866 (tp30) REVERT: F 569 SER cc_start: 0.8714 (m) cc_final: 0.8408 (p) REVERT: F 638 ASP cc_start: 0.7855 (p0) cc_final: 0.7538 (p0) REVERT: F 695 ARG cc_start: 0.8538 (tpp-160) cc_final: 0.8243 (tpt170) REVERT: F 775 THR cc_start: 0.8509 (m) cc_final: 0.8140 (p) REVERT: F 826 GLN cc_start: 0.8164 (mp10) cc_final: 0.7930 (mp10) REVERT: F 843 ILE cc_start: 0.8866 (mm) cc_final: 0.8643 (mt) REVERT: F 848 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7624 (mm-30) REVERT: F 898 LYS cc_start: 0.7930 (mmmm) cc_final: 0.7639 (mmmm) REVERT: F 904 ASP cc_start: 0.7902 (t0) cc_final: 0.7665 (t0) REVERT: F 910 GLN cc_start: 0.8508 (mt0) cc_final: 0.8297 (mt0) REVERT: F 917 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7320 (tm-30) outliers start: 84 outliers final: 74 residues processed: 923 average time/residue: 0.2317 time to fit residues: 354.0452 Evaluate side-chains 959 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 878 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 659 ARG Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 681 SER Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 703 GLU Chi-restraints excluded: chain C residue 899 GLN Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 688 MET Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 701 HIS Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 837 LEU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 571 GLN Chi-restraints excluded: chain E residue 659 ARG Chi-restraints excluded: chain E residue 681 SER Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain E residue 703 GLU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 748 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 596 GLU Chi-restraints excluded: chain F residue 599 ASP Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 681 SER Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 701 HIS Chi-restraints excluded: chain F residue 703 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 350 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 191 optimal weight: 0.6980 chunk 283 optimal weight: 7.9990 chunk 392 optimal weight: 0.9990 chunk 277 optimal weight: 0.0370 chunk 399 optimal weight: 0.6980 chunk 418 optimal weight: 0.9990 chunk 370 optimal weight: 0.0970 chunk 40 optimal weight: 9.9990 chunk 274 optimal weight: 1.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 GLN ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.183635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.139087 restraints weight = 53067.928| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.48 r_work: 0.3491 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.236 39198 Z= 0.183 Angle : 0.771 59.190 53256 Z= 0.434 Chirality : 0.049 1.940 6234 Planarity : 0.004 0.137 6708 Dihedral : 6.826 121.029 5328 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.16 % Favored : 93.82 % Rotamer: Outliers : 2.12 % Allowed : 20.25 % Favored : 77.63 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.12), residues: 4938 helix: 1.68 (0.10), residues: 2622 sheet: -1.73 (0.27), residues: 354 loop : -2.30 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 715 TYR 0.038 0.002 TYR B 432 PHE 0.019 0.001 PHE C 303 TRP 0.013 0.001 TRP A 846 HIS 0.007 0.001 HIS E 701 Details of bonding type rmsd covalent geometry : bond 0.00395 (39198) covalent geometry : angle 0.77139 (53256) hydrogen bonds : bond 0.03667 ( 2046) hydrogen bonds : angle 4.26331 ( 6066) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13631.42 seconds wall clock time: 232 minutes 59.90 seconds (13979.90 seconds total)