Starting phenix.real_space_refine on Sat Aug 8 14:09:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9e_65772/08_2026/9w9e_65772.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9e_65772/08_2026/9w9e_65772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w9e_65772/08_2026/9w9e_65772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9e_65772/08_2026/9w9e_65772.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w9e_65772/08_2026/9w9e_65772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9e_65772/08_2026/9w9e_65772.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 17512 2.51 5 N 4988 2.21 5 O 5120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27724 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6931 Classifications: {'peptide': 862} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 811} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: B, C, D Time building chain proxies: 8.80, per 1000 atoms: 0.32 Number of scatterers: 27724 At special positions: 0 Unit cell: (151.06, 220.78, 132.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 5120 8.00 N 4988 7.00 C 17512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.3 seconds 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6448 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 18 sheets defined 42.5% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 86 through 102 Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 182 through 191 removed outlier: 3.591A pdb=" N VAL A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 268 through 275 Processing helix chain 'A' and resid 275 through 299 removed outlier: 3.546A pdb=" N GLN A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 384 through 406 removed outlier: 4.286A pdb=" N MET A 388 " --> pdb=" O HIS A 384 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 389 " --> pdb=" O TYR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 418 removed outlier: 3.816A pdb=" N ILE A 411 " --> pdb=" O TYR A 407 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 444 Processing helix chain 'A' and resid 461 through 477 Processing helix chain 'A' and resid 526 through 538 Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 544 through 554 removed outlier: 3.664A pdb=" N GLY A 550 " --> pdb=" O ASP A 546 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 602 through 606 Processing helix chain 'A' and resid 610 through 616 Processing helix chain 'A' and resid 629 through 638 Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.974A pdb=" N GLY A 646 " --> pdb=" O THR A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 684 through 699 Processing helix chain 'A' and resid 710 through 720 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 744 through 757 Processing helix chain 'A' and resid 771 through 789 Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 804 through 806 No H-bonds generated for 'chain 'A' and resid 804 through 806' Processing helix chain 'A' and resid 849 through 866 Processing helix chain 'A' and resid 889 through 901 Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' Processing helix chain 'A' and resid 906 through 918 removed outlier: 3.713A pdb=" N PHE A 913 " --> pdb=" O ARG A 909 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG A 914 " --> pdb=" O LYS A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 946 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 182 through 191 removed outlier: 3.591A pdb=" N VAL B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 261 through 268 Processing helix chain 'B' and resid 268 through 275 Processing helix chain 'B' and resid 275 through 299 removed outlier: 3.546A pdb=" N GLN B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 384 through 406 removed outlier: 4.286A pdb=" N MET B 388 " --> pdb=" O HIS B 384 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 389 " --> pdb=" O TYR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 418 removed outlier: 3.815A pdb=" N ILE B 411 " --> pdb=" O TYR B 407 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN B 417 " --> pdb=" O ILE B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 444 Processing helix chain 'B' and resid 461 through 477 Processing helix chain 'B' and resid 526 through 538 Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 544 through 554 removed outlier: 3.664A pdb=" N GLY B 550 " --> pdb=" O ASP B 546 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 574 Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'B' and resid 602 through 606 Processing helix chain 'B' and resid 610 through 616 Processing helix chain 'B' and resid 629 through 638 Processing helix chain 'B' and resid 639 through 647 removed outlier: 3.975A pdb=" N GLY B 646 " --> pdb=" O THR B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 683 No H-bonds generated for 'chain 'B' and resid 681 through 683' Processing helix chain 'B' and resid 684 through 699 Processing helix chain 'B' and resid 710 through 720 Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 744 through 757 Processing helix chain 'B' and resid 771 through 789 Processing helix chain 'B' and resid 793 through 798 Processing helix chain 'B' and resid 804 through 806 No H-bonds generated for 'chain 'B' and resid 804 through 806' Processing helix chain 'B' and resid 849 through 866 Processing helix chain 'B' and resid 889 through 901 Processing helix chain 'B' and resid 903 through 905 No H-bonds generated for 'chain 'B' and resid 903 through 905' Processing helix chain 'B' and resid 906 through 918 removed outlier: 3.714A pdb=" N PHE B 913 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ARG B 914 " --> pdb=" O LYS B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 946 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 182 through 191 removed outlier: 3.591A pdb=" N VAL C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 245 Processing helix chain 'C' and resid 261 through 268 Processing helix chain 'C' and resid 268 through 275 Processing helix chain 'C' and resid 275 through 299 removed outlier: 3.545A pdb=" N GLN C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 384 through 406 removed outlier: 4.286A pdb=" N MET C 388 " --> pdb=" O HIS C 384 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 389 " --> pdb=" O TYR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 418 removed outlier: 3.816A pdb=" N ILE C 411 " --> pdb=" O TYR C 407 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN C 417 " --> pdb=" O ILE C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 461 through 477 Processing helix chain 'C' and resid 526 through 538 Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 544 through 554 removed outlier: 3.664A pdb=" N GLY C 550 " --> pdb=" O ASP C 546 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE C 551 " --> pdb=" O TYR C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 574 Processing helix chain 'C' and resid 577 through 581 Processing helix chain 'C' and resid 602 through 606 Processing helix chain 'C' and resid 610 through 616 Processing helix chain 'C' and resid 629 through 638 Processing helix chain 'C' and resid 639 through 647 removed outlier: 3.973A pdb=" N GLY C 646 " --> pdb=" O THR C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 683 No H-bonds generated for 'chain 'C' and resid 681 through 683' Processing helix chain 'C' and resid 684 through 699 Processing helix chain 'C' and resid 710 through 720 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 744 through 757 Processing helix chain 'C' and resid 771 through 789 Processing helix chain 'C' and resid 793 through 798 Processing helix chain 'C' and resid 804 through 806 No H-bonds generated for 'chain 'C' and resid 804 through 806' Processing helix chain 'C' and resid 849 through 866 Processing helix chain 'C' and resid 889 through 901 Processing helix chain 'C' and resid 903 through 905 No H-bonds generated for 'chain 'C' and resid 903 through 905' Processing helix chain 'C' and resid 906 through 918 removed outlier: 3.713A pdb=" N PHE C 913 " --> pdb=" O ARG C 909 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG C 914 " --> pdb=" O LYS C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 934 through 946 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 182 through 191 removed outlier: 3.590A pdb=" N VAL D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 268 through 275 Processing helix chain 'D' and resid 275 through 299 removed outlier: 3.547A pdb=" N GLN D 299 " --> pdb=" O SER D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 346 Processing helix chain 'D' and resid 384 through 406 removed outlier: 4.286A pdb=" N MET D 388 " --> pdb=" O HIS D 384 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 389 " --> pdb=" O TYR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 418 removed outlier: 3.817A pdb=" N ILE D 411 " --> pdb=" O TYR D 407 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN D 417 " --> pdb=" O ILE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 444 Processing helix chain 'D' and resid 461 through 477 Processing helix chain 'D' and resid 526 through 538 Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 544 through 554 removed outlier: 3.664A pdb=" N GLY D 550 " --> pdb=" O ASP D 546 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE D 551 " --> pdb=" O TYR D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 577 through 581 Processing helix chain 'D' and resid 602 through 606 Processing helix chain 'D' and resid 610 through 616 Processing helix chain 'D' and resid 629 through 638 Processing helix chain 'D' and resid 639 through 647 removed outlier: 3.973A pdb=" N GLY D 646 " --> pdb=" O THR D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 683 No H-bonds generated for 'chain 'D' and resid 681 through 683' Processing helix chain 'D' and resid 684 through 699 Processing helix chain 'D' and resid 710 through 720 Processing helix chain 'D' and resid 739 through 744 Processing helix chain 'D' and resid 744 through 757 Processing helix chain 'D' and resid 771 through 789 Processing helix chain 'D' and resid 793 through 798 Processing helix chain 'D' and resid 804 through 806 No H-bonds generated for 'chain 'D' and resid 804 through 806' Processing helix chain 'D' and resid 849 through 866 Processing helix chain 'D' and resid 889 through 901 Processing helix chain 'D' and resid 903 through 905 No H-bonds generated for 'chain 'D' and resid 903 through 905' Processing helix chain 'D' and resid 906 through 918 removed outlier: 3.714A pdb=" N PHE D 913 " --> pdb=" O ARG D 909 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ARG D 914 " --> pdb=" O LYS D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 934 through 946 Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 153 removed outlier: 6.903A pdb=" N VAL A 162 " --> pdb=" O HIS A 149 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE A 151 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE A 160 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG A 153 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N LEU A 158 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N HIS A 175 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 9.327A pdb=" N GLN A 225 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG A 201 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE A 226 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG A 199 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU A 228 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE A 197 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 302 through 303 removed outlier: 5.796A pdb=" N ILE A 302 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE A 354 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 564 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE A 517 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 510 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N SER A 519 " --> pdb=" O PHE A 508 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE A 508 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 432 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 309 through 310 removed outlier: 3.540A pdb=" N GLN A 322 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN D 322 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 651 through 654 removed outlier: 4.675A pdb=" N SER A 663 " --> pdb=" O PRO A 675 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 705 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR A 925 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU A 924 " --> pdb=" O CYS A 728 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N CYS A 728 " --> pdb=" O LEU A 924 " (cutoff:3.500A) removed outlier: 11.569A pdb=" N ARG A 724 " --> pdb=" O THR A 881 " (cutoff:3.500A) removed outlier: 12.080A pdb=" N THR A 881 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N LEU A 726 " --> pdb=" O THR A 879 " (cutoff:3.500A) removed outlier: 11.304A pdb=" N THR A 879 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N CYS A 728 " --> pdb=" O THR A 877 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 732 " --> pdb=" O GLY A 873 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLY A 873 " --> pdb=" O GLU A 732 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL A 734 " --> pdb=" O THR A 871 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N THR A 871 " --> pdb=" O VAL A 734 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 760 through 763 removed outlier: 4.202A pdb=" N ALA A 822 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS A 821 " --> pdb=" O ASP A 842 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASP A 842 " --> pdb=" O CYS A 821 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE A 823 " --> pdb=" O SER A 840 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER A 840 " --> pdb=" O PHE A 823 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA A 825 " --> pdb=" O LYS A 838 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 141 through 153 removed outlier: 6.902A pdb=" N VAL B 162 " --> pdb=" O HIS B 149 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE B 151 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE B 160 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG B 153 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N LEU B 158 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N HIS B 175 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N GLN B 225 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG B 201 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE B 226 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG B 199 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU B 228 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE B 197 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 302 through 303 removed outlier: 5.797A pdb=" N ILE B 302 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE B 354 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 564 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 517 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE B 510 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N SER B 519 " --> pdb=" O PHE B 508 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE B 508 " --> pdb=" O SER B 519 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 432 " --> pdb=" O ASP B 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 309 through 310 removed outlier: 3.577A pdb=" N GLN B 322 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN C 322 " --> pdb=" O ASN B 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 651 through 654 removed outlier: 4.675A pdb=" N SER B 663 " --> pdb=" O PRO B 675 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 705 " --> pdb=" O ALA B 672 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR B 925 " --> pdb=" O LEU B 708 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU B 924 " --> pdb=" O CYS B 728 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N CYS B 728 " --> pdb=" O LEU B 924 " (cutoff:3.500A) removed outlier: 11.569A pdb=" N ARG B 724 " --> pdb=" O THR B 881 " (cutoff:3.500A) removed outlier: 12.080A pdb=" N THR B 881 " --> pdb=" O ARG B 724 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N LEU B 726 " --> pdb=" O THR B 879 " (cutoff:3.500A) removed outlier: 11.304A pdb=" N THR B 879 " --> pdb=" O LEU B 726 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N CYS B 728 " --> pdb=" O THR B 877 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU B 732 " --> pdb=" O GLY B 873 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLY B 873 " --> pdb=" O GLU B 732 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 734 " --> pdb=" O THR B 871 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N THR B 871 " --> pdb=" O VAL B 734 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 760 through 763 removed outlier: 4.202A pdb=" N ALA B 822 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N CYS B 821 " --> pdb=" O ASP B 842 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASP B 842 " --> pdb=" O CYS B 821 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE B 823 " --> pdb=" O SER B 840 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER B 840 " --> pdb=" O PHE B 823 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA B 825 " --> pdb=" O LYS B 838 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 141 through 153 removed outlier: 6.902A pdb=" N VAL C 162 " --> pdb=" O HIS C 149 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE C 151 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N PHE C 160 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG C 153 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N LEU C 158 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N HIS C 175 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N GLN C 225 " --> pdb=" O HIS C 175 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG C 201 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE C 226 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG C 199 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU C 228 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE C 197 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 302 through 303 removed outlier: 5.797A pdb=" N ILE C 302 " --> pdb=" O TYR C 352 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE C 354 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY C 564 " --> pdb=" O ILE C 517 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE C 517 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 510 " --> pdb=" O ILE C 517 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N SER C 519 " --> pdb=" O PHE C 508 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE C 508 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE C 432 " --> pdb=" O ASP C 484 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 651 through 654 removed outlier: 4.675A pdb=" N SER C 663 " --> pdb=" O PRO C 675 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 705 " --> pdb=" O ALA C 672 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR C 925 " --> pdb=" O LEU C 708 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU C 924 " --> pdb=" O CYS C 728 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N CYS C 728 " --> pdb=" O LEU C 924 " (cutoff:3.500A) removed outlier: 11.569A pdb=" N ARG C 724 " --> pdb=" O THR C 881 " (cutoff:3.500A) removed outlier: 12.081A pdb=" N THR C 881 " --> pdb=" O ARG C 724 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N LEU C 726 " --> pdb=" O THR C 879 " (cutoff:3.500A) removed outlier: 11.304A pdb=" N THR C 879 " --> pdb=" O LEU C 726 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N CYS C 728 " --> pdb=" O THR C 877 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C 732 " --> pdb=" O GLY C 873 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLY C 873 " --> pdb=" O GLU C 732 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL C 734 " --> pdb=" O THR C 871 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N THR C 871 " --> pdb=" O VAL C 734 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 760 through 763 removed outlier: 4.203A pdb=" N ALA C 822 " --> pdb=" O ALA C 813 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS C 821 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASP C 842 " --> pdb=" O CYS C 821 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE C 823 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER C 840 " --> pdb=" O PHE C 823 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA C 825 " --> pdb=" O LYS C 838 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 153 removed outlier: 6.901A pdb=" N VAL D 162 " --> pdb=" O HIS D 149 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE D 151 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE D 160 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG D 153 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N LEU D 158 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N HIS D 175 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 9.327A pdb=" N GLN D 225 " --> pdb=" O HIS D 175 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG D 201 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE D 226 " --> pdb=" O ARG D 199 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG D 199 " --> pdb=" O ILE D 226 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU D 228 " --> pdb=" O ILE D 197 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE D 197 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 302 through 303 removed outlier: 5.796A pdb=" N ILE D 302 " --> pdb=" O TYR D 352 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE D 354 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY D 564 " --> pdb=" O ILE D 517 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE D 517 " --> pdb=" O GLY D 564 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE D 510 " --> pdb=" O ILE D 517 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N SER D 519 " --> pdb=" O PHE D 508 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE D 508 " --> pdb=" O SER D 519 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE D 432 " --> pdb=" O ASP D 484 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 651 through 654 removed outlier: 4.675A pdb=" N SER D 663 " --> pdb=" O PRO D 675 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 705 " --> pdb=" O ALA D 672 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR D 925 " --> pdb=" O LEU D 708 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU D 924 " --> pdb=" O CYS D 728 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N CYS D 728 " --> pdb=" O LEU D 924 " (cutoff:3.500A) removed outlier: 11.568A pdb=" N ARG D 724 " --> pdb=" O THR D 881 " (cutoff:3.500A) removed outlier: 12.080A pdb=" N THR D 881 " --> pdb=" O ARG D 724 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N LEU D 726 " --> pdb=" O THR D 879 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N THR D 879 " --> pdb=" O LEU D 726 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N CYS D 728 " --> pdb=" O THR D 877 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU D 732 " --> pdb=" O GLY D 873 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLY D 873 " --> pdb=" O GLU D 732 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL D 734 " --> pdb=" O THR D 871 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N THR D 871 " --> pdb=" O VAL D 734 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 760 through 763 removed outlier: 4.202A pdb=" N ALA D 822 " --> pdb=" O ALA D 813 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS D 821 " --> pdb=" O ASP D 842 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASP D 842 " --> pdb=" O CYS D 821 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE D 823 " --> pdb=" O SER D 840 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER D 840 " --> pdb=" O PHE D 823 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA D 825 " --> pdb=" O LYS D 838 " (cutoff:3.500A) 1257 hydrogen bonds defined for protein. 3555 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: 6.60 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9440 1.34 - 1.46: 6005 1.46 - 1.58: 12771 1.58 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 28400 Sorted by residual: bond pdb=" N ILE B 799 " pdb=" CA ILE B 799 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.04e-02 9.25e+03 1.48e+01 bond pdb=" N ILE A 799 " pdb=" CA ILE A 799 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.04e-02 9.25e+03 1.45e+01 bond pdb=" N ILE C 799 " pdb=" CA ILE C 799 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.04e-02 9.25e+03 1.45e+01 bond pdb=" N ILE D 799 " pdb=" CA ILE D 799 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.04e-02 9.25e+03 1.38e+01 bond pdb=" N HIS C 800 " pdb=" CA HIS C 800 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.21e-02 6.83e+03 8.39e+00 ... (remaining 28395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 36695 1.44 - 2.87: 1404 2.87 - 4.31: 285 4.31 - 5.75: 48 5.75 - 7.18: 12 Bond angle restraints: 38444 Sorted by residual: angle pdb=" C GLU C 349 " pdb=" CA GLU C 349 " pdb=" CB GLU C 349 " ideal model delta sigma weight residual 116.63 111.08 5.55 1.16e+00 7.43e-01 2.29e+01 angle pdb=" C GLU A 349 " pdb=" CA GLU A 349 " pdb=" CB GLU A 349 " ideal model delta sigma weight residual 116.63 111.11 5.52 1.16e+00 7.43e-01 2.27e+01 angle pdb=" C GLU B 349 " pdb=" CA GLU B 349 " pdb=" CB GLU B 349 " ideal model delta sigma weight residual 116.63 111.12 5.51 1.16e+00 7.43e-01 2.26e+01 angle pdb=" N ILE B 799 " pdb=" CA ILE B 799 " pdb=" C ILE B 799 " ideal model delta sigma weight residual 112.43 108.06 4.37 9.20e-01 1.18e+00 2.25e+01 angle pdb=" C GLU D 349 " pdb=" CA GLU D 349 " pdb=" CB GLU D 349 " ideal model delta sigma weight residual 116.63 111.13 5.50 1.16e+00 7.43e-01 2.25e+01 ... (remaining 38439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 15393 17.97 - 35.95: 1447 35.95 - 53.92: 228 53.92 - 71.89: 124 71.89 - 89.87: 4 Dihedral angle restraints: 17196 sinusoidal: 7200 harmonic: 9996 Sorted by residual: dihedral pdb=" CB LYS C 177 " pdb=" CG LYS C 177 " pdb=" CD LYS C 177 " pdb=" CE LYS C 177 " ideal model delta sinusoidal sigma weight residual 180.00 121.62 58.38 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB LYS A 177 " pdb=" CG LYS A 177 " pdb=" CD LYS A 177 " pdb=" CE LYS A 177 " ideal model delta sinusoidal sigma weight residual 180.00 121.64 58.36 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB LYS D 177 " pdb=" CG LYS D 177 " pdb=" CD LYS D 177 " pdb=" CE LYS D 177 " ideal model delta sinusoidal sigma weight residual 180.00 121.65 58.35 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 17193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2945 0.043 - 0.086: 772 0.086 - 0.129: 322 0.129 - 0.172: 41 0.172 - 0.215: 12 Chirality restraints: 4092 Sorted by residual: chirality pdb=" CA ILE B 799 " pdb=" N ILE B 799 " pdb=" C ILE B 799 " pdb=" CB ILE B 799 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE D 799 " pdb=" N ILE D 799 " pdb=" C ILE D 799 " pdb=" CB ILE D 799 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE A 799 " pdb=" N ILE A 799 " pdb=" C ILE A 799 " pdb=" CB ILE A 799 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 4089 not shown) Planarity restraints: 5068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 350 " -0.455 9.50e-02 1.11e+02 2.04e-01 2.56e+01 pdb=" NE ARG C 350 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG C 350 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 350 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 350 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 350 " 0.455 9.50e-02 1.11e+02 2.04e-01 2.56e+01 pdb=" NE ARG D 350 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG D 350 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D 350 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 350 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 350 " 0.455 9.50e-02 1.11e+02 2.04e-01 2.55e+01 pdb=" NE ARG A 350 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 350 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 350 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 350 " 0.015 2.00e-02 2.50e+03 ... (remaining 5065 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 475 2.70 - 3.25: 29279 3.25 - 3.80: 47005 3.80 - 4.35: 60035 4.35 - 4.90: 95755 Nonbonded interactions: 232549 Sorted by model distance: nonbonded pdb=" O GLY B 554 " pdb=" NH2 ARG C 274 " model vdw 2.155 3.120 nonbonded pdb=" NH2 ARG A 274 " pdb=" O GLY D 554 " model vdw 2.172 3.120 nonbonded pdb=" NH2 ARG B 328 " pdb=" O PRO C 588 " model vdw 2.179 3.120 nonbonded pdb=" O PRO A 588 " pdb=" NH2 ARG D 328 " model vdw 2.204 3.120 nonbonded pdb=" O PRO B 588 " pdb=" NH2 ARG C 328 " model vdw 2.325 3.120 ... (remaining 232544 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.050 Find NCS groups from input model: 0.280 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: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 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 : 0.004 0.040 28400 Z= 0.265 Angle : 0.662 7.185 38444 Z= 0.401 Chirality : 0.047 0.215 4092 Planarity : 0.011 0.204 5068 Dihedral : 14.646 89.868 10748 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.48 % Allowed : 12.65 % Favored : 85.86 % 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: 0.07 (0.14), residues: 3440 helix: 0.61 (0.14), residues: 1292 sheet: -1.24 (0.20), residues: 648 loop : 0.38 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 552 TYR 0.021 0.002 TYR C 352 PHE 0.018 0.002 PHE B 282 TRP 0.013 0.001 TRP C 553 HIS 0.005 0.001 HIS C 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.27 (28400) covalent geometry : angle 0.66231 / 0.40 (38444) hydrogen bonds : bond 0.15576 / 10.69 ( 1257) hydrogen bonds : angle 7.03368 / 5.00 ( 3555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 316 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.4697 (t70) cc_final: 0.4145 (t70) REVERT: A 377 ILE cc_start: 0.8601 (mm) cc_final: 0.8301 (mm) REVERT: A 379 MET cc_start: 0.8499 (ptm) cc_final: 0.8248 (ptm) REVERT: A 685 TYR cc_start: 0.7216 (m-10) cc_final: 0.6945 (m-80) REVERT: A 799 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8577 (mp) REVERT: A 835 MET cc_start: 0.7945 (mmt) cc_final: 0.7255 (mmm) REVERT: A 839 TYR cc_start: 0.6098 (m-80) cc_final: 0.5662 (m-10) REVERT: B 296 LEU cc_start: 0.8441 (mm) cc_final: 0.8107 (mt) REVERT: B 337 GLN cc_start: 0.6114 (pm20) cc_final: 0.5732 (mm-40) REVERT: B 342 MET cc_start: 0.8610 (tpp) cc_final: 0.8319 (mmt) REVERT: B 465 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6809 (pt0) REVERT: C 251 ASP cc_start: 0.4700 (t70) cc_final: 0.4135 (t70) REVERT: C 377 ILE cc_start: 0.8627 (mm) cc_final: 0.8348 (mm) REVERT: C 414 VAL cc_start: 0.9574 (m) cc_final: 0.9218 (p) REVERT: C 685 TYR cc_start: 0.7195 (m-10) cc_final: 0.6971 (m-80) REVERT: C 799 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8438 (mp) REVERT: C 835 MET cc_start: 0.7964 (mmt) cc_final: 0.7270 (mmm) REVERT: C 841 PHE cc_start: 0.7686 (m-80) cc_final: 0.7470 (m-80) REVERT: C 885 ASN cc_start: 0.8370 (m-40) cc_final: 0.8047 (m110) REVERT: D 296 LEU cc_start: 0.8530 (mm) cc_final: 0.8167 (mt) REVERT: D 337 GLN cc_start: 0.6097 (pm20) cc_final: 0.5756 (mm-40) REVERT: D 342 MET cc_start: 0.8615 (tpp) cc_final: 0.8307 (mmt) REVERT: D 465 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7044 (pt0) outliers start: 44 outliers final: 10 residues processed: 350 average time/residue: 0.1976 time to fit residues: 109.7022 Evaluate side-chains 204 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 796 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.4980 chunk 298 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 GLN A 793 GLN A 906 HIS ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 GLN C 285 GLN ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 793 GLN C 906 HIS D 285 GLN ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 793 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.171252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.133145 restraints weight = 79448.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.129560 restraints weight = 58584.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.131454 restraints weight = 54283.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.130626 restraints weight = 42916.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.130856 restraints weight = 40393.296| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28400 Z= 0.167 Angle : 0.592 10.057 38444 Z= 0.306 Chirality : 0.044 0.175 4092 Planarity : 0.005 0.048 5068 Dihedral : 4.760 58.928 3862 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.23 % Allowed : 12.89 % Favored : 84.89 % 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: 0.55 (0.15), residues: 3440 helix: 1.05 (0.14), residues: 1344 sheet: -1.08 (0.20), residues: 632 loop : 0.64 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 328 TYR 0.018 0.002 TYR C 325 PHE 0.024 0.002 PHE D 160 TRP 0.011 0.002 TRP A 188 HIS 0.011 0.001 HIS A 906 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (28400) covalent geometry : angle 0.59234 / 0.31 (38444) hydrogen bonds : bond 0.04188 / 2.83 ( 1257) hydrogen bonds : angle 5.30389 / 3.81 ( 3555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 198 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.7294 (mmt) cc_final: 0.7083 (mmt) REVERT: A 251 ASP cc_start: 0.4174 (t70) cc_final: 0.3927 (t70) REVERT: A 544 MET cc_start: 0.8283 (ttt) cc_final: 0.7917 (tpp) REVERT: A 572 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8722 (tp) REVERT: A 799 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8464 (mm) REVERT: B 297 ASP cc_start: 0.8752 (m-30) cc_final: 0.8133 (m-30) REVERT: B 342 MET cc_start: 0.8968 (tpp) cc_final: 0.8415 (mmm) REVERT: B 828 MET cc_start: 0.5612 (OUTLIER) cc_final: 0.5181 (tmm) REVERT: C 496 MET cc_start: 0.8833 (tpp) cc_final: 0.8585 (tpp) REVERT: C 529 MET cc_start: 0.8811 (ppp) cc_final: 0.8474 (ppp) REVERT: C 544 MET cc_start: 0.8478 (ttt) cc_final: 0.8216 (tpp) REVERT: C 572 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8780 (tp) REVERT: C 799 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8436 (mm) REVERT: C 841 PHE cc_start: 0.7617 (m-80) cc_final: 0.7158 (m-10) REVERT: D 154 MET cc_start: 0.4339 (mmt) cc_final: 0.3143 (mpp) REVERT: D 185 MET cc_start: 0.9172 (ttt) cc_final: 0.8891 (mtp) REVERT: D 297 ASP cc_start: 0.8497 (m-30) cc_final: 0.8099 (m-30) REVERT: D 342 MET cc_start: 0.8968 (tpp) cc_final: 0.8501 (mmm) REVERT: D 835 MET cc_start: 0.8532 (mmp) cc_final: 0.7808 (mmm) outliers start: 66 outliers final: 28 residues processed: 253 average time/residue: 0.1807 time to fit residues: 75.0296 Evaluate side-chains 190 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 709 CYS Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 796 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 72 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 308 optimal weight: 0.3980 chunk 265 optimal weight: 30.0000 chunk 108 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 198 optimal weight: 0.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN B 628 GLN C 285 GLN ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 GLN D 337 GLN D 628 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.164505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.119770 restraints weight = 79366.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.121166 restraints weight = 57014.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.121280 restraints weight = 38877.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.121368 restraints weight = 38399.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.121815 restraints weight = 34111.080| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28400 Z= 0.185 Angle : 0.573 9.788 38444 Z= 0.296 Chirality : 0.043 0.180 4092 Planarity : 0.004 0.050 5068 Dihedral : 4.530 57.950 3856 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.60 % Allowed : 14.34 % Favored : 83.06 % 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: 0.55 (0.15), residues: 3440 helix: 1.02 (0.14), residues: 1344 sheet: -0.93 (0.20), residues: 652 loop : 0.61 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 350 TYR 0.015 0.002 TYR B 325 PHE 0.022 0.002 PHE B 292 TRP 0.028 0.002 TRP D 653 HIS 0.008 0.001 HIS D 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (28400) covalent geometry : angle 0.57279 / 0.30 (38444) hydrogen bonds : bond 0.04154 / 2.85 ( 1257) hydrogen bonds : angle 5.10365 / 3.67 ( 3555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 162 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 MET cc_start: 0.6726 (mtt) cc_final: 0.6522 (mtt) REVERT: A 496 MET cc_start: 0.8573 (tpp) cc_final: 0.8133 (tpp) REVERT: A 799 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8528 (mm) REVERT: A 835 MET cc_start: 0.7868 (mmt) cc_final: 0.7253 (mmm) REVERT: A 841 PHE cc_start: 0.7128 (m-10) cc_final: 0.6559 (m-10) REVERT: A 894 LEU cc_start: 0.8299 (mp) cc_final: 0.8092 (mp) REVERT: B 342 MET cc_start: 0.8902 (tpp) cc_final: 0.8538 (mmm) REVERT: B 835 MET cc_start: 0.8512 (tpp) cc_final: 0.7563 (tpp) REVERT: B 893 MET cc_start: 0.0739 (ptt) cc_final: 0.0081 (ppp) REVERT: C 379 MET cc_start: 0.8221 (ptm) cc_final: 0.7575 (ppp) REVERT: C 496 MET cc_start: 0.8843 (tpp) cc_final: 0.8363 (tpp) REVERT: C 529 MET cc_start: 0.8763 (ppp) cc_final: 0.8426 (ppp) REVERT: C 572 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8855 (tp) REVERT: C 721 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8358 (mt) REVERT: C 799 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8389 (mm) REVERT: C 835 MET cc_start: 0.7896 (mmt) cc_final: 0.7295 (mmm) REVERT: C 841 PHE cc_start: 0.7801 (m-80) cc_final: 0.7201 (m-10) REVERT: D 154 MET cc_start: 0.4398 (mmt) cc_final: 0.4023 (mpp) REVERT: D 185 MET cc_start: 0.9316 (ttt) cc_final: 0.7086 (ttt) REVERT: D 297 ASP cc_start: 0.8521 (m-30) cc_final: 0.8318 (m-30) REVERT: D 342 MET cc_start: 0.8902 (tpp) cc_final: 0.8570 (mmm) REVERT: D 828 MET cc_start: 0.5286 (tmm) cc_final: 0.4418 (tmm) REVERT: D 835 MET cc_start: 0.8626 (mmp) cc_final: 0.8258 (mmp) REVERT: D 893 MET cc_start: 0.2243 (tmm) cc_final: 0.1956 (tmm) outliers start: 77 outliers final: 37 residues processed: 226 average time/residue: 0.1809 time to fit residues: 67.6302 Evaluate side-chains 183 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 680 CYS Chi-restraints excluded: chain C residue 721 LEU Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 709 CYS Chi-restraints excluded: chain D residue 750 LYS Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 796 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 23 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 340 optimal weight: 50.0000 chunk 246 optimal weight: 0.6980 chunk 235 optimal weight: 5.9990 chunk 196 optimal weight: 0.4980 chunk 157 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN C 285 GLN ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.165757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.132761 restraints weight = 79178.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.128162 restraints weight = 59687.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.129138 restraints weight = 54749.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.129834 restraints weight = 39432.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.130061 restraints weight = 38627.990| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28400 Z= 0.107 Angle : 0.511 8.454 38444 Z= 0.260 Chirality : 0.041 0.153 4092 Planarity : 0.004 0.041 5068 Dihedral : 4.393 57.590 3856 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.43 % Allowed : 14.88 % Favored : 82.69 % 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: 0.76 (0.15), residues: 3440 helix: 1.28 (0.14), residues: 1344 sheet: -0.85 (0.21), residues: 596 loop : 0.58 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 110 TYR 0.018 0.001 TYR A 853 PHE 0.020 0.001 PHE A 282 TRP 0.011 0.001 TRP B 653 HIS 0.005 0.001 HIS D 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (28400) covalent geometry : angle 0.51065 / 0.26 (38444) hydrogen bonds : bond 0.03374 / 2.30 ( 1257) hydrogen bonds : angle 4.84815 / 3.48 ( 3555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 162 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.8623 (tpp) cc_final: 0.8206 (tpp) REVERT: A 615 GLU cc_start: 0.9087 (tp30) cc_final: 0.8425 (tm-30) REVERT: A 721 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8272 (mt) REVERT: A 799 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8491 (mm) REVERT: A 835 MET cc_start: 0.7916 (mmt) cc_final: 0.7303 (mmm) REVERT: A 841 PHE cc_start: 0.6872 (m-10) cc_final: 0.6342 (m-10) REVERT: A 945 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.7366 (t80) REVERT: B 342 MET cc_start: 0.8802 (tpp) cc_final: 0.8596 (mmm) REVERT: B 835 MET cc_start: 0.8265 (tpp) cc_final: 0.7066 (tpp) REVERT: B 893 MET cc_start: 0.0830 (ptt) cc_final: 0.0433 (ptm) REVERT: C 496 MET cc_start: 0.8834 (tpp) cc_final: 0.8434 (tpp) REVERT: C 529 MET cc_start: 0.8896 (ppp) cc_final: 0.8633 (ppp) REVERT: C 572 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8829 (tp) REVERT: C 615 GLU cc_start: 0.9173 (tp30) cc_final: 0.8539 (tp30) REVERT: C 799 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8499 (mm) REVERT: C 835 MET cc_start: 0.7936 (mmt) cc_final: 0.7328 (mmm) REVERT: C 841 PHE cc_start: 0.7363 (m-80) cc_final: 0.7123 (m-80) REVERT: C 894 LEU cc_start: 0.8170 (mp) cc_final: 0.7905 (mp) REVERT: C 945 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.7477 (t80) REVERT: D 154 MET cc_start: 0.3125 (mmt) cc_final: 0.2859 (mmt) REVERT: D 185 MET cc_start: 0.8962 (ttt) cc_final: 0.8547 (ttt) REVERT: D 377 ILE cc_start: 0.8793 (mt) cc_final: 0.8512 (pt) REVERT: D 828 MET cc_start: 0.4999 (tmm) cc_final: 0.4403 (tmm) REVERT: D 893 MET cc_start: 0.2392 (tmm) cc_final: 0.1981 (tmm) outliers start: 72 outliers final: 37 residues processed: 221 average time/residue: 0.1809 time to fit residues: 65.4219 Evaluate side-chains 189 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 680 CYS Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 750 LYS Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 945 PHE Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 544 MET Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 709 CYS Chi-restraints excluded: chain D residue 750 LYS Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain D residue 763 GLU Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 796 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 262 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 165 optimal weight: 50.0000 chunk 312 optimal weight: 40.0000 chunk 48 optimal weight: 0.3980 chunk 132 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 256 optimal weight: 0.1980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 GLN ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.165341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.133814 restraints weight = 79614.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.132218 restraints weight = 66912.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.133365 restraints weight = 56528.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.133531 restraints weight = 37512.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.136788 restraints weight = 36209.905| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28400 Z= 0.109 Angle : 0.507 10.871 38444 Z= 0.257 Chirality : 0.041 0.263 4092 Planarity : 0.004 0.039 5068 Dihedral : 4.328 57.527 3856 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.99 % Allowed : 15.49 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.85 (0.15), residues: 3440 helix: 1.38 (0.14), residues: 1344 sheet: -0.84 (0.20), residues: 600 loop : 0.63 (0.17), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 749 TYR 0.016 0.001 TYR A 547 PHE 0.017 0.001 PHE A 282 TRP 0.036 0.001 TRP B 706 HIS 0.003 0.000 HIS C 906 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (28400) covalent geometry : angle 0.50739 / 0.26 (38444) hydrogen bonds : bond 0.03273 / 2.23 ( 1257) hydrogen bonds : angle 4.73731 / 3.40 ( 3555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 151 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ASP cc_start: 0.7458 (t0) cc_final: 0.7101 (t0) REVERT: A 496 MET cc_start: 0.8590 (tpp) cc_final: 0.8258 (tpp) REVERT: A 529 MET cc_start: 0.8953 (ppp) cc_final: 0.8555 (ppp) REVERT: A 615 GLU cc_start: 0.8533 (tp30) cc_final: 0.8313 (tm-30) REVERT: A 721 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8292 (mt) REVERT: A 799 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8547 (mm) REVERT: A 835 MET cc_start: 0.7971 (mmt) cc_final: 0.7406 (mmm) REVERT: A 841 PHE cc_start: 0.6439 (m-10) cc_final: 0.6079 (m-10) REVERT: A 945 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.7380 (t80) REVERT: B 893 MET cc_start: 0.0585 (ptt) cc_final: 0.0136 (ptm) REVERT: C 272 ASP cc_start: 0.7530 (t0) cc_final: 0.7136 (t0) REVERT: C 496 MET cc_start: 0.8795 (tpp) cc_final: 0.8508 (tpp) REVERT: C 529 MET cc_start: 0.8825 (ppp) cc_final: 0.8600 (ppp) REVERT: C 572 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8879 (tp) REVERT: C 615 GLU cc_start: 0.8755 (tp30) cc_final: 0.8206 (tp30) REVERT: C 799 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8533 (mm) REVERT: C 835 MET cc_start: 0.7991 (mmt) cc_final: 0.7438 (mmm) REVERT: C 945 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.7501 (t80) REVERT: D 154 MET cc_start: 0.2562 (mmt) cc_final: 0.2336 (mmt) REVERT: D 185 MET cc_start: 0.8328 (ttt) cc_final: 0.8024 (ttt) REVERT: D 377 ILE cc_start: 0.8791 (mt) cc_final: 0.8478 (pt) REVERT: D 835 MET cc_start: 0.7365 (mmp) cc_final: 0.6883 (tpp) REVERT: D 893 MET cc_start: 0.2749 (tmm) cc_final: 0.2021 (tmm) outliers start: 59 outliers final: 39 residues processed: 198 average time/residue: 0.1849 time to fit residues: 60.0191 Evaluate side-chains 185 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 750 LYS Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 945 PHE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 544 MET Chi-restraints excluded: chain D residue 709 CYS Chi-restraints excluded: chain D residue 763 GLU Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 796 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 324 optimal weight: 10.0000 chunk 320 optimal weight: 20.0000 chunk 263 optimal weight: 20.0000 chunk 201 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 chunk 249 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 HIS C 334 GLN ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.162152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.114541 restraints weight = 77093.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.116352 restraints weight = 50716.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.115288 restraints weight = 38609.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.116006 restraints weight = 36412.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.116243 restraints weight = 32739.964| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 28400 Z= 0.239 Angle : 0.606 9.472 38444 Z= 0.311 Chirality : 0.044 0.221 4092 Planarity : 0.005 0.051 5068 Dihedral : 4.552 57.244 3856 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.70 % Allowed : 15.18 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3440 helix: 1.11 (0.14), residues: 1344 sheet: -0.98 (0.19), residues: 668 loop : 0.63 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 101 TYR 0.016 0.002 TYR B 325 PHE 0.026 0.002 PHE C 508 TRP 0.030 0.002 TRP B 706 HIS 0.009 0.001 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.24 (28400) covalent geometry : angle 0.60588 / 0.31 (38444) hydrogen bonds : bond 0.03903 / 2.70 ( 1257) hydrogen bonds : angle 4.97619 / 3.58 ( 3555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 135 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.8749 (tpp) cc_final: 0.8289 (tpp) REVERT: A 615 GLU cc_start: 0.9059 (tp30) cc_final: 0.8807 (tp30) REVERT: A 721 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8378 (mt) REVERT: A 799 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8540 (mm) REVERT: A 835 MET cc_start: 0.8017 (mmt) cc_final: 0.7184 (mmm) REVERT: A 841 PHE cc_start: 0.7177 (m-10) cc_final: 0.6547 (m-10) REVERT: B 835 MET cc_start: 0.8191 (tpp) cc_final: 0.7232 (tpp) REVERT: B 893 MET cc_start: 0.1879 (ptt) cc_final: 0.1649 (ptm) REVERT: C 496 MET cc_start: 0.8948 (tpp) cc_final: 0.8541 (tpp) REVERT: C 529 MET cc_start: 0.8899 (ppp) cc_final: 0.8667 (ppp) REVERT: C 572 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8891 (tp) REVERT: C 721 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8407 (mt) REVERT: C 799 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8657 (mm) REVERT: C 835 MET cc_start: 0.8101 (mmt) cc_final: 0.7248 (mmm) REVERT: D 185 MET cc_start: 0.9357 (ttt) cc_final: 0.9080 (ttt) REVERT: D 377 ILE cc_start: 0.9150 (mt) cc_final: 0.8838 (pt) REVERT: D 835 MET cc_start: 0.8709 (mmp) cc_final: 0.7597 (mmm) REVERT: D 893 MET cc_start: 0.2978 (tmm) cc_final: 0.2530 (tmm) outliers start: 80 outliers final: 54 residues processed: 202 average time/residue: 0.1770 time to fit residues: 58.4344 Evaluate side-chains 188 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 129 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 750 LYS Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 721 LEU Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 945 PHE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain D residue 709 CYS Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain D residue 763 GLU Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 796 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 192 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 325 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.162936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.118561 restraints weight = 79156.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.120366 restraints weight = 54647.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.119517 restraints weight = 39041.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.120411 restraints weight = 38118.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.120565 restraints weight = 34115.117| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28400 Z= 0.134 Angle : 0.527 10.882 38444 Z= 0.267 Chirality : 0.041 0.156 4092 Planarity : 0.004 0.038 5068 Dihedral : 4.382 57.133 3856 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.26 % Allowed : 16.09 % Favored : 81.65 % 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: 0.73 (0.15), residues: 3440 helix: 1.29 (0.14), residues: 1348 sheet: -0.95 (0.21), residues: 596 loop : 0.56 (0.17), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 101 TYR 0.022 0.001 TYR D 241 PHE 0.019 0.001 PHE B 292 TRP 0.025 0.001 TRP B 706 HIS 0.004 0.001 HIS D 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (28400) covalent geometry : angle 0.52706 / 0.27 (38444) hydrogen bonds : bond 0.03362 / 2.30 ( 1257) hydrogen bonds : angle 4.78990 / 3.43 ( 3555) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 140 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.8686 (tpp) cc_final: 0.8207 (tpp) REVERT: A 544 MET cc_start: 0.7874 (tpp) cc_final: 0.7653 (tpp) REVERT: A 615 GLU cc_start: 0.9066 (tp30) cc_final: 0.8236 (tm-30) REVERT: A 721 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8371 (mt) REVERT: A 799 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8687 (mm) REVERT: A 835 MET cc_start: 0.8127 (mmt) cc_final: 0.7403 (mmm) REVERT: A 841 PHE cc_start: 0.7340 (m-10) cc_final: 0.6800 (m-10) REVERT: A 945 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.7403 (t80) REVERT: B 241 TYR cc_start: 0.8000 (t80) cc_final: 0.7728 (t80) REVERT: B 578 ILE cc_start: 0.9162 (tt) cc_final: 0.8880 (tt) REVERT: B 835 MET cc_start: 0.8020 (tpp) cc_final: 0.7548 (tpp) REVERT: B 893 MET cc_start: 0.1958 (ptt) cc_final: 0.1710 (ptm) REVERT: C 496 MET cc_start: 0.8900 (tpp) cc_final: 0.8506 (tpp) REVERT: C 529 MET cc_start: 0.8927 (ppp) cc_final: 0.8657 (ppp) REVERT: C 572 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8827 (tp) REVERT: C 799 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8769 (mm) REVERT: C 835 MET cc_start: 0.8226 (mmt) cc_final: 0.7479 (mmm) REVERT: C 903 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6908 (pttm) REVERT: C 945 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.7505 (t80) REVERT: D 185 MET cc_start: 0.9257 (ttt) cc_final: 0.8946 (ttt) REVERT: D 377 ILE cc_start: 0.9067 (mt) cc_final: 0.8672 (pt) REVERT: D 578 ILE cc_start: 0.9157 (tt) cc_final: 0.8916 (tt) REVERT: D 835 MET cc_start: 0.8640 (mmp) cc_final: 0.7523 (tpp) REVERT: D 893 MET cc_start: 0.3132 (tmm) cc_final: 0.1425 (ptt) outliers start: 67 outliers final: 48 residues processed: 192 average time/residue: 0.1780 time to fit residues: 55.7744 Evaluate side-chains 194 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 139 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 750 LYS Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 903 LYS Chi-restraints excluded: chain C residue 945 PHE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 544 MET Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 709 CYS Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain D residue 763 GLU Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 796 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 12 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 290 optimal weight: 2.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 386 HIS A 857 HIS C 386 HIS C 857 HIS D 525 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.160882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.115793 restraints weight = 79690.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.117692 restraints weight = 53614.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.117164 restraints weight = 36023.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.117459 restraints weight = 36299.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.117623 restraints weight = 34746.499| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 28400 Z= 0.226 Angle : 0.601 13.847 38444 Z= 0.305 Chirality : 0.043 0.152 4092 Planarity : 0.005 0.047 5068 Dihedral : 4.541 56.894 3856 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.56 % Allowed : 16.03 % Favored : 81.41 % 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: 0.54 (0.15), residues: 3440 helix: 1.11 (0.14), residues: 1352 sheet: -1.05 (0.20), residues: 644 loop : 0.55 (0.18), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 101 TYR 0.016 0.002 TYR B 325 PHE 0.021 0.002 PHE B 292 TRP 0.023 0.002 TRP B 706 HIS 0.011 0.001 HIS A 857 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.23 (28400) covalent geometry : angle 0.60090 / 0.31 (38444) hydrogen bonds : bond 0.03777 / 2.59 ( 1257) hydrogen bonds : angle 4.94801 / 3.56 ( 3555) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 135 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 TYR cc_start: 0.7851 (t80) cc_final: 0.7645 (t80) REVERT: A 496 MET cc_start: 0.8728 (tpp) cc_final: 0.8259 (tpp) REVERT: A 544 MET cc_start: 0.7993 (tpp) cc_final: 0.7656 (tpp) REVERT: A 721 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8392 (mt) REVERT: A 799 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8647 (mm) REVERT: A 841 PHE cc_start: 0.7229 (m-10) cc_final: 0.6370 (m-10) REVERT: B 128 ILE cc_start: 0.9278 (tp) cc_final: 0.9061 (tp) REVERT: B 241 TYR cc_start: 0.8065 (t80) cc_final: 0.7816 (t80) REVERT: B 828 MET cc_start: 0.5485 (tmm) cc_final: 0.4911 (tmm) REVERT: B 835 MET cc_start: 0.8219 (tpp) cc_final: 0.7715 (tpp) REVERT: B 893 MET cc_start: 0.1995 (ptt) cc_final: 0.1745 (ptm) REVERT: C 496 MET cc_start: 0.8937 (tpp) cc_final: 0.8542 (tpp) REVERT: C 529 MET cc_start: 0.8974 (ppp) cc_final: 0.8679 (ppp) REVERT: C 544 MET cc_start: 0.8157 (tpp) cc_final: 0.7928 (tpp) REVERT: C 572 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8878 (tp) REVERT: C 721 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8416 (mt) REVERT: C 799 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8692 (mm) REVERT: C 835 MET cc_start: 0.8202 (mmt) cc_final: 0.7397 (mmm) REVERT: C 903 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7205 (pttm) REVERT: C 945 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.7467 (t80) REVERT: D 185 MET cc_start: 0.9272 (ttt) cc_final: 0.8942 (ttt) REVERT: D 377 ILE cc_start: 0.9100 (mt) cc_final: 0.8758 (pt) REVERT: D 468 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9121 (mt) REVERT: D 835 MET cc_start: 0.8687 (mmp) cc_final: 0.7484 (mmm) REVERT: D 893 MET cc_start: 0.3151 (tmm) cc_final: 0.1408 (ptt) outliers start: 76 outliers final: 57 residues processed: 200 average time/residue: 0.1694 time to fit residues: 55.9259 Evaluate side-chains 198 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 133 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 750 LYS Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 721 LEU Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 903 LYS Chi-restraints excluded: chain C residue 945 PHE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain D residue 763 GLU Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 796 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 287 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 342 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 139 optimal weight: 20.0000 chunk 170 optimal weight: 50.0000 chunk 259 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.161910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.116996 restraints weight = 79476.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.118741 restraints weight = 52660.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.118209 restraints weight = 36617.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.118736 restraints weight = 38678.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.118995 restraints weight = 34496.376| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28400 Z= 0.145 Angle : 0.543 13.048 38444 Z= 0.275 Chirality : 0.042 0.152 4092 Planarity : 0.004 0.052 5068 Dihedral : 4.440 56.759 3856 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.13 % Allowed : 16.53 % Favored : 81.34 % 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: 0.65 (0.15), residues: 3440 helix: 1.21 (0.14), residues: 1352 sheet: -1.03 (0.21), residues: 596 loop : 0.55 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.000 ARG C 101 TYR 0.019 0.001 TYR C 547 PHE 0.018 0.001 PHE D 292 TRP 0.022 0.001 TRP B 706 HIS 0.006 0.001 HIS A 857 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (28400) covalent geometry : angle 0.54267 / 0.27 (38444) hydrogen bonds : bond 0.03406 / 2.34 ( 1257) hydrogen bonds : angle 4.84516 / 3.47 ( 3555) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 138 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.8676 (tpp) cc_final: 0.8304 (tpp) REVERT: A 544 MET cc_start: 0.7985 (tpp) cc_final: 0.7695 (tpp) REVERT: A 721 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8387 (mt) REVERT: A 799 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8659 (mm) REVERT: A 835 MET cc_start: 0.8003 (mmt) cc_final: 0.7440 (mmm) REVERT: A 841 PHE cc_start: 0.7360 (m-10) cc_final: 0.6761 (m-10) REVERT: A 945 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.7415 (t80) REVERT: B 241 TYR cc_start: 0.8074 (t80) cc_final: 0.7818 (t80) REVERT: B 342 MET cc_start: 0.8546 (mmt) cc_final: 0.8233 (mmm) REVERT: B 578 ILE cc_start: 0.9068 (tt) cc_final: 0.8798 (tt) REVERT: B 835 MET cc_start: 0.8252 (tpp) cc_final: 0.7723 (tpp) REVERT: B 893 MET cc_start: 0.2008 (ptt) cc_final: 0.1763 (ptm) REVERT: C 496 MET cc_start: 0.8893 (tpp) cc_final: 0.8515 (tpp) REVERT: C 529 MET cc_start: 0.8986 (ppp) cc_final: 0.8666 (ppp) REVERT: C 572 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8839 (tp) REVERT: C 721 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8412 (mt) REVERT: C 799 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8686 (mm) REVERT: C 903 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.7066 (pttm) REVERT: C 945 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.7519 (t80) REVERT: D 128 ILE cc_start: 0.9217 (mp) cc_final: 0.8837 (tp) REVERT: D 185 MET cc_start: 0.9247 (ttt) cc_final: 0.8905 (ttt) REVERT: D 377 ILE cc_start: 0.9121 (mt) cc_final: 0.8804 (pt) REVERT: D 578 ILE cc_start: 0.9153 (tt) cc_final: 0.8924 (tt) REVERT: D 835 MET cc_start: 0.8658 (mmp) cc_final: 0.7568 (mmm) REVERT: D 893 MET cc_start: 0.3392 (tmm) cc_final: 0.1665 (ptt) outliers start: 63 outliers final: 51 residues processed: 190 average time/residue: 0.1755 time to fit residues: 54.0871 Evaluate side-chains 196 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 137 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 750 LYS Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 721 LEU Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 903 LYS Chi-restraints excluded: chain C residue 945 PHE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 544 MET Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 796 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 74 optimal weight: 0.0570 chunk 82 optimal weight: 4.9990 chunk 205 optimal weight: 0.6980 chunk 194 optimal weight: 0.0970 chunk 115 optimal weight: 0.7980 chunk 257 optimal weight: 0.9980 chunk 241 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 310 optimal weight: 30.0000 chunk 141 optimal weight: 9.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.163271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.118992 restraints weight = 79556.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.121445 restraints weight = 51917.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.120569 restraints weight = 37091.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.121198 restraints weight = 35383.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.121387 restraints weight = 33373.163| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28400 Z= 0.095 Angle : 0.530 14.638 38444 Z= 0.264 Chirality : 0.041 0.170 4092 Planarity : 0.004 0.040 5068 Dihedral : 4.266 56.900 3856 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.86 % Allowed : 16.90 % Favored : 81.24 % 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: 0.84 (0.15), residues: 3440 helix: 1.39 (0.14), residues: 1348 sheet: -0.91 (0.20), residues: 596 loop : 0.63 (0.17), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 101 TYR 0.037 0.001 TYR C 547 PHE 0.017 0.001 PHE A 282 TRP 0.023 0.001 TRP B 706 HIS 0.004 0.001 HIS A 857 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 (28400) covalent geometry : angle 0.52998 / 0.26 (38444) hydrogen bonds : bond 0.03051 / 2.09 ( 1257) hydrogen bonds : angle 4.71351 / 3.37 ( 3555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 150 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.8584 (tpp) cc_final: 0.8150 (tpp) REVERT: A 529 MET cc_start: 0.8954 (ppp) cc_final: 0.8594 (ppp) REVERT: A 544 MET cc_start: 0.7921 (tpp) cc_final: 0.7652 (tpp) REVERT: A 615 GLU cc_start: 0.9036 (tp30) cc_final: 0.8529 (tm-30) REVERT: A 799 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8685 (mm) REVERT: A 835 MET cc_start: 0.7903 (mmt) cc_final: 0.7600 (mmm) REVERT: A 841 PHE cc_start: 0.7371 (m-10) cc_final: 0.6798 (m-10) REVERT: A 864 ARG cc_start: 0.7447 (tmm160) cc_final: 0.7167 (ptt90) REVERT: A 945 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7441 (t80) REVERT: B 241 TYR cc_start: 0.8050 (t80) cc_final: 0.7763 (t80) REVERT: B 578 ILE cc_start: 0.9029 (tt) cc_final: 0.8750 (tt) REVERT: B 828 MET cc_start: 0.5289 (tmm) cc_final: 0.4739 (tmm) REVERT: B 835 MET cc_start: 0.8230 (tpp) cc_final: 0.7720 (tpp) REVERT: B 893 MET cc_start: 0.1708 (ptt) cc_final: 0.1475 (ptm) REVERT: C 124 ARG cc_start: 0.7956 (mtp85) cc_final: 0.7596 (ttm110) REVERT: C 272 ASP cc_start: 0.7452 (t0) cc_final: 0.7071 (t0) REVERT: C 496 MET cc_start: 0.8831 (tpp) cc_final: 0.8433 (tpp) REVERT: C 553 TRP cc_start: 0.7955 (m100) cc_final: 0.7589 (m100) REVERT: C 572 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8786 (tp) REVERT: C 799 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8660 (mm) REVERT: C 835 MET cc_start: 0.8142 (mmt) cc_final: 0.7704 (mmm) REVERT: C 945 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.7545 (t80) REVERT: D 185 MET cc_start: 0.9188 (ttt) cc_final: 0.8932 (ttt) REVERT: D 377 ILE cc_start: 0.8946 (mt) cc_final: 0.8672 (pt) REVERT: D 578 ILE cc_start: 0.9022 (tt) cc_final: 0.8775 (tt) REVERT: D 709 CYS cc_start: 0.4700 (p) cc_final: 0.4496 (p) REVERT: D 835 MET cc_start: 0.8652 (mmp) cc_final: 0.7454 (mmm) REVERT: D 893 MET cc_start: 0.3394 (tmm) cc_final: 0.3060 (tmm) outliers start: 55 outliers final: 44 residues processed: 195 average time/residue: 0.1890 time to fit residues: 59.1927 Evaluate side-chains 191 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 750 LYS Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 945 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 750 LYS Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 945 PHE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 796 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 102 optimal weight: 5.9990 chunk 315 optimal weight: 50.0000 chunk 77 optimal weight: 5.9990 chunk 331 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 chunk 99 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 225 GLN C 632 HIS C 904 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.154572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.109783 restraints weight = 76738.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.107527 restraints weight = 53349.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.107460 restraints weight = 48556.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.108011 restraints weight = 43934.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.108448 restraints weight = 36142.386| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.132 28400 Z= 0.327 Angle : 0.706 15.856 38444 Z= 0.358 Chirality : 0.045 0.189 4092 Planarity : 0.005 0.059 5068 Dihedral : 4.655 56.621 3854 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.40 % Allowed : 16.30 % Favored : 81.31 % 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: 0.43 (0.15), residues: 3440 helix: 0.96 (0.14), residues: 1352 sheet: -1.05 (0.20), residues: 652 loop : 0.54 (0.18), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 101 TYR 0.027 0.002 TYR C 547 PHE 0.025 0.002 PHE C 508 TRP 0.019 0.002 TRP D 706 HIS 0.013 0.002 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.33 (28400) covalent geometry : angle 0.70625 / 0.36 (38444) hydrogen bonds : bond 0.04133 / 2.84 ( 1257) hydrogen bonds : angle 5.11609 / 3.68 ( 3555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4468.69 seconds wall clock time: 78 minutes 13.73 seconds (4693.73 seconds total)