Starting phenix.real_space_refine on Tue Aug 26 12:58:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wks_37606/08_2025/8wks_37606.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wks_37606/08_2025/8wks_37606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wks_37606/08_2025/8wks_37606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wks_37606/08_2025/8wks_37606.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wks_37606/08_2025/8wks_37606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wks_37606/08_2025/8wks_37606.map" } resolution = 3.58 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= 0.039 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 136 5.16 5 C 23835 2.51 5 N 5931 2.21 5 O 6997 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36899 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 8190 Classifications: {'peptide': 984} Link IDs: {'PTRANS': 19, 'TRANS': 964} Chain: "B" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1037 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1037 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain breaks: 1 Chain: "D" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 8190 Classifications: {'peptide': 984} Link IDs: {'PTRANS': 19, 'TRANS': 964} Chain: "E" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1028 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "F" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 8190 Classifications: {'peptide': 984} Link IDs: {'PTRANS': 19, 'TRANS': 964} Chain: "G" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1037 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain breaks: 1 Chain: "H" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 8190 Classifications: {'peptide': 984} Link IDs: {'PTRANS': 19, 'TRANS': 964} Time building chain proxies: 9.03, per 1000 atoms: 0.24 Number of scatterers: 36899 At special positions: 0 Unit cell: (100, 130, 257, 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 136 16.00 O 6997 8.00 N 5931 7.00 C 23835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8486 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 17 sheets defined 61.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 23 through 40 removed outlier: 3.749A pdb=" N SER A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 4.205A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 Processing helix chain 'A' and resid 80 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.588A pdb=" N GLY A 102 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 removed outlier: 3.777A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.604A pdb=" N TYR A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.530A pdb=" N ALA A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 235 removed outlier: 3.949A pdb=" N LEU A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.547A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 removed outlier: 4.021A pdb=" N ASP A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.064A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 334' Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 366 through 373 removed outlier: 3.778A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 392 removed outlier: 4.482A pdb=" N ARG A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.936A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 425 removed outlier: 3.946A pdb=" N LYS A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 461 Processing helix chain 'A' and resid 468 through 491 removed outlier: 3.590A pdb=" N GLN A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 520 Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 546 removed outlier: 4.516A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 546 " --> pdb=" O GLU A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 571 Processing helix chain 'A' and resid 579 through 597 removed outlier: 3.555A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.861A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 628 Processing helix chain 'A' and resid 648 through 659 removed outlier: 3.553A pdb=" N ASN A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 removed outlier: 3.740A pdb=" N ASN A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 700 Processing helix chain 'A' and resid 709 through 723 removed outlier: 4.350A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 743 Processing helix chain 'A' and resid 750 through 765 removed outlier: 3.571A pdb=" N TYR A 755 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 756 " --> pdb=" O GLY A 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 761 " --> pdb=" O TRP A 757 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.560A pdb=" N ASP A 776 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.711A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.748A pdb=" N THR A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 825 " --> pdb=" O SER A 821 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 840 removed outlier: 4.013A pdb=" N ILE A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 846 through 857 removed outlier: 3.735A pdb=" N HIS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 853 " --> pdb=" O ALA A 849 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 854 " --> pdb=" O LYS A 850 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 871 removed outlier: 4.101A pdb=" N ARG A 870 " --> pdb=" O MET A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 899 removed outlier: 3.562A pdb=" N GLU A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 922 removed outlier: 3.557A pdb=" N PHE A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 918 " --> pdb=" O SER A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 933 Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 955 removed outlier: 6.098A pdb=" N ILE A 955 " --> pdb=" O LYS A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 962 removed outlier: 4.135A pdb=" N LYS A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 975 through 991 removed outlier: 3.759A pdb=" N HIS A 979 " --> pdb=" O HIS A 975 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS A 989 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1002 removed outlier: 3.649A pdb=" N LEU A 997 " --> pdb=" O ASP A 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'C' and resid 69 through 75 removed outlier: 4.413A pdb=" N MET C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 40 removed outlier: 3.502A pdb=" N GLU D 28 " --> pdb=" O ASN D 24 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 removed outlier: 3.794A pdb=" N THR D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 53 " --> pdb=" O GLY D 49 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 54' Processing helix chain 'D' and resid 58 through 72 Processing helix chain 'D' and resid 80 through 95 removed outlier: 3.648A pdb=" N LEU D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 95 through 109 removed outlier: 4.089A pdb=" N ALA D 99 " --> pdb=" O LYS D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.805A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 removed outlier: 3.641A pdb=" N ALA D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 160 Processing helix chain 'D' and resid 173 through 177 removed outlier: 4.101A pdb=" N LYS D 176 " --> pdb=" O ASP D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 192 removed outlier: 3.661A pdb=" N TYR D 190 " --> pdb=" O LYS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.745A pdb=" N ILE D 208 " --> pdb=" O MET D 204 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR D 210 " --> pdb=" O THR D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 235 removed outlier: 3.588A pdb=" N LEU D 235 " --> pdb=" O TRP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 296 Processing helix chain 'D' and resid 298 through 302 Processing helix chain 'D' and resid 305 through 317 removed outlier: 4.314A pdb=" N ASP D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 322 Processing helix chain 'D' and resid 327 through 332 removed outlier: 4.011A pdb=" N LYS D 331 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 366 removed outlier: 4.219A pdb=" N GLU D 365 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER D 366 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 372 removed outlier: 3.785A pdb=" N ARG D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 371 " --> pdb=" O CYS D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 391 Processing helix chain 'D' and resid 417 through 426 removed outlier: 3.695A pdb=" N LYS D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU D 426 " --> pdb=" O LYS D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 Processing helix chain 'D' and resid 447 through 461 removed outlier: 3.660A pdb=" N LEU D 460 " --> pdb=" O SER D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 494 Processing helix chain 'D' and resid 495 through 501 removed outlier: 3.917A pdb=" N THR D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 519 removed outlier: 3.512A pdb=" N GLU D 516 " --> pdb=" O LEU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 539 removed outlier: 3.531A pdb=" N GLN D 536 " --> pdb=" O PRO D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 546 removed outlier: 4.258A pdb=" N PHE D 544 " --> pdb=" O ILE D 541 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER D 546 " --> pdb=" O GLU D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 572 Processing helix chain 'D' and resid 579 through 597 Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.540A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 628 Processing helix chain 'D' and resid 648 through 658 Processing helix chain 'D' and resid 660 through 671 Processing helix chain 'D' and resid 681 through 701 removed outlier: 4.125A pdb=" N GLU D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR D 687 " --> pdb=" O LYS D 683 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU D 694 " --> pdb=" O GLY D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 722 removed outlier: 3.529A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 726 Processing helix chain 'D' and resid 729 through 743 Processing helix chain 'D' and resid 750 through 765 removed outlier: 3.763A pdb=" N TYR D 755 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 756 " --> pdb=" O GLY D 752 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN D 765 " --> pdb=" O LEU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 785 removed outlier: 3.521A pdb=" N ILE D 772 " --> pdb=" O PRO D 768 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 774 " --> pdb=" O SER D 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 788 No H-bonds generated for 'chain 'D' and resid 786 through 788' Processing helix chain 'D' and resid 800 through 812 removed outlier: 3.927A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 823 removed outlier: 3.538A pdb=" N ILE D 823 " --> pdb=" O ARG D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 840 removed outlier: 3.815A pdb=" N PHE D 839 " --> pdb=" O ILE D 835 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS D 840 " --> pdb=" O ASP D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 845 Processing helix chain 'D' and resid 846 through 855 Processing helix chain 'D' and resid 862 through 872 removed outlier: 4.142A pdb=" N MET D 866 " --> pdb=" O ILE D 862 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN D 867 " --> pdb=" O ASN D 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 902 removed outlier: 3.503A pdb=" N THR D 891 " --> pdb=" O GLU D 887 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG D 892 " --> pdb=" O TYR D 888 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS D 893 " --> pdb=" O LEU D 889 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL D 894 " --> pdb=" O GLU D 890 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN D 895 " --> pdb=" O THR D 891 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL D 898 " --> pdb=" O VAL D 894 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU D 901 " --> pdb=" O ILE D 897 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D 902 " --> pdb=" O VAL D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 911 through 922 removed outlier: 3.648A pdb=" N LEU D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 933 removed outlier: 3.677A pdb=" N PHE D 933 " --> pdb=" O LYS D 929 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 945 Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 955 through 962 Processing helix chain 'D' and resid 964 through 970 Processing helix chain 'D' and resid 976 through 991 removed outlier: 3.854A pdb=" N VAL D 980 " --> pdb=" O MET D 976 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU D 982 " --> pdb=" O HIS D 978 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL D 983 " --> pdb=" O HIS D 979 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D 988 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS D 989 " --> pdb=" O LYS D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1003 removed outlier: 3.613A pdb=" N LEU D 997 " --> pdb=" O ASP D 993 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 48 Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'F' and resid 23 through 40 removed outlier: 3.649A pdb=" N GLU F 28 " --> pdb=" O ASN F 24 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 54 removed outlier: 3.968A pdb=" N SER F 51 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 71 removed outlier: 3.568A pdb=" N ASP F 64 " --> pdb=" O TRP F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 95 removed outlier: 3.526A pdb=" N LEU F 85 " --> pdb=" O SER F 81 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 96 through 109 removed outlier: 3.650A pdb=" N ILE F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 122 removed outlier: 4.057A pdb=" N ASP F 119 " --> pdb=" O ASN F 115 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS F 120 " --> pdb=" O PRO F 116 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU F 122 " --> pdb=" O HIS F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 146 Processing helix chain 'F' and resid 154 through 160 removed outlier: 3.891A pdb=" N VAL F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 183 Processing helix chain 'F' and resid 186 through 192 Processing helix chain 'F' and resid 192 through 197 Processing helix chain 'F' and resid 197 through 211 removed outlier: 3.591A pdb=" N MET F 204 " --> pdb=" O ILE F 200 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 233 Processing helix chain 'F' and resid 254 through 265 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 281 through 296 removed outlier: 4.209A pdb=" N ARG F 285 " --> pdb=" O ASP F 281 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU F 293 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE F 294 " --> pdb=" O MET F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 302 removed outlier: 3.976A pdb=" N PHE F 301 " --> pdb=" O GLN F 297 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE F 302 " --> pdb=" O GLU F 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 297 through 302' Processing helix chain 'F' and resid 304 through 317 removed outlier: 4.093A pdb=" N ILE F 309 " --> pdb=" O ASP F 305 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP F 310 " --> pdb=" O ASP F 306 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR F 311 " --> pdb=" O GLU F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 322 removed outlier: 3.653A pdb=" N ALA F 321 " --> pdb=" O PRO F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 334 removed outlier: 4.123A pdb=" N VAL F 333 " --> pdb=" O ASP F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 366 removed outlier: 3.540A pdb=" N GLU F 365 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 373 removed outlier: 3.801A pdb=" N LEU F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 391 Processing helix chain 'F' and resid 412 through 416 removed outlier: 3.596A pdb=" N HIS F 415 " --> pdb=" O LEU F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 427 removed outlier: 3.603A pdb=" N MET F 421 " --> pdb=" O LYS F 417 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS F 422 " --> pdb=" O TYR F 418 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS F 423 " --> pdb=" O ASP F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 446 Processing helix chain 'F' and resid 448 through 462 removed outlier: 3.917A pdb=" N ASP F 453 " --> pdb=" O GLU F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 493 removed outlier: 3.578A pdb=" N THR F 490 " --> pdb=" O THR F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 501 Processing helix chain 'F' and resid 508 through 519 Processing helix chain 'F' and resid 523 through 525 No H-bonds generated for 'chain 'F' and resid 523 through 525' Processing helix chain 'F' and resid 526 through 531 Processing helix chain 'F' and resid 532 through 539 Processing helix chain 'F' and resid 542 through 547 removed outlier: 3.779A pdb=" N SER F 546 " --> pdb=" O LEU F 542 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP F 547 " --> pdb=" O GLU F 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 542 through 547' Processing helix chain 'F' and resid 552 through 572 removed outlier: 3.633A pdb=" N SER F 570 " --> pdb=" O ARG F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 597 Processing helix chain 'F' and resid 600 through 604 removed outlier: 3.777A pdb=" N VAL F 603 " --> pdb=" O LEU F 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 629 removed outlier: 3.862A pdb=" N TYR F 611 " --> pdb=" O GLU F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 657 Processing helix chain 'F' and resid 660 through 671 removed outlier: 3.745A pdb=" N ASN F 666 " --> pdb=" O ASP F 662 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU F 667 " --> pdb=" O ASP F 663 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU F 668 " --> pdb=" O ILE F 664 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 676 removed outlier: 3.729A pdb=" N LYS F 675 " --> pdb=" O SER F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 680 through 701 removed outlier: 3.769A pdb=" N GLN F 698 " --> pdb=" O GLU F 694 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE F 699 " --> pdb=" O ILE F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 722 removed outlier: 4.286A pdb=" N SER F 714 " --> pdb=" O THR F 710 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU F 715 " --> pdb=" O GLN F 711 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA F 718 " --> pdb=" O SER F 714 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE F 722 " --> pdb=" O ALA F 718 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 743 removed outlier: 3.596A pdb=" N LYS F 738 " --> pdb=" O GLY F 734 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA F 739 " --> pdb=" O LYS F 735 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 740 " --> pdb=" O ILE F 736 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU F 741 " --> pdb=" O VAL F 737 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR F 743 " --> pdb=" O ALA F 739 " (cutoff:3.500A) Processing helix chain 'F' and resid 751 through 762 removed outlier: 4.184A pdb=" N VAL F 756 " --> pdb=" O GLY F 752 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP F 757 " --> pdb=" O LYS F 753 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU F 761 " --> pdb=" O TRP F 757 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR F 762 " --> pdb=" O LEU F 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 768 through 786 removed outlier: 3.541A pdb=" N ILE F 772 " --> pdb=" O PRO F 768 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE F 775 " --> pdb=" O ILE F 771 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP F 776 " --> pdb=" O ILE F 772 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE F 778 " --> pdb=" O ILE F 774 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU F 779 " --> pdb=" O ILE F 775 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL F 780 " --> pdb=" O ASP F 776 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU F 781 " --> pdb=" O ASP F 777 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN F 782 " --> pdb=" O PHE F 778 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA F 783 " --> pdb=" O LEU F 779 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU F 784 " --> pdb=" O VAL F 780 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS F 786 " --> pdb=" O GLN F 782 " (cutoff:3.500A) Processing helix chain 'F' and resid 800 through 812 removed outlier: 3.998A pdb=" N TYR F 804 " --> pdb=" O TYR F 800 " (cutoff:3.500A) Processing helix chain 'F' and resid 817 through 827 removed outlier: 3.781A pdb=" N GLU F 822 " --> pdb=" O LYS F 818 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE F 823 " --> pdb=" O ARG F 819 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS F 826 " --> pdb=" O GLU F 822 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU F 827 " --> pdb=" O ILE F 823 " (cutoff:3.500A) Processing helix chain 'F' and resid 832 through 840 removed outlier: 4.220A pdb=" N ASP F 836 " --> pdb=" O GLN F 832 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE F 837 " --> pdb=" O LYS F 833 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS F 840 " --> pdb=" O ASP F 836 " (cutoff:3.500A) Processing helix chain 'F' and resid 846 through 853 Processing helix chain 'F' and resid 861 through 872 removed outlier: 3.574A pdb=" N ILE F 869 " --> pdb=" O LEU F 865 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG F 870 " --> pdb=" O MET F 866 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 902 removed outlier: 3.605A pdb=" N GLU F 899 " --> pdb=" O ASN F 895 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS F 900 " --> pdb=" O TYR F 896 " (cutoff:3.500A) Processing helix chain 'F' and resid 911 through 922 removed outlier: 3.690A pdb=" N PHE F 916 " --> pdb=" O TYR F 912 " (cutoff:3.500A) Processing helix chain 'F' and resid 928 through 933 removed outlier: 3.935A pdb=" N GLU F 932 " --> pdb=" O SER F 928 " (cutoff:3.500A) Processing helix chain 'F' and resid 937 through 945 Processing helix chain 'F' and resid 957 through 962 removed outlier: 4.014A pdb=" N ASN F 961 " --> pdb=" O SER F 957 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR F 962 " --> pdb=" O TRP F 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 957 through 962' Processing helix chain 'F' and resid 963 through 973 Processing helix chain 'F' and resid 974 through 976 No H-bonds generated for 'chain 'F' and resid 974 through 976' Processing helix chain 'F' and resid 977 through 990 removed outlier: 3.808A pdb=" N GLU F 986 " --> pdb=" O GLU F 982 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS F 989 " --> pdb=" O LYS F 985 " (cutoff:3.500A) Processing helix chain 'F' and resid 993 through 1003 removed outlier: 3.827A pdb=" N LEU F 997 " --> pdb=" O ASP F 993 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F1000 " --> pdb=" O TYR F 996 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR F1003 " --> pdb=" O ILE F 999 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 74 removed outlier: 3.815A pdb=" N LEU G 73 " --> pdb=" O ASP G 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 38 removed outlier: 3.535A pdb=" N CYS H 29 " --> pdb=" O ASN H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 54 removed outlier: 3.792A pdb=" N THR H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU H 53 " --> pdb=" O GLY H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 71 Processing helix chain 'H' and resid 80 through 108 Proline residue: H 88 - end of helix removed outlier: 6.439A pdb=" N GLU H 97 " --> pdb=" O ASN H 93 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N MET H 98 " --> pdb=" O VAL H 94 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA H 99 " --> pdb=" O LYS H 95 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE H 103 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU H 104 " --> pdb=" O PHE H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 124 removed outlier: 3.903A pdb=" N ASP H 119 " --> pdb=" O ASN H 115 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU H 122 " --> pdb=" O HIS H 118 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 146 Processing helix chain 'H' and resid 154 through 160 Processing helix chain 'H' and resid 186 through 192 removed outlier: 3.701A pdb=" N TYR H 190 " --> pdb=" O LYS H 186 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 197 Processing helix chain 'H' and resid 197 through 211 removed outlier: 3.659A pdb=" N LYS H 205 " --> pdb=" O SER H 201 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR H 210 " --> pdb=" O THR H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 236 Processing helix chain 'H' and resid 254 through 265 Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.550A pdb=" N LEU H 274 " --> pdb=" O ASP H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 296 removed outlier: 3.553A pdb=" N VAL H 289 " --> pdb=" O ARG H 285 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU H 292 " --> pdb=" O ALA H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 302 removed outlier: 3.681A pdb=" N ILE H 302 " --> pdb=" O GLU H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 317 removed outlier: 4.327A pdb=" N ASP H 310 " --> pdb=" O ASP H 306 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR H 311 " --> pdb=" O GLU H 307 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS H 315 " --> pdb=" O TYR H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 318 through 321 removed outlier: 3.588A pdb=" N ALA H 321 " --> pdb=" O PRO H 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 318 through 321' Processing helix chain 'H' and resid 326 through 332 removed outlier: 4.151A pdb=" N LYS H 331 " --> pdb=" O ILE H 328 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 366 Processing helix chain 'H' and resid 366 through 373 removed outlier: 3.892A pdb=" N ARG H 370 " --> pdb=" O SER H 366 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER H 371 " --> pdb=" O CYS H 367 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS H 372 " --> pdb=" O ASP H 368 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU H 373 " --> pdb=" O GLU H 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 366 through 373' Processing helix chain 'H' and resid 374 through 392 removed outlier: 4.334A pdb=" N ARG H 380 " --> pdb=" O LYS H 376 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU H 389 " --> pdb=" O PHE H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 396 through 400 removed outlier: 3.715A pdb=" N ASP H 399 " --> pdb=" O MET H 396 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 426 removed outlier: 3.546A pdb=" N MET H 421 " --> pdb=" O LYS H 417 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS H 422 " --> pdb=" O TYR H 418 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS H 423 " --> pdb=" O ASP H 419 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU H 426 " --> pdb=" O LYS H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 445 Processing helix chain 'H' and resid 447 through 461 removed outlier: 4.022A pdb=" N ASP H 453 " --> pdb=" O GLU H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 467 through 494 removed outlier: 4.060A pdb=" N LEU H 473 " --> pdb=" O CYS H 469 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER H 474 " --> pdb=" O VAL H 470 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN H 487 " --> pdb=" O GLN H 483 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 501 removed outlier: 3.727A pdb=" N THR H 499 " --> pdb=" O LEU H 495 " (cutoff:3.500A) Processing helix chain 'H' and resid 508 through 519 removed outlier: 3.842A pdb=" N LEU H 512 " --> pdb=" O THR H 508 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA H 513 " --> pdb=" O ASP H 509 " (cutoff:3.500A) Processing helix chain 'H' and resid 526 through 531 Processing helix chain 'H' and resid 532 through 539 Processing helix chain 'H' and resid 542 through 547 removed outlier: 3.951A pdb=" N SER H 546 " --> pdb=" O LEU H 542 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP H 547 " --> pdb=" O GLU H 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 542 through 547' Processing helix chain 'H' and resid 550 through 572 removed outlier: 4.109A pdb=" N ASP H 554 " --> pdb=" O PHE H 550 " (cutoff:3.500A) Processing helix chain 'H' and resid 579 through 597 removed outlier: 3.698A pdb=" N VAL H 583 " --> pdb=" O SER H 579 " (cutoff:3.500A) Processing helix chain 'H' and resid 598 through 604 removed outlier: 6.619A pdb=" N TRP H 601 " --> pdb=" O ASN H 598 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N SER H 602 " --> pdb=" O CYS H 599 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL H 603 " --> pdb=" O LEU H 600 " (cutoff:3.500A) Processing helix chain 'H' and resid 605 through 628 removed outlier: 3.502A pdb=" N MET H 616 " --> pdb=" O ILE H 612 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU H 618 " --> pdb=" O ASN H 614 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU H 619 " --> pdb=" O SER H 615 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG H 627 " --> pdb=" O ALA H 623 " (cutoff:3.500A) Processing helix chain 'H' and resid 648 through 659 Processing helix chain 'H' and resid 660 through 671 removed outlier: 3.900A pdb=" N LYS H 665 " --> pdb=" O ILE H 661 " (cutoff:3.500A) Processing helix chain 'H' and resid 682 through 701 removed outlier: 3.659A pdb=" N GLU H 686 " --> pdb=" O GLU H 682 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA H 701 " --> pdb=" O LYS H 697 " (cutoff:3.500A) Processing helix chain 'H' and resid 705 through 722 removed outlier: 3.535A pdb=" N TYR H 709 " --> pdb=" O ASN H 705 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR H 710 " --> pdb=" O VAL H 706 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN H 711 " --> pdb=" O VAL H 707 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER H 714 " --> pdb=" O THR H 710 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU H 715 " --> pdb=" O GLN H 711 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA H 718 " --> pdb=" O SER H 714 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR H 721 " --> pdb=" O LYS H 717 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE H 722 " --> pdb=" O ALA H 718 " (cutoff:3.500A) Processing helix chain 'H' and resid 723 through 725 No H-bonds generated for 'chain 'H' and resid 723 through 725' Processing helix chain 'H' and resid 729 through 741 removed outlier: 3.959A pdb=" N VAL H 737 " --> pdb=" O LEU H 733 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU H 741 " --> pdb=" O VAL H 737 " (cutoff:3.500A) Processing helix chain 'H' and resid 750 through 761 removed outlier: 3.533A pdb=" N ARG H 754 " --> pdb=" O ASP H 750 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP H 757 " --> pdb=" O LYS H 753 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU H 761 " --> pdb=" O TRP H 757 " (cutoff:3.500A) Processing helix chain 'H' and resid 768 through 785 removed outlier: 3.650A pdb=" N ILE H 772 " --> pdb=" O PRO H 768 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER H 773 " --> pdb=" O LYS H 769 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE H 778 " --> pdb=" O ILE H 774 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU H 779 " --> pdb=" O ILE H 775 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL H 780 " --> pdb=" O ASP H 776 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU H 781 " --> pdb=" O ASP H 777 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN H 782 " --> pdb=" O PHE H 778 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA H 783 " --> pdb=" O LEU H 779 " (cutoff:3.500A) Processing helix chain 'H' and resid 786 through 788 No H-bonds generated for 'chain 'H' and resid 786 through 788' Processing helix chain 'H' and resid 801 through 812 removed outlier: 4.015A pdb=" N GLY H 805 " --> pdb=" O SER H 801 " (cutoff:3.500A) Processing helix chain 'H' and resid 817 through 824 removed outlier: 3.889A pdb=" N THR H 824 " --> pdb=" O LEU H 820 " (cutoff:3.500A) Processing helix chain 'H' and resid 832 through 840 removed outlier: 4.021A pdb=" N ASP H 836 " --> pdb=" O GLN H 832 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE H 837 " --> pdb=" O LYS H 833 " (cutoff:3.500A) Processing helix chain 'H' and resid 841 through 845 Processing helix chain 'H' and resid 846 through 856 removed outlier: 3.513A pdb=" N SER H 851 " --> pdb=" O THR H 847 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS H 852 " --> pdb=" O ASN H 848 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE H 856 " --> pdb=" O HIS H 852 " (cutoff:3.500A) Processing helix chain 'H' and resid 862 through 872 removed outlier: 3.705A pdb=" N MET H 866 " --> pdb=" O ILE H 862 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG H 870 " --> pdb=" O MET H 866 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 871 " --> pdb=" O ASN H 867 " (cutoff:3.500A) Processing helix chain 'H' and resid 878 through 903 removed outlier: 4.057A pdb=" N LEU H 884 " --> pdb=" O GLU H 880 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE H 885 " --> pdb=" O HIS H 881 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE H 886 " --> pdb=" O GLU H 882 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU H 887 " --> pdb=" O GLU H 883 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR H 888 " --> pdb=" O LEU H 884 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS H 893 " --> pdb=" O LEU H 889 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS H 900 " --> pdb=" O TYR H 896 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU H 901 " --> pdb=" O ILE H 897 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS H 902 " --> pdb=" O VAL H 898 " (cutoff:3.500A) Processing helix chain 'H' and resid 912 through 922 removed outlier: 3.812A pdb=" N GLY H 917 " --> pdb=" O MET H 913 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE H 918 " --> pdb=" O SER H 914 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP H 919 " --> pdb=" O THR H 915 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR H 920 " --> pdb=" O PHE H 916 " (cutoff:3.500A) Processing helix chain 'H' and resid 929 through 933 Processing helix chain 'H' and resid 937 through 945 Processing helix chain 'H' and resid 955 through 962 removed outlier: 3.616A pdb=" N TYR H 962 " --> pdb=" O LEU H 959 " (cutoff:3.500A) Processing helix chain 'H' and resid 963 through 971 Processing helix chain 'H' and resid 976 through 990 removed outlier: 3.583A pdb=" N GLU H 982 " --> pdb=" O HIS H 978 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS H 989 " --> pdb=" O LYS H 985 " (cutoff:3.500A) Processing helix chain 'H' and resid 994 through 1003 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 8.043A pdb=" N ILE A 130 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.860A pdb=" N PHE B 13 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR B 24 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 11 " --> pdb=" O THR B 24 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP B 10 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 178 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.318A pdb=" N THR B 29 " --> pdb=" O THR B 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 198 through 200 removed outlier: 3.509A pdb=" N GLU B 221 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.511A pdb=" N THR C 62 " --> pdb=" O GLN C 28 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA C 30 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASN C 60 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE C 32 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU C 58 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE C 59 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA C 222 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 61 " --> pdb=" O PHE C 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'D' and resid 150 through 152 removed outlier: 5.928A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL D 129 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU D 42 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE D 130 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AB1, first strand: chain 'E' and resid 21 through 25 removed outlier: 6.715A pdb=" N PHE E 13 " --> pdb=" O VAL E 22 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR E 24 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL E 11 " --> pdb=" O THR E 24 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP E 10 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 178 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 198 through 199 removed outlier: 3.640A pdb=" N SER E 199 " --> pdb=" O GLU E 221 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU E 221 " --> pdb=" O SER E 199 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU E 61 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE E 59 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN E 60 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA E 30 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR E 62 " --> pdb=" O GLN E 28 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR H 574 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 150 through 152 removed outlier: 5.791A pdb=" N SER F 150 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS F 169 " --> pdb=" O SER F 150 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE F 152 " --> pdb=" O LYS F 169 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL F 129 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU F 42 " --> pdb=" O HIS F 128 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ILE F 130 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE F 44 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL F 43 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE F 216 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE F 45 " --> pdb=" O ILE F 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 338 through 340 Processing sheet with id=AB5, first strand: chain 'G' and resid 14 through 15 removed outlier: 3.861A pdb=" N LYS G 14 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU G 174 " --> pdb=" O LYS G 14 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 27 through 30 removed outlier: 6.421A pdb=" N THR G 62 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 150 through 152 removed outlier: 6.037A pdb=" N PHE H 44 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 338 through 340 1583 hydrogen bonds defined for protein. 4530 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: 8.21 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11554 1.34 - 1.46: 6510 1.46 - 1.58: 19442 1.58 - 1.70: 1 1.70 - 1.82: 232 Bond restraints: 37739 Sorted by residual: bond pdb=" N ILE A 515 " pdb=" CA ILE A 515 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.68e+00 bond pdb=" N VAL H 584 " pdb=" CA VAL H 584 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.26e+00 bond pdb=" N ASN H 192 " pdb=" CA ASN H 192 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.12e-02 7.97e+03 7.14e+00 bond pdb=" N ILE H 582 " pdb=" CA ILE H 582 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.21e-02 6.83e+03 6.96e+00 bond pdb=" N ARG A 517 " pdb=" CA ARG A 517 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.16e-02 7.43e+03 6.91e+00 ... (remaining 37734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 50417 2.45 - 4.89: 370 4.89 - 7.34: 53 7.34 - 9.78: 20 9.78 - 12.23: 4 Bond angle restraints: 50864 Sorted by residual: angle pdb=" CB GLN B 28 " pdb=" CG GLN B 28 " pdb=" CD GLN B 28 " ideal model delta sigma weight residual 112.60 119.87 -7.27 1.70e+00 3.46e-01 1.83e+01 angle pdb=" CB MET D 396 " pdb=" CG MET D 396 " pdb=" SD MET D 396 " ideal model delta sigma weight residual 112.70 124.93 -12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" CA PRO C 49 " pdb=" N PRO C 49 " pdb=" CD PRO C 49 " ideal model delta sigma weight residual 112.00 106.35 5.65 1.40e+00 5.10e-01 1.63e+01 angle pdb=" CB MET F 204 " pdb=" CG MET F 204 " pdb=" SD MET F 204 " ideal model delta sigma weight residual 112.70 123.99 -11.29 3.00e+00 1.11e-01 1.42e+01 angle pdb=" N SER D 54 " pdb=" CA SER D 54 " pdb=" C SER D 54 " ideal model delta sigma weight residual 113.21 108.90 4.31 1.15e+00 7.56e-01 1.41e+01 ... (remaining 50859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 19414 17.96 - 35.93: 2415 35.93 - 53.89: 459 53.89 - 71.85: 202 71.85 - 89.82: 28 Dihedral angle restraints: 22518 sinusoidal: 9309 harmonic: 13209 Sorted by residual: dihedral pdb=" CA ALA E 179 " pdb=" C ALA E 179 " pdb=" N TYR E 180 " pdb=" CA TYR E 180 " ideal model delta harmonic sigma weight residual 180.00 155.24 24.76 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA GLN B 194 " pdb=" C GLN B 194 " pdb=" N PHE B 195 " pdb=" CA PHE B 195 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA MET A 704 " pdb=" C MET A 704 " pdb=" N ASN A 705 " pdb=" CA ASN A 705 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 22515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 4032 0.040 - 0.080: 1070 0.080 - 0.120: 275 0.120 - 0.159: 31 0.159 - 0.199: 3 Chirality restraints: 5411 Sorted by residual: chirality pdb=" CA ILE H 582 " pdb=" N ILE H 582 " pdb=" C ILE H 582 " pdb=" CB ILE H 582 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CA LEU H 585 " pdb=" N LEU H 585 " pdb=" C LEU H 585 " pdb=" CB LEU H 585 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA VAL H 583 " pdb=" N VAL H 583 " pdb=" C VAL H 583 " pdb=" CB VAL H 583 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.61e-01 ... (remaining 5408 not shown) Planarity restraints: 6518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 56 " -0.043 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A 57 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 125 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C ASN H 125 " -0.030 2.00e-02 2.50e+03 pdb=" O ASN H 125 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO H 126 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 52 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C ILE G 52 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE G 52 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU G 53 " -0.010 2.00e-02 2.50e+03 ... (remaining 6515 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3144 2.74 - 3.28: 40879 3.28 - 3.82: 63541 3.82 - 4.36: 77064 4.36 - 4.90: 124274 Nonbonded interactions: 308902 Sorted by model distance: nonbonded pdb=" O SER D 817 " pdb=" OG SER D 821 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR A 800 " pdb=" O ASP B 225 " model vdw 2.207 3.040 nonbonded pdb=" O GLU D 181 " pdb=" OH TYR D 197 " model vdw 2.209 3.040 nonbonded pdb=" O VAL C 11 " pdb=" OG1 THR C 24 " model vdw 2.211 3.040 nonbonded pdb=" O GLU A 362 " pdb=" OG SER A 366 " model vdw 2.211 3.040 ... (remaining 308897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'B' and (resid 9 through 76 or resid 173 through 234)) selection = (chain 'C' and (resid 9 through 76 or resid 173 through 234)) selection = chain 'E' selection = (chain 'G' and (resid 9 through 76 or resid 173 through 234)) } 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: 5.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 35.510 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 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 : 0.003 0.115 37739 Z= 0.136 Angle : 0.563 12.226 50864 Z= 0.300 Chirality : 0.039 0.199 5411 Planarity : 0.003 0.064 6518 Dihedral : 16.804 89.818 14032 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.37 % Allowed : 22.37 % Favored : 77.26 % 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 aren not related in a simple way. whole: -0.31 (0.12), residues: 4435 helix: 0.67 (0.11), residues: 2126 sheet: -1.65 (0.34), residues: 230 loop : -0.92 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 629 TYR 0.022 0.001 TYR A 356 PHE 0.018 0.001 PHE F 742 TRP 0.013 0.001 TRP A 60 HIS 0.006 0.001 HIS F 658 Details of bonding type rmsd covalent geometry : bond 0.00259 (37739) covalent geometry : angle 0.56309 (50864) hydrogen bonds : bond 0.27347 ( 1583) hydrogen bonds : angle 7.58586 ( 4530) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 307 time to evaluate : 1.584 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 974 LYS cc_start: 0.7959 (tptp) cc_final: 0.7652 (mmmt) REVERT: C 53 LEU cc_start: 0.6968 (mm) cc_final: 0.6406 (tp) REVERT: C 175 TYR cc_start: 0.6170 (p90) cc_final: 0.5958 (p90) REVERT: C 231 MET cc_start: 0.6440 (mtt) cc_final: 0.6173 (mtt) REVERT: D 976 MET cc_start: 0.5785 (pmm) cc_final: 0.5238 (mpp) REVERT: E 75 MET cc_start: 0.0340 (pmm) cc_final: -0.1619 (tpp) REVERT: F 519 MET cc_start: 0.7189 (mmm) cc_final: 0.6987 (tpt) REVERT: F 722 PHE cc_start: 0.8723 (m-80) cc_final: 0.8365 (m-80) REVERT: F 763 LYS cc_start: 0.5134 (tptt) cc_final: 0.4518 (mttp) REVERT: H 498 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6977 (pp) REVERT: H 519 MET cc_start: 0.6937 (tmm) cc_final: 0.6553 (tmm) REVERT: H 526 ASP cc_start: 0.8601 (p0) cc_final: 0.8369 (p0) REVERT: H 569 MET cc_start: 0.8933 (tmm) cc_final: 0.8637 (tpp) REVERT: H 702 ASN cc_start: 0.8243 (t0) cc_final: 0.8042 (p0) REVERT: H 758 LEU cc_start: 0.8674 (mt) cc_final: 0.8312 (pp) REVERT: H 913 MET cc_start: 0.7125 (tmm) cc_final: 0.6663 (tmm) outliers start: 15 outliers final: 3 residues processed: 317 average time/residue: 0.2379 time to fit residues: 124.6622 Evaluate side-chains 226 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 222 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain H residue 584 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0060 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 8.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN A 786 HIS B 194 GLN D 377 GLN ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 563 ASN D 961 ASN ** F 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 711 GLN ** F 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN H 323 GLN ** H 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.069895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.054864 restraints weight = 214264.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.056728 restraints weight = 126092.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.057694 restraints weight = 75920.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.057862 restraints weight = 54413.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.058006 restraints weight = 55607.834| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 37739 Z= 0.131 Angle : 0.563 11.124 50864 Z= 0.297 Chirality : 0.040 0.163 5411 Planarity : 0.003 0.044 6518 Dihedral : 3.981 40.204 4899 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.05 % Allowed : 19.80 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.13), residues: 4435 helix: 0.72 (0.11), residues: 2300 sheet: -1.97 (0.32), residues: 230 loop : -1.08 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 892 TYR 0.020 0.001 TYR A 755 PHE 0.015 0.001 PHE D 943 TRP 0.015 0.001 TRP A 231 HIS 0.008 0.001 HIS F 503 Details of bonding type rmsd covalent geometry : bond 0.00268 (37739) covalent geometry : angle 0.56337 (50864) hydrogen bonds : bond 0.05046 ( 1583) hydrogen bonds : angle 5.15702 ( 4530) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 245 time to evaluate : 1.265 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 204 MET cc_start: 0.8969 (tmm) cc_final: 0.8256 (tmm) REVERT: A 913 MET cc_start: 0.7991 (mmm) cc_final: 0.7678 (mmt) REVERT: A 974 LYS cc_start: 0.7847 (tptp) cc_final: 0.7555 (mmmt) REVERT: C 231 MET cc_start: 0.6358 (mtt) cc_final: 0.6082 (mtt) REVERT: D 135 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7658 (m-30) REVERT: D 683 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8814 (ttpp) REVERT: D 976 MET cc_start: 0.5704 (pmm) cc_final: 0.5068 (mpp) REVERT: E 68 PHE cc_start: 0.4387 (OUTLIER) cc_final: 0.3857 (t80) REVERT: E 75 MET cc_start: 0.0881 (pmm) cc_final: 0.0378 (ppp) REVERT: E 231 MET cc_start: 0.0531 (mmt) cc_final: -0.1425 (mmp) REVERT: F 204 MET cc_start: 0.8497 (tmm) cc_final: 0.8250 (tmm) REVERT: F 368 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8546 (p0) REVERT: F 722 PHE cc_start: 0.8724 (m-80) cc_final: 0.8502 (m-80) REVERT: F 763 LYS cc_start: 0.5232 (tptt) cc_final: 0.4614 (mttp) REVERT: F 979 HIS cc_start: 0.7233 (OUTLIER) cc_final: 0.5898 (m-70) REVERT: G 14 LYS cc_start: 0.6294 (pttp) cc_final: 0.6025 (ttpp) REVERT: H 445 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8797 (mm) REVERT: H 519 MET cc_start: 0.6808 (tmm) cc_final: 0.6478 (tmm) REVERT: H 913 MET cc_start: 0.6972 (tmm) cc_final: 0.6596 (tmm) outliers start: 83 outliers final: 30 residues processed: 321 average time/residue: 0.1993 time to fit residues: 108.7047 Evaluate side-chains 256 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 683 LYS Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 961 ASN Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 915 THR Chi-restraints excluded: chain F residue 928 SER Chi-restraints excluded: chain F residue 930 MET Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 979 HIS Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 764 CYS Chi-restraints excluded: chain H residue 883 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 123 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 230 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 346 optimal weight: 10.0000 chunk 180 optimal weight: 0.7980 chunk 306 optimal weight: 0.0270 chunk 258 optimal weight: 1.9990 chunk 315 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 263 ASN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN D 477 ASN ** D 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 ASN F 881 HIS ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 867 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.068686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.053844 restraints weight = 213465.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.055665 restraints weight = 123368.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.056601 restraints weight = 75182.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.056693 restraints weight = 53939.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.056886 restraints weight = 54860.991| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37739 Z= 0.132 Angle : 0.529 12.674 50864 Z= 0.275 Chirality : 0.040 0.167 5411 Planarity : 0.003 0.045 6518 Dihedral : 3.812 24.609 4891 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.35 % Favored : 95.63 % Rotamer: Outliers : 2.15 % Allowed : 20.15 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.13), residues: 4435 helix: 0.85 (0.11), residues: 2323 sheet: -1.99 (0.33), residues: 219 loop : -1.01 (0.15), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 359 TYR 0.024 0.001 TYR H 888 PHE 0.022 0.001 PHE B 220 TRP 0.011 0.001 TRP D 143 HIS 0.008 0.001 HIS F 658 Details of bonding type rmsd covalent geometry : bond 0.00284 (37739) covalent geometry : angle 0.52888 (50864) hydrogen bonds : bond 0.04227 ( 1583) hydrogen bonds : angle 4.80123 ( 4530) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 221 time to evaluate : 1.518 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 204 MET cc_start: 0.9066 (tmm) cc_final: 0.8293 (tmm) REVERT: A 913 MET cc_start: 0.8056 (mmm) cc_final: 0.7671 (mmt) REVERT: A 974 LYS cc_start: 0.7880 (tptp) cc_final: 0.7654 (mmmt) REVERT: B 205 GLU cc_start: 0.7296 (pp20) cc_final: 0.7057 (pp20) REVERT: D 135 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8087 (m-30) REVERT: D 683 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8800 (ttpp) REVERT: D 976 MET cc_start: 0.6055 (pmm) cc_final: 0.5425 (mpp) REVERT: E 68 PHE cc_start: 0.4186 (OUTLIER) cc_final: 0.3529 (t80) REVERT: E 175 TYR cc_start: 0.7273 (t80) cc_final: 0.6598 (t80) REVERT: E 228 THR cc_start: 0.5740 (m) cc_final: 0.5471 (m) REVERT: E 231 MET cc_start: 0.0546 (mmt) cc_final: -0.0458 (mmt) REVERT: F 368 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8590 (p0) REVERT: F 396 MET cc_start: 0.7729 (ttt) cc_final: 0.7487 (ttt) REVERT: F 569 MET cc_start: 0.6968 (ptp) cc_final: 0.6154 (mtm) REVERT: F 763 LYS cc_start: 0.5103 (tptt) cc_final: 0.4469 (mttm) REVERT: F 979 HIS cc_start: 0.7461 (OUTLIER) cc_final: 0.6339 (m-70) REVERT: G 14 LYS cc_start: 0.6356 (pttp) cc_final: 0.6128 (ttpp) REVERT: H 421 MET cc_start: 0.7243 (mmt) cc_final: 0.7026 (mpp) REVERT: H 432 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8560 (mt) REVERT: H 519 MET cc_start: 0.6879 (tmm) cc_final: 0.6416 (tmm) REVERT: H 913 MET cc_start: 0.6988 (tmm) cc_final: 0.6709 (tmm) outliers start: 87 outliers final: 39 residues processed: 297 average time/residue: 0.1971 time to fit residues: 99.9409 Evaluate side-chains 254 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 683 LYS Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 866 MET Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 979 HIS Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 524 ILE Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 673 ILE Chi-restraints excluded: chain H residue 693 GLU Chi-restraints excluded: chain H residue 742 PHE Chi-restraints excluded: chain H residue 810 HIS Chi-restraints excluded: chain H residue 883 GLU Chi-restraints excluded: chain H residue 1004 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 6.9990 chunk 174 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 282 optimal weight: 10.0000 chunk 202 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 443 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 347 optimal weight: 0.5980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 786 HIS D 133 ASN D 230 ASN ** D 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 GLN D 961 ASN ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 810 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.067993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.053233 restraints weight = 213275.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.054691 restraints weight = 114427.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.055647 restraints weight = 75591.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.056265 restraints weight = 56957.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.056630 restraints weight = 47022.772| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37739 Z= 0.129 Angle : 0.513 14.095 50864 Z= 0.266 Chirality : 0.039 0.163 5411 Planarity : 0.003 0.045 6518 Dihedral : 3.838 24.519 4891 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.49 % Favored : 95.49 % Rotamer: Outliers : 2.64 % Allowed : 20.02 % Favored : 77.34 % 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 aren not related in a simple way. whole: -0.05 (0.13), residues: 4435 helix: 0.95 (0.11), residues: 2338 sheet: -2.15 (0.32), residues: 226 loop : -0.97 (0.15), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 627 TYR 0.020 0.001 TYR A1003 PHE 0.025 0.001 PHE B 220 TRP 0.010 0.001 TRP A 59 HIS 0.009 0.001 HIS A 786 Details of bonding type rmsd covalent geometry : bond 0.00279 (37739) covalent geometry : angle 0.51344 (50864) hydrogen bonds : bond 0.03567 ( 1583) hydrogen bonds : angle 4.59264 ( 4530) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 216 time to evaluate : 1.549 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 279 GLU cc_start: 0.8626 (pm20) cc_final: 0.8195 (mm-30) REVERT: B 205 GLU cc_start: 0.7457 (pp20) cc_final: 0.7077 (pp20) REVERT: C 62 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8459 (p) REVERT: D 531 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8263 (tmm) REVERT: D 976 MET cc_start: 0.5960 (pmm) cc_final: 0.5483 (mpp) REVERT: E 68 PHE cc_start: 0.3990 (OUTLIER) cc_final: 0.3405 (t80) REVERT: E 175 TYR cc_start: 0.7136 (t80) cc_final: 0.6399 (t80) REVERT: E 228 THR cc_start: 0.5873 (m) cc_final: 0.5608 (m) REVERT: E 231 MET cc_start: 0.0567 (mmt) cc_final: -0.0428 (mmt) REVERT: F 368 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8612 (p0) REVERT: F 569 MET cc_start: 0.7118 (ptp) cc_final: 0.6283 (mtm) REVERT: F 722 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8438 (m-80) REVERT: F 763 LYS cc_start: 0.5137 (tptt) cc_final: 0.4432 (mtmm) REVERT: F 936 MET cc_start: 0.3383 (mtp) cc_final: 0.3038 (mtp) REVERT: F 979 HIS cc_start: 0.7487 (OUTLIER) cc_final: 0.6548 (m-70) REVERT: H 280 TYR cc_start: 0.8412 (t80) cc_final: 0.7602 (t80) REVERT: H 432 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8582 (mt) REVERT: H 445 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8826 (mm) REVERT: H 519 MET cc_start: 0.6902 (tmm) cc_final: 0.6454 (tmm) outliers start: 107 outliers final: 56 residues processed: 313 average time/residue: 0.2100 time to fit residues: 113.3347 Evaluate side-chains 265 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 201 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 613 ARG Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 961 ASN Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 722 PHE Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 814 ASN Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 979 HIS Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 524 ILE Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 558 LEU Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 673 ILE Chi-restraints excluded: chain H residue 684 ILE Chi-restraints excluded: chain H residue 726 VAL Chi-restraints excluded: chain H residue 764 CYS Chi-restraints excluded: chain H residue 810 HIS Chi-restraints excluded: chain H residue 883 GLU Chi-restraints excluded: chain H residue 930 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 62 optimal weight: 0.3980 chunk 220 optimal weight: 0.9990 chunk 422 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 277 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 192 optimal weight: 0.0020 chunk 338 optimal weight: 5.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 961 ASN G 210 ASN ** H 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 810 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.068243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.053607 restraints weight = 210071.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.055039 restraints weight = 112353.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.055986 restraints weight = 73735.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.056587 restraints weight = 55556.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.056991 restraints weight = 45999.292| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 37739 Z= 0.101 Angle : 0.499 14.698 50864 Z= 0.257 Chirality : 0.039 0.157 5411 Planarity : 0.003 0.045 6518 Dihedral : 3.786 24.273 4891 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.44 % Favored : 95.54 % Rotamer: Outliers : 2.19 % Allowed : 20.74 % Favored : 77.07 % 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 aren not related in a simple way. whole: 0.00 (0.13), residues: 4435 helix: 0.99 (0.11), residues: 2339 sheet: -2.20 (0.32), residues: 228 loop : -0.93 (0.15), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 15 TYR 0.020 0.001 TYR A 755 PHE 0.029 0.001 PHE B 220 TRP 0.019 0.001 TRP E 72 HIS 0.015 0.001 HIS H 810 Details of bonding type rmsd covalent geometry : bond 0.00219 (37739) covalent geometry : angle 0.49897 (50864) hydrogen bonds : bond 0.03341 ( 1583) hydrogen bonds : angle 4.46859 ( 4530) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 212 time to evaluate : 1.487 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 204 MET cc_start: 0.9173 (tmm) cc_final: 0.8434 (tmm) REVERT: A 279 GLU cc_start: 0.8574 (pm20) cc_final: 0.8195 (mm-30) REVERT: B 39 GLU cc_start: 0.6061 (OUTLIER) cc_final: 0.5064 (mp0) REVERT: B 205 GLU cc_start: 0.7463 (pp20) cc_final: 0.7066 (pp20) REVERT: C 62 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8454 (p) REVERT: D 135 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8029 (m-30) REVERT: D 200 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8826 (mt) REVERT: D 683 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8845 (ttpp) REVERT: D 976 MET cc_start: 0.5855 (pmm) cc_final: 0.5346 (mpp) REVERT: E 68 PHE cc_start: 0.3976 (OUTLIER) cc_final: 0.3413 (t80) REVERT: E 175 TYR cc_start: 0.7284 (t80) cc_final: 0.6664 (t80) REVERT: E 228 THR cc_start: 0.5893 (m) cc_final: 0.5644 (m) REVERT: E 231 MET cc_start: 0.0962 (mmt) cc_final: -0.0043 (mmt) REVERT: F 569 MET cc_start: 0.7176 (ptp) cc_final: 0.6507 (mtm) REVERT: F 722 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8465 (m-80) REVERT: F 763 LYS cc_start: 0.5143 (tptt) cc_final: 0.4297 (mtmm) REVERT: F 936 MET cc_start: 0.4226 (mtp) cc_final: 0.3958 (mtp) REVERT: F 979 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.6633 (m-70) REVERT: H 432 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8596 (mt) REVERT: H 445 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8810 (mm) REVERT: H 519 MET cc_start: 0.6857 (tmm) cc_final: 0.6428 (tmm) outliers start: 89 outliers final: 50 residues processed: 290 average time/residue: 0.2087 time to fit residues: 104.5711 Evaluate side-chains 258 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 198 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 613 ARG Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 683 LYS Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 603 VAL Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 722 PHE Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 866 MET Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 979 HIS Chi-restraints excluded: chain F residue 1004 PHE Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 673 ILE Chi-restraints excluded: chain H residue 684 ILE Chi-restraints excluded: chain H residue 726 VAL Chi-restraints excluded: chain H residue 764 CYS Chi-restraints excluded: chain H residue 883 GLU Chi-restraints excluded: chain H residue 930 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 368 optimal weight: 0.0770 chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 375 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 332 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 219 optimal weight: 0.5980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 477 ASN ** 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 = 0.3903 r_free = 0.3903 target = 0.068091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.053517 restraints weight = 210921.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.054934 restraints weight = 113808.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.055891 restraints weight = 74925.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.056506 restraints weight = 56488.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.056825 restraints weight = 46522.890| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 37739 Z= 0.100 Angle : 0.503 14.819 50864 Z= 0.256 Chirality : 0.038 0.165 5411 Planarity : 0.003 0.045 6518 Dihedral : 3.741 24.348 4891 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.33 % Favored : 95.65 % Rotamer: Outliers : 2.39 % Allowed : 20.67 % Favored : 76.94 % 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 aren not related in a simple way. whole: 0.06 (0.13), residues: 4435 helix: 1.03 (0.11), residues: 2344 sheet: -2.22 (0.32), residues: 229 loop : -0.89 (0.15), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 15 TYR 0.022 0.001 TYR A 755 PHE 0.029 0.001 PHE B 220 TRP 0.033 0.001 TRP E 72 HIS 0.007 0.001 HIS F 658 Details of bonding type rmsd covalent geometry : bond 0.00218 (37739) covalent geometry : angle 0.50340 (50864) hydrogen bonds : bond 0.03166 ( 1583) hydrogen bonds : angle 4.37718 ( 4530) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 211 time to evaluate : 1.356 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 118 HIS cc_start: 0.8465 (OUTLIER) cc_final: 0.8190 (m90) REVERT: A 204 MET cc_start: 0.9138 (tmm) cc_final: 0.8407 (tmm) REVERT: A 279 GLU cc_start: 0.8567 (pm20) cc_final: 0.8182 (mm-30) REVERT: A 631 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8220 (mp) REVERT: B 39 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5188 (mp0) REVERT: B 177 THR cc_start: 0.5416 (OUTLIER) cc_final: 0.5047 (p) REVERT: B 205 GLU cc_start: 0.7446 (pp20) cc_final: 0.6967 (pp20) REVERT: C 62 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8452 (p) REVERT: D 135 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8025 (m-30) REVERT: D 200 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8830 (mt) REVERT: D 683 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8832 (ttpp) REVERT: D 976 MET cc_start: 0.6044 (pmm) cc_final: 0.5508 (mpp) REVERT: E 68 PHE cc_start: 0.4044 (OUTLIER) cc_final: 0.3422 (t80) REVERT: E 175 TYR cc_start: 0.7131 (t80) cc_final: 0.6421 (t80) REVERT: E 228 THR cc_start: 0.5780 (m) cc_final: 0.5518 (m) REVERT: E 231 MET cc_start: 0.0990 (mmt) cc_final: -0.0010 (mmt) REVERT: F 569 MET cc_start: 0.7156 (ptp) cc_final: 0.6451 (mtm) REVERT: F 722 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: F 763 LYS cc_start: 0.5146 (tptt) cc_final: 0.4296 (mtmm) REVERT: F 979 HIS cc_start: 0.7508 (OUTLIER) cc_final: 0.6683 (m-70) REVERT: H 445 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8800 (mm) REVERT: H 519 MET cc_start: 0.6850 (tmm) cc_final: 0.6464 (tmm) outliers start: 97 outliers final: 57 residues processed: 297 average time/residue: 0.1905 time to fit residues: 98.1290 Evaluate side-chains 267 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 198 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 613 ARG Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 683 LYS Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 603 VAL Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 722 PHE Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 979 HIS Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 558 LEU Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 673 ILE Chi-restraints excluded: chain H residue 684 ILE Chi-restraints excluded: chain H residue 726 VAL Chi-restraints excluded: chain H residue 764 CYS Chi-restraints excluded: chain H residue 810 HIS Chi-restraints excluded: chain H residue 883 GLU Chi-restraints excluded: chain H residue 930 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 24 optimal weight: 8.9990 chunk 290 optimal weight: 3.9990 chunk 379 optimal weight: 9.9990 chunk 420 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 302 optimal weight: 3.9990 chunk 205 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 228 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 782 GLN A 961 ASN D 487 GLN ** D 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 829 GLN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 829 GLN H 477 ASN H 536 GLN H 654 ASN H 711 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.065306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.050543 restraints weight = 216233.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.052407 restraints weight = 123399.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.052636 restraints weight = 70671.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.053020 restraints weight = 62301.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.053098 restraints weight = 55253.788| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 37739 Z= 0.241 Angle : 0.608 15.227 50864 Z= 0.318 Chirality : 0.041 0.165 5411 Planarity : 0.004 0.067 6518 Dihedral : 4.133 24.823 4891 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.28 % Favored : 94.70 % Rotamer: Outliers : 2.86 % Allowed : 20.81 % Favored : 76.33 % 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 aren not related in a simple way. whole: -0.10 (0.13), residues: 4435 helix: 0.85 (0.11), residues: 2359 sheet: -2.13 (0.32), residues: 249 loop : -0.91 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 15 TYR 0.027 0.002 TYR A1003 PHE 0.019 0.002 PHE D 174 TRP 0.041 0.002 TRP E 72 HIS 0.010 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00511 (37739) covalent geometry : angle 0.60836 (50864) hydrogen bonds : bond 0.03639 ( 1583) hydrogen bonds : angle 4.63391 ( 4530) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 203 time to evaluate : 1.593 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: A 118 HIS cc_start: 0.8516 (OUTLIER) cc_final: 0.8223 (m90) REVERT: A 204 MET cc_start: 0.9093 (tmm) cc_final: 0.8344 (tmm) REVERT: A 227 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8308 (mpp) REVERT: A 279 GLU cc_start: 0.8653 (pm20) cc_final: 0.8161 (mm-30) REVERT: A 499 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7735 (p) REVERT: A 631 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8406 (mp) REVERT: B 39 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.4844 (mp0) REVERT: B 177 THR cc_start: 0.5903 (OUTLIER) cc_final: 0.5604 (p) REVERT: B 205 GLU cc_start: 0.7563 (pp20) cc_final: 0.7131 (pp20) REVERT: C 62 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8526 (p) REVERT: D 80 SER cc_start: 0.8051 (OUTLIER) cc_final: 0.7827 (p) REVERT: D 135 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: D 683 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8845 (ttpp) REVERT: D 936 MET cc_start: 0.5753 (tpp) cc_final: 0.5468 (tpp) REVERT: E 175 TYR cc_start: 0.7171 (t80) cc_final: 0.6362 (t80) REVERT: E 228 THR cc_start: 0.5730 (m) cc_final: 0.5487 (m) REVERT: F 396 MET cc_start: 0.7685 (ttt) cc_final: 0.7049 (tmm) REVERT: F 763 LYS cc_start: 0.5220 (tptt) cc_final: 0.4268 (mtmm) REVERT: F 976 MET cc_start: 0.3889 (mmm) cc_final: 0.3671 (mmm) REVERT: F 979 HIS cc_start: 0.7165 (OUTLIER) cc_final: 0.6386 (m-70) REVERT: H 445 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8963 (mm) REVERT: H 519 MET cc_start: 0.7048 (tmm) cc_final: 0.6677 (tmm) outliers start: 116 outliers final: 68 residues processed: 304 average time/residue: 0.2175 time to fit residues: 114.3501 Evaluate side-chains 271 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 191 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 683 LYS Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 722 PHE Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 814 ASN Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 866 MET Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 979 HIS Chi-restraints excluded: chain F residue 1004 PHE Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 547 ASP Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 558 LEU Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 673 ILE Chi-restraints excluded: chain H residue 684 ILE Chi-restraints excluded: chain H residue 726 VAL Chi-restraints excluded: chain H residue 764 CYS Chi-restraints excluded: chain H residue 810 HIS Chi-restraints excluded: chain H residue 824 THR Chi-restraints excluded: chain H residue 883 GLU Chi-restraints excluded: chain H residue 1004 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 290 optimal weight: 20.0000 chunk 284 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 246 optimal weight: 0.8980 chunk 8 optimal weight: 0.0170 chunk 55 optimal weight: 9.9990 chunk 252 optimal weight: 1.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 415 HIS H 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.067667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.051573 restraints weight = 210890.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.053366 restraints weight = 131854.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.053613 restraints weight = 81961.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.053998 restraints weight = 71537.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.054122 restraints weight = 63346.226| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 37739 Z= 0.109 Angle : 0.544 15.207 50864 Z= 0.274 Chirality : 0.039 0.173 5411 Planarity : 0.003 0.049 6518 Dihedral : 3.964 23.910 4891 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.17 % Favored : 95.81 % Rotamer: Outliers : 2.05 % Allowed : 21.43 % Favored : 76.52 % 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 aren not related in a simple way. whole: 0.05 (0.13), residues: 4435 helix: 1.00 (0.11), residues: 2347 sheet: -2.09 (0.33), residues: 233 loop : -0.88 (0.15), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 15 TYR 0.029 0.001 TYR A 755 PHE 0.026 0.001 PHE B 220 TRP 0.009 0.001 TRP E 72 HIS 0.008 0.001 HIS F 658 Details of bonding type rmsd covalent geometry : bond 0.00238 (37739) covalent geometry : angle 0.54366 (50864) hydrogen bonds : bond 0.03168 ( 1583) hydrogen bonds : angle 4.42682 ( 4530) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 207 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 HIS cc_start: 0.8468 (OUTLIER) cc_final: 0.8149 (m90) REVERT: A 204 MET cc_start: 0.9068 (tmm) cc_final: 0.8349 (tmm) REVERT: A 227 MET cc_start: 0.8876 (mpp) cc_final: 0.8428 (mpp) REVERT: A 279 GLU cc_start: 0.8818 (pm20) cc_final: 0.8283 (mm-30) REVERT: A 613 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8116 (ttm170) REVERT: B 39 GLU cc_start: 0.5728 (OUTLIER) cc_final: 0.4700 (mp0) REVERT: B 177 THR cc_start: 0.5600 (OUTLIER) cc_final: 0.5307 (p) REVERT: B 205 GLU cc_start: 0.7498 (pp20) cc_final: 0.6995 (pp20) REVERT: C 62 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8492 (p) REVERT: D 80 SER cc_start: 0.8197 (OUTLIER) cc_final: 0.7994 (p) REVERT: D 135 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7835 (m-30) REVERT: D 683 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8803 (ttpp) REVERT: D 784 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8429 (mt-10) REVERT: D 936 MET cc_start: 0.5801 (tpp) cc_final: 0.5565 (tpp) REVERT: E 68 PHE cc_start: 0.4277 (OUTLIER) cc_final: 0.3679 (t80) REVERT: E 175 TYR cc_start: 0.7103 (t80) cc_final: 0.6221 (t80) REVERT: E 228 THR cc_start: 0.5693 (m) cc_final: 0.5452 (m) REVERT: F 763 LYS cc_start: 0.5358 (tptt) cc_final: 0.4546 (mtmm) REVERT: F 936 MET cc_start: 0.4093 (mtp) cc_final: 0.3862 (mtp) REVERT: F 979 HIS cc_start: 0.7388 (OUTLIER) cc_final: 0.6751 (m-70) REVERT: H 445 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8901 (mm) REVERT: H 519 MET cc_start: 0.6920 (tmm) cc_final: 0.6055 (tmm) outliers start: 83 outliers final: 58 residues processed: 279 average time/residue: 0.2097 time to fit residues: 101.1576 Evaluate side-chains 267 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 198 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 613 ARG Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 683 LYS Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 722 PHE Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 814 ASN Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 866 MET Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 979 HIS Chi-restraints excluded: chain F residue 1004 PHE Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain H residue 134 TYR Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 280 TYR Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 463 ILE Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 673 ILE Chi-restraints excluded: chain H residue 684 ILE Chi-restraints excluded: chain H residue 726 VAL Chi-restraints excluded: chain H residue 764 CYS Chi-restraints excluded: chain H residue 810 HIS Chi-restraints excluded: chain H residue 824 THR Chi-restraints excluded: chain H residue 883 GLU Chi-restraints excluded: chain H residue 930 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 441 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 384 optimal weight: 7.9990 chunk 320 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 409 optimal weight: 0.9980 chunk 350 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 290 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 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 = 0.3865 r_free = 0.3865 target = 0.067102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.052240 restraints weight = 212761.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.054311 restraints weight = 125558.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.054657 restraints weight = 70098.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.054754 restraints weight = 57393.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.054857 restraints weight = 55837.593| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 37739 Z= 0.109 Angle : 0.544 14.996 50864 Z= 0.271 Chirality : 0.039 0.175 5411 Planarity : 0.003 0.048 6518 Dihedral : 3.880 23.963 4891 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.55 % Favored : 95.42 % Rotamer: Outliers : 2.00 % Allowed : 21.78 % Favored : 76.23 % 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 aren not related in a simple way. whole: 0.07 (0.13), residues: 4435 helix: 1.04 (0.11), residues: 2347 sheet: -2.09 (0.32), residues: 243 loop : -0.88 (0.15), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 15 TYR 0.032 0.001 TYR A 755 PHE 0.026 0.001 PHE B 220 TRP 0.009 0.001 TRP A 59 HIS 0.008 0.001 HIS F 658 Details of bonding type rmsd covalent geometry : bond 0.00241 (37739) covalent geometry : angle 0.54439 (50864) hydrogen bonds : bond 0.03065 ( 1583) hydrogen bonds : angle 4.35806 ( 4530) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 208 time to evaluate : 1.317 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: A 118 HIS cc_start: 0.8321 (OUTLIER) cc_final: 0.8102 (m90) REVERT: A 204 MET cc_start: 0.9037 (tmm) cc_final: 0.8334 (tmm) REVERT: A 279 GLU cc_start: 0.8712 (pm20) cc_final: 0.8216 (mm-30) REVERT: A 613 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.8032 (ttm170) REVERT: B 39 GLU cc_start: 0.5755 (OUTLIER) cc_final: 0.4717 (mp0) REVERT: B 177 THR cc_start: 0.5727 (OUTLIER) cc_final: 0.5463 (p) REVERT: B 205 GLU cc_start: 0.7423 (pp20) cc_final: 0.6988 (pp20) REVERT: C 62 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8509 (p) REVERT: D 80 SER cc_start: 0.8019 (OUTLIER) cc_final: 0.7799 (p) REVERT: D 135 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7923 (m-30) REVERT: D 683 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8799 (ttpp) REVERT: D 784 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8441 (mt-10) REVERT: D 936 MET cc_start: 0.5825 (tpp) cc_final: 0.5614 (tpp) REVERT: E 175 TYR cc_start: 0.7247 (t80) cc_final: 0.6305 (t80) REVERT: E 228 THR cc_start: 0.5519 (m) cc_final: 0.5263 (m) REVERT: E 231 MET cc_start: 0.1415 (mmp) cc_final: 0.0980 (mmp) REVERT: F 396 MET cc_start: 0.7426 (ttt) cc_final: 0.6767 (tmm) REVERT: F 763 LYS cc_start: 0.5241 (tptt) cc_final: 0.4441 (mtmm) REVERT: H 445 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8910 (mm) REVERT: H 519 MET cc_start: 0.6972 (tmm) cc_final: 0.6096 (tmm) REVERT: H 951 TYR cc_start: 0.5229 (OUTLIER) cc_final: 0.5021 (m-80) outliers start: 81 outliers final: 59 residues processed: 275 average time/residue: 0.2164 time to fit residues: 102.7118 Evaluate side-chains 273 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 204 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 613 ARG Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 683 LYS Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 722 PHE Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 814 ASN Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 866 MET Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 1004 PHE Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 134 TYR Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 280 TYR Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 673 ILE Chi-restraints excluded: chain H residue 684 ILE Chi-restraints excluded: chain H residue 726 VAL Chi-restraints excluded: chain H residue 764 CYS Chi-restraints excluded: chain H residue 810 HIS Chi-restraints excluded: chain H residue 883 GLU Chi-restraints excluded: chain H residue 930 MET Chi-restraints excluded: chain H residue 951 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 57 optimal weight: 0.9990 chunk 441 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 297 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 407 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 317 optimal weight: 2.9990 chunk 171 optimal weight: 0.0670 chunk 67 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 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 = 0.3905 r_free = 0.3905 target = 0.068855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.053812 restraints weight = 225665.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.056077 restraints weight = 126716.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.056320 restraints weight = 74006.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.056531 restraints weight = 56943.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.056678 restraints weight = 57511.739| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 37739 Z= 0.101 Angle : 0.544 14.965 50864 Z= 0.269 Chirality : 0.039 0.179 5411 Planarity : 0.003 0.048 6518 Dihedral : 3.843 23.593 4891 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.37 % Favored : 95.60 % Rotamer: Outliers : 1.68 % Allowed : 22.12 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.13), residues: 4435 helix: 1.03 (0.11), residues: 2355 sheet: -2.07 (0.32), residues: 243 loop : -0.88 (0.15), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 15 TYR 0.033 0.001 TYR A 755 PHE 0.025 0.001 PHE B 220 TRP 0.009 0.001 TRP A 60 HIS 0.008 0.001 HIS F 658 Details of bonding type rmsd covalent geometry : bond 0.00224 (37739) covalent geometry : angle 0.54350 (50864) hydrogen bonds : bond 0.02982 ( 1583) hydrogen bonds : angle 4.31379 ( 4530) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8870 Ramachandran restraints generated. 4435 Oldfield, 0 Emsley, 4435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 217 time to evaluate : 1.365 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: A 204 MET cc_start: 0.9044 (tmm) cc_final: 0.8345 (tmm) REVERT: A 279 GLU cc_start: 0.8697 (pm20) cc_final: 0.8251 (mm-30) REVERT: A 613 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7933 (ttm170) REVERT: B 39 GLU cc_start: 0.5702 (OUTLIER) cc_final: 0.4664 (mp0) REVERT: B 75 MET cc_start: 0.7748 (pmm) cc_final: 0.7485 (pmm) REVERT: B 177 THR cc_start: 0.5706 (OUTLIER) cc_final: 0.5359 (p) REVERT: B 205 GLU cc_start: 0.7380 (pp20) cc_final: 0.6857 (pp20) REVERT: C 62 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8494 (p) REVERT: D 80 SER cc_start: 0.8035 (OUTLIER) cc_final: 0.7813 (p) REVERT: D 135 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: D 683 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8828 (ttpp) REVERT: D 784 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8478 (mt-10) REVERT: E 175 TYR cc_start: 0.7535 (t80) cc_final: 0.6888 (t80) REVERT: E 228 THR cc_start: 0.5492 (m) cc_final: 0.5257 (m) REVERT: E 231 MET cc_start: 0.2306 (mmp) cc_final: 0.2021 (mmp) REVERT: F 396 MET cc_start: 0.7408 (ttt) cc_final: 0.6692 (tmm) REVERT: F 763 LYS cc_start: 0.5218 (tptt) cc_final: 0.4434 (mtmm) REVERT: H 445 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8903 (mm) REVERT: H 519 MET cc_start: 0.6898 (tmm) cc_final: 0.6028 (tmm) REVERT: H 576 PHE cc_start: 0.7015 (m-80) cc_final: 0.6810 (m-80) outliers start: 68 outliers final: 54 residues processed: 274 average time/residue: 0.2032 time to fit residues: 96.1210 Evaluate side-chains 272 residues out of total 4055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 210 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 613 ARG Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 683 LYS Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 301 PHE Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 658 HIS Chi-restraints excluded: chain F residue 722 PHE Chi-restraints excluded: chain F residue 807 LEU Chi-restraints excluded: chain F residue 823 ILE Chi-restraints excluded: chain F residue 866 MET Chi-restraints excluded: chain F residue 955 ILE Chi-restraints excluded: chain F residue 1004 PHE Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 134 TYR Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 399 ASP Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 463 ILE Chi-restraints excluded: chain H residue 636 PHE Chi-restraints excluded: chain H residue 673 ILE Chi-restraints excluded: chain H residue 684 ILE Chi-restraints excluded: chain H residue 726 VAL Chi-restraints excluded: chain H residue 810 HIS Chi-restraints excluded: chain H residue 883 GLU Chi-restraints excluded: chain H residue 930 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 249 optimal weight: 8.9990 chunk 386 optimal weight: 6.9990 chunk 368 optimal weight: 0.9980 chunk 349 optimal weight: 2.9990 chunk 283 optimal weight: 0.9980 chunk 290 optimal weight: 30.0000 chunk 392 optimal weight: 3.9990 chunk 336 optimal weight: 0.9980 chunk 294 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 370 optimal weight: 0.9980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 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 = 0.3859 r_free = 0.3859 target = 0.066780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.051986 restraints weight = 211699.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.053840 restraints weight = 126259.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.054437 restraints weight = 71024.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.054658 restraints weight = 56155.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.054768 restraints weight = 53033.461| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37739 Z= 0.123 Angle : 0.554 15.838 50864 Z= 0.275 Chirality : 0.039 0.162 5411 Planarity : 0.003 0.047 6518 Dihedral : 3.845 23.770 4891 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.98 % Favored : 94.99 % Rotamer: Outliers : 1.78 % Allowed : 21.97 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.13), residues: 4435 helix: 1.08 (0.11), residues: 2347 sheet: -2.09 (0.32), residues: 243 loop : -0.86 (0.15), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 15 TYR 0.032 0.001 TYR A 755 PHE 0.023 0.001 PHE B 220 TRP 0.011 0.001 TRP A 59 HIS 0.007 0.001 HIS F 658 Details of bonding type rmsd covalent geometry : bond 0.00272 (37739) covalent geometry : angle 0.55383 (50864) hydrogen bonds : bond 0.03014 ( 1583) hydrogen bonds : angle 4.31118 ( 4530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6228.57 seconds wall clock time: 109 minutes 15.29 seconds (6555.29 seconds total)