Starting phenix.real_space_refine on Sun Aug 24 18:20:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wkt_37607/08_2025/8wkt_37607.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wkt_37607/08_2025/8wkt_37607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wkt_37607/08_2025/8wkt_37607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wkt_37607/08_2025/8wkt_37607.map" model { file = "/net/cci-nas-00/data/ceres_data/8wkt_37607/08_2025/8wkt_37607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wkt_37607/08_2025/8wkt_37607.cif" } resolution = 3.86 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 81 5.16 5 C 14203 2.51 5 N 3548 2.21 5 O 4112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 139 residue(s): 0.02s 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: 21944 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 8264 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 19, 'TRANS': 972} Chain: "B" Number of atoms: 8115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 8115 Classifications: {'peptide': 972} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 952} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 900 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "D" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2330 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "E" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2335 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Time building chain proxies: 5.03, per 1000 atoms: 0.23 Number of scatterers: 21944 At special positions: 0 Unit cell: (99.84, 128.96, 185.12, 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 81 16.00 O 4112 8.00 N 3548 7.00 C 14203 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 908.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5034 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 8 sheets defined 63.3% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 removed outlier: 3.642A pdb=" N LEU A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 50 through 54 removed outlier: 3.914A pdb=" N SER A 54 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.916A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 108 removed outlier: 3.756A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.650A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.915A pdb=" N VAL A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.539A pdb=" N ARG A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.823A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 322 removed outlier: 3.791A pdb=" N ILE A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) Proline residue: A 318 - end of helix removed outlier: 4.109A pdb=" N ALA A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU A 322 " --> pdb=" O PRO A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 355 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 376 through 391 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.563A pdb=" N ASP A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 494 Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.862A pdb=" N LEU A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 500 " --> pdb=" O GLY A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 520 Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.675A pdb=" N GLU A 543 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP A 547 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 572 removed outlier: 3.698A pdb=" N TYR A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 553 " --> pdb=" O GLN A 549 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP A 554 " --> pdb=" O PHE A 550 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS A 557 " --> pdb=" O ASP A 553 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 561 " --> pdb=" O LYS A 557 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN A 563 " --> pdb=" O PHE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 583 removed outlier: 3.555A pdb=" N ILE A 582 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 583 " --> pdb=" O SER A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 579 through 583' Processing helix chain 'A' and resid 584 through 598 removed outlier: 3.545A pdb=" N TYR A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG A 593 " --> pdb=" O TYR A 589 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.680A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 660 through 669 Processing helix chain 'A' and resid 670 through 671 No H-bonds generated for 'chain 'A' and resid 670 through 671' Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 699 Processing helix chain 'A' and resid 711 through 722 removed outlier: 3.554A pdb=" N LEU A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 750 through 762 Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.611A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 825 Processing helix chain 'A' and resid 832 through 841 Processing helix chain 'A' and resid 846 through 855 removed outlier: 3.612A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 870 removed outlier: 4.129A pdb=" N ARG A 870 " --> pdb=" O MET A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 903 Processing helix chain 'A' and resid 912 through 921 removed outlier: 4.197A pdb=" N TRP A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 934 removed outlier: 3.954A pdb=" N MET A 930 " --> pdb=" O ASN A 927 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 957 through 962 removed outlier: 4.242A pdb=" N TYR A 962 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 972 Processing helix chain 'A' and resid 973 through 990 removed outlier: 3.941A pdb=" N LYS A 977 " --> pdb=" O ASN A 973 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS A 978 " --> pdb=" O LYS A 974 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N HIS A 979 " --> pdb=" O HIS A 975 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU A 982 " --> pdb=" O HIS A 978 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 983 " --> pdb=" O HIS A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1003 removed outlier: 3.508A pdb=" N GLU A 998 " --> pdb=" O LYS A 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 20 removed outlier: 4.588A pdb=" N GLY B 12 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 38 Processing helix chain 'B' and resid 47 through 53 removed outlier: 4.141A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.592A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.560A pdb=" N ARG B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 97 through 109 removed outlier: 4.030A pdb=" N PHE B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.915A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.594A pdb=" N TYR B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 222 through 236 removed outlier: 3.693A pdb=" N TRP B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.878A pdb=" N ILE B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 275' Processing helix chain 'B' and resid 281 through 298 removed outlier: 3.899A pdb=" N VAL B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.644A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.732A pdb=" N VAL B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 329 through 334' Processing helix chain 'B' and resid 355 through 366 removed outlier: 3.801A pdb=" N GLU B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 374 through 392 removed outlier: 4.193A pdb=" N GLU B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.743A pdb=" N ALA B 400 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 468 through 490 Processing helix chain 'B' and resid 495 through 500 removed outlier: 4.194A pdb=" N LEU B 498 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 526 through 531 removed outlier: 3.659A pdb=" N MET B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 543 removed outlier: 3.539A pdb=" N GLU B 543 " --> pdb=" O LYS B 540 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 540 through 543' Processing helix chain 'B' and resid 555 through 561 removed outlier: 3.557A pdb=" N LEU B 558 " --> pdb=" O THR B 555 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 561 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 596 removed outlier: 3.650A pdb=" N LEU B 585 " --> pdb=" O ASP B 581 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 595 " --> pdb=" O ASN B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 627 removed outlier: 3.719A pdb=" N TYR B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER B 617 " --> pdb=" O ARG B 613 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 620 " --> pdb=" O MET B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 635 removed outlier: 4.127A pdb=" N GLU B 633 " --> pdb=" O ARG B 629 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY B 635 " --> pdb=" O ILE B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 659 removed outlier: 3.876A pdb=" N ASN B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 701 Processing helix chain 'B' and resid 705 through 723 removed outlier: 3.802A pdb=" N TYR B 709 " --> pdb=" O ASN B 705 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 750 through 762 Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 800 through 812 removed outlier: 4.199A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 Processing helix chain 'B' and resid 831 through 841 Processing helix chain 'B' and resid 842 through 845 Processing helix chain 'B' and resid 846 through 855 removed outlier: 3.991A pdb=" N SER B 855 " --> pdb=" O SER B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'B' and resid 878 through 897 Processing helix chain 'B' and resid 912 through 922 Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.706A pdb=" N LYS B 953 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 962 removed outlier: 3.905A pdb=" N TYR B 962 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 973 through 990 removed outlier: 4.513A pdb=" N HIS B 978 " --> pdb=" O LYS B 974 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS B 979 " --> pdb=" O HIS B 975 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1004 removed outlier: 3.718A pdb=" N LEU B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 101 Processing helix chain 'D' and resid 14 through 22 removed outlier: 3.778A pdb=" N VAL D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 39 removed outlier: 4.022A pdb=" N CYS D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.760A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 97 through 108 removed outlier: 4.112A pdb=" N ILE D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU D 104 " --> pdb=" O PHE D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.635A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 155 through 161 removed outlier: 3.517A pdb=" N VAL D 158 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA D 161 " --> pdb=" O VAL D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 222 through 234 Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.657A pdb=" N ARG D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 22 removed outlier: 4.298A pdb=" N PHE E 19 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET E 21 " --> pdb=" O GLU E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 40 Processing helix chain 'E' and resid 47 through 54 removed outlier: 3.954A pdb=" N SER E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 71 removed outlier: 3.801A pdb=" N LEU E 62 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.752A pdb=" N TYR E 84 " --> pdb=" O SER E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 95 removed outlier: 3.519A pdb=" N VAL E 94 " --> pdb=" O ILE E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 109 Processing helix chain 'E' and resid 115 through 124 removed outlier: 3.589A pdb=" N ASP E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 146 Processing helix chain 'E' and resid 155 through 160 removed outlier: 4.479A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN E 160 " --> pdb=" O GLU E 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 155 through 160' Processing helix chain 'E' and resid 187 through 192 Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 222 through 234 removed outlier: 3.938A pdb=" N LYS E 234 " --> pdb=" O ASN E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 240 removed outlier: 3.576A pdb=" N PHE E 240 " --> pdb=" O LYS E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 263 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 296 removed outlier: 4.008A pdb=" N ARG E 285 " --> pdb=" O ASP E 281 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER E 296 " --> pdb=" O LEU E 292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.100A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A 42 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ILE A 130 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (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 'A' and resid 573 through 575 removed outlier: 3.959A pdb=" N THR C 22 " --> pdb=" O HIS C 17 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N PHE C 23 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.169A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU B 42 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE B 130 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE B 44 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA6, first strand: chain 'C' and resid 65 through 67 removed outlier: 4.048A pdb=" N LYS C 41 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N PHE C 29 " --> pdb=" O LYS C 41 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.483A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 129 " --> pdb=" O TYR D 166 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU D 42 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE D 130 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE D 216 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY D 217 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 150 through 152 removed outlier: 6.412A pdb=" N SER E 150 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS E 169 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE E 152 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS E 128 " --> pdb=" O LEU E 42 " (cutoff:3.500A) 1028 hydrogen bonds defined for protein. 2949 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: 3.33 Time building geometry restraints manager: 2.27 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: 6936 1.34 - 1.46: 5202 1.46 - 1.58: 10186 1.58 - 1.70: 0 1.70 - 1.83: 135 Bond restraints: 22459 Sorted by residual: bond pdb=" N GLN B 323 " pdb=" CA GLN B 323 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.23e-02 6.61e+03 1.59e+01 bond pdb=" N ILE B 862 " pdb=" CA ILE B 862 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.06e-02 8.90e+03 1.41e+01 bond pdb=" N TYR B 324 " pdb=" CA TYR B 324 " ideal model delta sigma weight residual 1.456 1.504 -0.047 1.27e-02 6.20e+03 1.39e+01 bond pdb=" N VAL B 603 " pdb=" CA VAL B 603 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.07e-02 8.73e+03 1.17e+01 bond pdb=" N ILE B 934 " pdb=" CA ILE B 934 " ideal model delta sigma weight residual 1.455 1.495 -0.039 1.18e-02 7.18e+03 1.12e+01 ... (remaining 22454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 29919 2.42 - 4.84: 331 4.84 - 7.26: 36 7.26 - 9.68: 4 9.68 - 12.09: 2 Bond angle restraints: 30292 Sorted by residual: angle pdb=" N VAL D 50 " pdb=" CA VAL D 50 " pdb=" C VAL D 50 " ideal model delta sigma weight residual 113.43 107.04 6.39 1.09e+00 8.42e-01 3.43e+01 angle pdb=" N ILE A 582 " pdb=" CA ILE A 582 " pdb=" C ILE A 582 " ideal model delta sigma weight residual 113.53 108.58 4.95 9.80e-01 1.04e+00 2.55e+01 angle pdb=" C ASN B 861 " pdb=" CA ASN B 861 " pdb=" CB ASN B 861 " ideal model delta sigma weight residual 116.54 110.88 5.66 1.15e+00 7.56e-01 2.42e+01 angle pdb=" N ASP A 590 " pdb=" CA ASP A 590 " pdb=" C ASP A 590 " ideal model delta sigma weight residual 112.93 107.06 5.87 1.33e+00 5.65e-01 1.95e+01 angle pdb=" CB LYS A 540 " pdb=" CG LYS A 540 " pdb=" CD LYS A 540 " ideal model delta sigma weight residual 111.30 121.03 -9.73 2.30e+00 1.89e-01 1.79e+01 ... (remaining 30287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 11165 17.87 - 35.73: 1677 35.73 - 53.60: 434 53.60 - 71.46: 76 71.46 - 89.33: 25 Dihedral angle restraints: 13377 sinusoidal: 5538 harmonic: 7839 Sorted by residual: dihedral pdb=" CA PHE A 107 " pdb=" C PHE A 107 " pdb=" N PHE A 108 " pdb=" CA PHE A 108 " ideal model delta harmonic sigma weight residual -180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ILE A 871 " pdb=" C ILE A 871 " pdb=" N GLY A 872 " pdb=" CA GLY A 872 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA PRO E 74 " pdb=" C PRO E 74 " pdb=" N LYS E 75 " pdb=" CA LYS E 75 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 13374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2301 0.043 - 0.085: 755 0.085 - 0.128: 150 0.128 - 0.171: 20 0.171 - 0.213: 6 Chirality restraints: 3232 Sorted by residual: chirality pdb=" CG LEU E 266 " pdb=" CB LEU E 266 " pdb=" CD1 LEU E 266 " pdb=" CD2 LEU E 266 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA LEU A 841 " pdb=" N LEU A 841 " pdb=" C LEU A 841 " pdb=" CB LEU A 841 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE A 695 " pdb=" CA ILE A 695 " pdb=" CG1 ILE A 695 " pdb=" CG2 ILE A 695 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.32e-01 ... (remaining 3229 not shown) Planarity restraints: 3864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 73 " -0.077 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO A 74 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 52 " 0.236 9.50e-02 1.11e+02 1.06e-01 6.86e+00 pdb=" NE ARG C 52 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 52 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 52 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 52 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 933 " 0.011 2.00e-02 2.50e+03 1.62e-02 4.59e+00 pdb=" CG PHE B 933 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 933 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 933 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE B 933 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 933 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 933 " 0.002 2.00e-02 2.50e+03 ... (remaining 3861 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1778 2.74 - 3.28: 22665 3.28 - 3.82: 36880 3.82 - 4.36: 42342 4.36 - 4.90: 72983 Nonbonded interactions: 176648 Sorted by model distance: nonbonded pdb=" OH TYR A 687 " pdb=" OE2 GLU A 715 " model vdw 2.197 3.040 nonbonded pdb=" OE2 GLU B 730 " pdb=" OG SER B 770 " model vdw 2.214 3.040 nonbonded pdb=" OG1 THR B 257 " pdb=" OH TYR E 71 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR B 414 " pdb=" OD1 ASN B 654 " model vdw 2.219 3.040 nonbonded pdb=" OD2 ASP D 249 " pdb=" OG SER D 251 " model vdw 2.222 3.040 ... (remaining 176643 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 565 or (resid 580 and (name N or name CA or nam \ e C or name O or name CB )) or resid 581 through 897 or resid 911 through 1005)) \ selection = (chain 'B' and resid 14 through 1005) } ncs_group { reference = (chain 'D' and resid 13 through 296) selection = (chain 'E' and resid 13 through 296) } 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: 16.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.320 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 22459 Z= 0.215 Angle : 0.632 12.094 30292 Z= 0.371 Chirality : 0.043 0.213 3232 Planarity : 0.004 0.113 3864 Dihedral : 18.080 89.330 8343 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.62 % Allowed : 26.37 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.40 (0.16), residues: 2630 helix: 0.57 (0.14), residues: 1455 sheet: -1.79 (0.47), residues: 100 loop : -1.22 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 233 TYR 0.020 0.001 TYR B 625 PHE 0.036 0.001 PHE B 933 TRP 0.026 0.002 TRP B 143 HIS 0.007 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00392 (22459) covalent geometry : angle 0.63216 (30292) hydrogen bonds : bond 0.16808 ( 1028) hydrogen bonds : angle 6.03659 ( 2949) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 363 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6704 (m-10) cc_final: 0.6380 (m-10) REVERT: A 208 ILE cc_start: 0.8870 (mt) cc_final: 0.8538 (mt) REVERT: B 10 ARG cc_start: 0.8320 (mmp-170) cc_final: 0.7726 (ttt180) REVERT: B 14 LYS cc_start: 0.7942 (tttt) cc_final: 0.7464 (mmtp) REVERT: B 396 MET cc_start: 0.8315 (mmm) cc_final: 0.7828 (mmm) REVERT: B 662 ASP cc_start: 0.8530 (p0) cc_final: 0.7957 (t0) REVERT: C 12 HIS cc_start: 0.7766 (p-80) cc_final: 0.7517 (p-80) REVERT: C 74 LEU cc_start: 0.8042 (mp) cc_final: 0.7436 (tp) REVERT: C 120 ASP cc_start: 0.7908 (m-30) cc_final: 0.7073 (t0) REVERT: D 28 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8946 (tp30) REVERT: D 32 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8772 (mm-30) REVERT: D 122 LEU cc_start: 0.8988 (mt) cc_final: 0.8624 (mp) REVERT: E 27 VAL cc_start: 0.8686 (t) cc_final: 0.8396 (t) REVERT: E 268 ILE cc_start: 0.9131 (mm) cc_final: 0.8683 (tp) outliers start: 15 outliers final: 4 residues processed: 373 average time/residue: 0.1467 time to fit residues: 83.4636 Evaluate side-chains 179 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 175 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain E residue 134 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.0270 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.0980 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN B 349 HIS ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN C 80 ASN D 118 HIS ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.056494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.044302 restraints weight = 123317.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.045865 restraints weight = 70089.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.046955 restraints weight = 47874.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.047705 restraints weight = 36572.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.048218 restraints weight = 30186.724| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22459 Z= 0.127 Angle : 0.575 11.141 30292 Z= 0.296 Chirality : 0.041 0.199 3232 Planarity : 0.004 0.076 3864 Dihedral : 4.274 52.239 2914 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.27 % Allowed : 26.12 % Favored : 71.61 % 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: -0.23 (0.17), residues: 2630 helix: 0.68 (0.14), residues: 1493 sheet: -1.77 (0.47), residues: 108 loop : -1.13 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 247 TYR 0.011 0.001 TYR B 962 PHE 0.015 0.001 PHE B 943 TRP 0.010 0.001 TRP D 60 HIS 0.006 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00278 (22459) covalent geometry : angle 0.57545 (30292) hydrogen bonds : bond 0.03889 ( 1028) hydrogen bonds : angle 4.55316 ( 2949) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ILE cc_start: 0.8940 (mt) cc_final: 0.8652 (mm) REVERT: A 421 MET cc_start: 0.9324 (ptp) cc_final: 0.9020 (ptp) REVERT: A 647 MET cc_start: 0.8549 (mtp) cc_final: 0.8303 (mtp) REVERT: A 913 MET cc_start: 0.8590 (tpp) cc_final: 0.8174 (tpp) REVERT: A 936 MET cc_start: 0.6040 (mmm) cc_final: 0.5542 (tpt) REVERT: A 976 MET cc_start: 0.8594 (mmm) cc_final: 0.8322 (mmm) REVERT: B 10 ARG cc_start: 0.8426 (mmp-170) cc_final: 0.7708 (ttt180) REVERT: B 14 LYS cc_start: 0.7786 (ttpt) cc_final: 0.7444 (mmtp) REVERT: B 124 MET cc_start: 0.8612 (mmt) cc_final: 0.8368 (mmm) REVERT: B 531 MET cc_start: 0.9331 (mmm) cc_final: 0.9002 (mmm) REVERT: B 662 ASP cc_start: 0.8530 (p0) cc_final: 0.7982 (t0) REVERT: B 938 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7730 (p0) REVERT: B 1001 MET cc_start: 0.9222 (mtp) cc_final: 0.8923 (mpp) REVERT: C 12 HIS cc_start: 0.8185 (p-80) cc_final: 0.7912 (p-80) REVERT: C 29 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7802 (p90) REVERT: C 74 LEU cc_start: 0.8302 (mp) cc_final: 0.7675 (tp) REVERT: C 88 HIS cc_start: 0.7728 (t70) cc_final: 0.7123 (t70) REVERT: C 115 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7841 (tm-30) REVERT: C 120 ASP cc_start: 0.8260 (m-30) cc_final: 0.7475 (t0) REVERT: D 134 TYR cc_start: 0.7562 (OUTLIER) cc_final: 0.6492 (m-10) REVERT: E 145 ARG cc_start: 0.8460 (mtp-110) cc_final: 0.7617 (ttp-170) REVERT: E 171 HIS cc_start: 0.8760 (OUTLIER) cc_final: 0.8395 (m-70) REVERT: E 268 ILE cc_start: 0.9163 (mm) cc_final: 0.8899 (tp) REVERT: E 290 MET cc_start: 0.9462 (mmm) cc_final: 0.9180 (mtm) REVERT: E 294 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8593 (mm) outliers start: 55 outliers final: 17 residues processed: 233 average time/residue: 0.1329 time to fit residues: 48.6817 Evaluate side-chains 168 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 171 HIS Chi-restraints excluded: chain E residue 294 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 224 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 chunk 201 optimal weight: 0.0040 chunk 166 optimal weight: 3.9990 chunk 140 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 391 ASN B 834 GLN ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 115 ASN E 118 HIS E 171 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.055884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.043713 restraints weight = 123306.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.045241 restraints weight = 69922.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.046309 restraints weight = 47799.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.047040 restraints weight = 36598.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.047491 restraints weight = 30348.220| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22459 Z= 0.109 Angle : 0.522 8.680 30292 Z= 0.266 Chirality : 0.040 0.189 3232 Planarity : 0.003 0.059 3864 Dihedral : 4.024 40.281 2910 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.52 % Allowed : 25.22 % Favored : 72.27 % 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: -0.08 (0.17), residues: 2630 helix: 0.84 (0.14), residues: 1493 sheet: -1.60 (0.50), residues: 97 loop : -1.17 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 61 TYR 0.010 0.001 TYR B 134 PHE 0.018 0.001 PHE B 301 TRP 0.014 0.001 TRP B 231 HIS 0.011 0.001 HIS E 171 Details of bonding type rmsd covalent geometry : bond 0.00234 (22459) covalent geometry : angle 0.52180 (30292) hydrogen bonds : bond 0.03395 ( 1028) hydrogen bonds : angle 4.26730 ( 2949) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 153 time to evaluate : 0.884 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: A 124 MET cc_start: 0.8300 (mmt) cc_final: 0.7923 (mmt) REVERT: A 208 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8728 (mm) REVERT: A 229 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9406 (mm) REVERT: A 421 MET cc_start: 0.9313 (ptp) cc_final: 0.8774 (ttp) REVERT: A 569 MET cc_start: 0.8401 (tpp) cc_final: 0.8057 (mmm) REVERT: A 913 MET cc_start: 0.8618 (tpp) cc_final: 0.8226 (tpp) REVERT: A 976 MET cc_start: 0.8589 (mmm) cc_final: 0.8314 (mmm) REVERT: B 10 ARG cc_start: 0.8451 (mmp-170) cc_final: 0.7721 (ttt180) REVERT: B 14 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7427 (mmtp) REVERT: B 227 MET cc_start: 0.8583 (mmm) cc_final: 0.8308 (mmm) REVERT: B 519 MET cc_start: 0.8910 (tpp) cc_final: 0.8550 (mmt) REVERT: B 531 MET cc_start: 0.9373 (mmm) cc_final: 0.9075 (mmm) REVERT: B 647 MET cc_start: 0.9060 (mmm) cc_final: 0.8423 (mmm) REVERT: B 662 ASP cc_start: 0.8482 (p0) cc_final: 0.7956 (t0) REVERT: B 1001 MET cc_start: 0.9176 (mtp) cc_final: 0.8942 (mtt) REVERT: C 12 HIS cc_start: 0.8242 (p-80) cc_final: 0.7973 (p-80) REVERT: C 26 ASP cc_start: 0.8567 (t0) cc_final: 0.8168 (p0) REVERT: C 29 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7798 (p90) REVERT: C 72 ARG cc_start: 0.7686 (mmm160) cc_final: 0.7138 (mmm160) REVERT: C 74 LEU cc_start: 0.8456 (mp) cc_final: 0.7742 (tp) REVERT: C 76 GLU cc_start: 0.6404 (tt0) cc_final: 0.6003 (tp30) REVERT: C 88 HIS cc_start: 0.7785 (t70) cc_final: 0.7104 (t70) REVERT: C 115 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7603 (tm-30) REVERT: D 21 MET cc_start: 0.7754 (ppp) cc_final: 0.7422 (ppp) REVERT: D 134 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.6539 (m-10) REVERT: D 165 ARG cc_start: 0.8417 (ptp90) cc_final: 0.8144 (ptp90) REVERT: E 82 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7849 (p0) REVERT: E 124 MET cc_start: 0.8705 (mmm) cc_final: 0.8438 (mmm) REVERT: E 145 ARG cc_start: 0.8452 (mtp-110) cc_final: 0.7898 (tmm-80) REVERT: E 171 HIS cc_start: 0.8890 (OUTLIER) cc_final: 0.8555 (m-70) REVERT: E 297 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7554 (pm20) outliers start: 61 outliers final: 24 residues processed: 206 average time/residue: 0.1348 time to fit residues: 44.5827 Evaluate side-chains 170 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 171 HIS Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 297 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 179 optimal weight: 3.9990 chunk 249 optimal weight: 0.1980 chunk 44 optimal weight: 0.9990 chunk 246 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 160 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 391 ASN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS E 118 HIS E 171 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.055424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.043345 restraints weight = 123456.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.044863 restraints weight = 69881.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.045927 restraints weight = 47730.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.046645 restraints weight = 36522.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.047097 restraints weight = 30306.176| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22459 Z= 0.104 Angle : 0.498 8.626 30292 Z= 0.254 Chirality : 0.040 0.298 3232 Planarity : 0.003 0.058 3864 Dihedral : 3.946 41.263 2910 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.48 % Allowed : 24.72 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.08 (0.17), residues: 2630 helix: 0.98 (0.14), residues: 1498 sheet: -2.00 (0.51), residues: 87 loop : -1.08 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 61 TYR 0.014 0.001 TYR B 71 PHE 0.012 0.001 PHE B 301 TRP 0.032 0.001 TRP B 143 HIS 0.012 0.001 HIS E 171 Details of bonding type rmsd covalent geometry : bond 0.00229 (22459) covalent geometry : angle 0.49840 (30292) hydrogen bonds : bond 0.03077 ( 1028) hydrogen bonds : angle 4.11039 ( 2949) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 147 time to evaluate : 1.009 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 124 MET cc_start: 0.8267 (mmt) cc_final: 0.7858 (mmm) REVERT: A 208 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8699 (mm) REVERT: A 421 MET cc_start: 0.9272 (ptp) cc_final: 0.9034 (ptp) REVERT: A 445 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9201 (mm) REVERT: A 913 MET cc_start: 0.8613 (tpp) cc_final: 0.8231 (tpp) REVERT: B 10 ARG cc_start: 0.8419 (mmp-170) cc_final: 0.7704 (ttt180) REVERT: B 14 LYS cc_start: 0.7794 (ttpt) cc_final: 0.7423 (mmtp) REVERT: B 124 MET cc_start: 0.9191 (mmm) cc_final: 0.8697 (mmm) REVERT: B 531 MET cc_start: 0.9427 (mmm) cc_final: 0.9219 (mmm) REVERT: B 662 ASP cc_start: 0.8506 (p0) cc_final: 0.7951 (t0) REVERT: B 977 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8185 (tptm) REVERT: B 1001 MET cc_start: 0.9161 (mtp) cc_final: 0.8921 (mtt) REVERT: C 12 HIS cc_start: 0.8162 (p-80) cc_final: 0.7878 (p-80) REVERT: C 26 ASP cc_start: 0.8587 (t0) cc_final: 0.8100 (p0) REVERT: C 29 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7914 (p90) REVERT: C 41 LYS cc_start: 0.9059 (mtmm) cc_final: 0.8774 (mmtt) REVERT: C 72 ARG cc_start: 0.7600 (mmm160) cc_final: 0.7057 (mmm160) REVERT: C 74 LEU cc_start: 0.8456 (mp) cc_final: 0.7715 (tp) REVERT: C 76 GLU cc_start: 0.6527 (tt0) cc_final: 0.6119 (tp30) REVERT: C 88 HIS cc_start: 0.7737 (t70) cc_final: 0.6904 (t70) REVERT: C 98 ILE cc_start: 0.8977 (mp) cc_final: 0.8366 (tp) REVERT: C 115 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7395 (tm-30) REVERT: D 134 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.6457 (m-10) REVERT: D 165 ARG cc_start: 0.8307 (ptp90) cc_final: 0.8061 (ptp90) REVERT: E 82 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7770 (p0) REVERT: E 124 MET cc_start: 0.8834 (mmm) cc_final: 0.8414 (mmm) REVERT: E 145 ARG cc_start: 0.8406 (mtp-110) cc_final: 0.7993 (tmm-80) REVERT: E 171 HIS cc_start: 0.8989 (OUTLIER) cc_final: 0.8734 (m-70) outliers start: 60 outliers final: 29 residues processed: 201 average time/residue: 0.1396 time to fit residues: 44.8356 Evaluate side-chains 171 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 977 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 171 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 164 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 56 optimal weight: 0.0060 chunk 140 optimal weight: 0.6980 chunk 237 optimal weight: 0.0770 chunk 155 optimal weight: 0.0670 chunk 24 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 173 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 overall best weight: 0.3092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 563 ASN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS D 224 ASN E 118 HIS E 171 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.055702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.043705 restraints weight = 121234.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.045275 restraints weight = 68102.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.046342 restraints weight = 46207.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.047037 restraints weight = 35240.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.047555 restraints weight = 29246.249| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22459 Z= 0.093 Angle : 0.497 11.012 30292 Z= 0.250 Chirality : 0.039 0.192 3232 Planarity : 0.003 0.057 3864 Dihedral : 3.915 41.857 2910 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.06 % Allowed : 25.51 % Favored : 72.43 % 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: 0.21 (0.17), residues: 2630 helix: 1.10 (0.14), residues: 1485 sheet: -1.77 (0.46), residues: 109 loop : -1.02 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 61 TYR 0.013 0.001 TYR A 223 PHE 0.010 0.001 PHE C 79 TRP 0.041 0.001 TRP B 143 HIS 0.004 0.000 HIS E 171 Details of bonding type rmsd covalent geometry : bond 0.00201 (22459) covalent geometry : angle 0.49667 (30292) hydrogen bonds : bond 0.02959 ( 1028) hydrogen bonds : angle 4.08829 ( 2949) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8261 (mmt) cc_final: 0.7832 (mmm) REVERT: A 421 MET cc_start: 0.9222 (ptp) cc_final: 0.8810 (ptm) REVERT: A 445 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9165 (mm) REVERT: A 526 ASP cc_start: 0.9286 (t0) cc_final: 0.8933 (t0) REVERT: A 571 GLU cc_start: 0.8697 (tt0) cc_final: 0.8182 (mm-30) REVERT: A 874 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7154 (tp) REVERT: A 936 MET cc_start: 0.5692 (mmm) cc_final: 0.5212 (tpt) REVERT: B 10 ARG cc_start: 0.8376 (mmp-170) cc_final: 0.7933 (ttt180) REVERT: B 124 MET cc_start: 0.9273 (mmm) cc_final: 0.8548 (mmm) REVERT: B 227 MET cc_start: 0.8847 (ppp) cc_final: 0.8537 (tmm) REVERT: B 519 MET cc_start: 0.8941 (tpp) cc_final: 0.8710 (mmm) REVERT: B 662 ASP cc_start: 0.8498 (p0) cc_final: 0.7915 (t0) REVERT: B 976 MET cc_start: 0.8826 (ptp) cc_final: 0.8475 (mpp) REVERT: B 1001 MET cc_start: 0.9191 (mtp) cc_final: 0.8926 (mtt) REVERT: C 12 HIS cc_start: 0.8252 (p-80) cc_final: 0.7987 (p-80) REVERT: C 26 ASP cc_start: 0.8611 (t0) cc_final: 0.8090 (p0) REVERT: C 29 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7846 (p90) REVERT: C 41 LYS cc_start: 0.9011 (mtmm) cc_final: 0.8724 (mmtt) REVERT: C 74 LEU cc_start: 0.8461 (mp) cc_final: 0.7746 (tp) REVERT: C 76 GLU cc_start: 0.6545 (tt0) cc_final: 0.6150 (tp30) REVERT: C 88 HIS cc_start: 0.7861 (t70) cc_final: 0.7015 (t70) REVERT: C 115 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7295 (tm-30) REVERT: C 120 ASP cc_start: 0.8169 (m-30) cc_final: 0.7428 (t0) REVERT: D 21 MET cc_start: 0.7723 (ppp) cc_final: 0.7413 (ppp) REVERT: D 134 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6289 (m-10) REVERT: E 82 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7756 (p0) REVERT: E 145 ARG cc_start: 0.8372 (mtp-110) cc_final: 0.7782 (tmm-80) outliers start: 50 outliers final: 23 residues processed: 191 average time/residue: 0.1319 time to fit residues: 41.3360 Evaluate side-chains 158 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 183 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 187 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 166 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN E 118 HIS E 133 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.054218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.042274 restraints weight = 123800.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.043793 restraints weight = 69273.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.044827 restraints weight = 47021.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.045529 restraints weight = 35873.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.046032 restraints weight = 29687.337| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22459 Z= 0.124 Angle : 0.531 17.171 30292 Z= 0.264 Chirality : 0.039 0.165 3232 Planarity : 0.003 0.056 3864 Dihedral : 3.945 41.938 2910 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.19 % Allowed : 25.42 % Favored : 72.39 % 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: 0.37 (0.17), residues: 2630 helix: 1.23 (0.14), residues: 1490 sheet: -1.77 (0.45), residues: 109 loop : -0.95 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 72 TYR 0.012 0.001 TYR B 134 PHE 0.022 0.001 PHE D 19 TRP 0.061 0.001 TRP B 143 HIS 0.006 0.001 HIS E 171 Details of bonding type rmsd covalent geometry : bond 0.00277 (22459) covalent geometry : angle 0.53104 (30292) hydrogen bonds : bond 0.02945 ( 1028) hydrogen bonds : angle 4.04083 ( 2949) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 136 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8222 (mmt) cc_final: 0.7822 (mmm) REVERT: A 204 MET cc_start: 0.9184 (tmm) cc_final: 0.8957 (tmm) REVERT: A 421 MET cc_start: 0.9237 (ptp) cc_final: 0.8845 (ptm) REVERT: A 445 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9189 (mm) REVERT: A 605 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: A 874 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.6957 (tp) REVERT: A 913 MET cc_start: 0.9185 (mtp) cc_final: 0.8214 (tpp) REVERT: A 936 MET cc_start: 0.6075 (mmm) cc_final: 0.5682 (tpt) REVERT: A 976 MET cc_start: 0.8439 (mmm) cc_final: 0.7796 (mmm) REVERT: B 10 ARG cc_start: 0.8397 (mmp-170) cc_final: 0.7934 (ttt180) REVERT: B 124 MET cc_start: 0.9389 (mmm) cc_final: 0.8528 (mmm) REVERT: B 227 MET cc_start: 0.8819 (ppp) cc_final: 0.8491 (tmm) REVERT: B 454 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9194 (tp) REVERT: B 519 MET cc_start: 0.9029 (tpp) cc_final: 0.8808 (mmm) REVERT: B 662 ASP cc_start: 0.8536 (p0) cc_final: 0.7942 (t0) REVERT: B 711 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8428 (tm-30) REVERT: B 1001 MET cc_start: 0.9227 (mtp) cc_final: 0.8939 (mtp) REVERT: C 12 HIS cc_start: 0.8384 (p-80) cc_final: 0.8103 (p-80) REVERT: C 26 ASP cc_start: 0.8627 (t0) cc_final: 0.8185 (p0) REVERT: C 29 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.8047 (p90) REVERT: C 41 LYS cc_start: 0.9037 (mtmm) cc_final: 0.8762 (mmtt) REVERT: C 51 TYR cc_start: 0.8029 (m-10) cc_final: 0.7754 (m-10) REVERT: C 74 LEU cc_start: 0.8469 (mp) cc_final: 0.7717 (tp) REVERT: C 76 GLU cc_start: 0.6741 (tt0) cc_final: 0.6320 (tp30) REVERT: C 98 ILE cc_start: 0.9024 (mp) cc_final: 0.8410 (tp) REVERT: C 115 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7273 (tm-30) REVERT: C 120 ASP cc_start: 0.7997 (m-30) cc_final: 0.7250 (t0) REVERT: D 21 MET cc_start: 0.7894 (ppp) cc_final: 0.7619 (ppp) REVERT: D 134 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6306 (m-10) REVERT: E 82 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7747 (p0) REVERT: E 124 MET cc_start: 0.8686 (mmm) cc_final: 0.8350 (mmm) REVERT: E 145 ARG cc_start: 0.8399 (mtp-110) cc_final: 0.7874 (tmm-80) outliers start: 53 outliers final: 35 residues processed: 184 average time/residue: 0.1339 time to fit residues: 39.8813 Evaluate side-chains 166 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 190 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 209 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 221 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 237 optimal weight: 1.9990 chunk 116 optimal weight: 0.4980 chunk 5 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 152 optimal weight: 0.0970 chunk 210 optimal weight: 0.0000 chunk 17 optimal weight: 0.0030 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 HIS ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN C 88 HIS E 118 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.055144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.043213 restraints weight = 122603.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.044738 restraints weight = 68413.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.045801 restraints weight = 46476.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.046377 restraints weight = 35287.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.046953 restraints weight = 29987.993| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22459 Z= 0.091 Angle : 0.514 10.704 30292 Z= 0.253 Chirality : 0.039 0.217 3232 Planarity : 0.003 0.055 3864 Dihedral : 3.878 42.458 2910 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.69 % Allowed : 26.17 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.17), residues: 2630 helix: 1.26 (0.14), residues: 1482 sheet: -1.68 (0.45), residues: 109 loop : -0.91 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 72 TYR 0.018 0.001 TYR A 223 PHE 0.018 0.001 PHE D 19 TRP 0.033 0.001 TRP B 143 HIS 0.003 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00198 (22459) covalent geometry : angle 0.51387 (30292) hydrogen bonds : bond 0.02769 ( 1028) hydrogen bonds : angle 3.95397 ( 2949) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8144 (mmt) cc_final: 0.7754 (mmm) REVERT: A 204 MET cc_start: 0.9158 (tmm) cc_final: 0.8885 (tmm) REVERT: A 526 ASP cc_start: 0.9309 (t0) cc_final: 0.8977 (t0) REVERT: A 571 GLU cc_start: 0.8739 (tt0) cc_final: 0.8233 (mm-30) REVERT: A 605 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7819 (m-10) REVERT: A 874 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.6998 (tp) REVERT: A 902 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.6845 (pttt) REVERT: A 913 MET cc_start: 0.9218 (mtp) cc_final: 0.8241 (tpp) REVERT: A 936 MET cc_start: 0.6035 (mmm) cc_final: 0.5677 (tpt) REVERT: A 976 MET cc_start: 0.8443 (mmm) cc_final: 0.8068 (mmm) REVERT: B 10 ARG cc_start: 0.8367 (mmp-170) cc_final: 0.7953 (ttt180) REVERT: B 124 MET cc_start: 0.9374 (mmm) cc_final: 0.8536 (mmm) REVERT: B 227 MET cc_start: 0.8837 (ppp) cc_final: 0.8469 (tmm) REVERT: B 519 MET cc_start: 0.9029 (tpp) cc_final: 0.8812 (mmm) REVERT: B 662 ASP cc_start: 0.8554 (p0) cc_final: 0.7935 (t0) REVERT: B 704 MET cc_start: 0.6596 (tpt) cc_final: 0.6347 (tpt) REVERT: B 976 MET cc_start: 0.8848 (ptp) cc_final: 0.8470 (mpp) REVERT: B 977 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8264 (tptm) REVERT: B 1001 MET cc_start: 0.9252 (mtp) cc_final: 0.9026 (mtt) REVERT: C 12 HIS cc_start: 0.8420 (p-80) cc_final: 0.8177 (p-80) REVERT: C 26 ASP cc_start: 0.8641 (t0) cc_final: 0.8166 (p0) REVERT: C 29 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.8001 (p90) REVERT: C 41 LYS cc_start: 0.9038 (mtmm) cc_final: 0.8758 (mmtt) REVERT: C 51 TYR cc_start: 0.8040 (m-10) cc_final: 0.7761 (m-10) REVERT: C 74 LEU cc_start: 0.8497 (mp) cc_final: 0.7896 (tp) REVERT: C 76 GLU cc_start: 0.6738 (tt0) cc_final: 0.6299 (tp30) REVERT: C 88 HIS cc_start: 0.7061 (t-170) cc_final: 0.6236 (t70) REVERT: C 98 ILE cc_start: 0.9071 (mp) cc_final: 0.8511 (tp) REVERT: C 115 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7141 (tm-30) REVERT: C 120 ASP cc_start: 0.8002 (m-30) cc_final: 0.7236 (t0) REVERT: D 21 MET cc_start: 0.7797 (ppp) cc_final: 0.7530 (ppp) REVERT: D 134 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.6968 (m-80) REVERT: E 21 MET cc_start: 0.8708 (ppp) cc_final: 0.8503 (ppp) REVERT: E 82 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7744 (p0) REVERT: E 124 MET cc_start: 0.8660 (mmm) cc_final: 0.8416 (mmm) REVERT: E 145 ARG cc_start: 0.8363 (mtp-110) cc_final: 0.7757 (tmm-80) outliers start: 41 outliers final: 22 residues processed: 180 average time/residue: 0.1354 time to fit residues: 39.2810 Evaluate side-chains 156 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 902 LYS Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 190 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 41 optimal weight: 0.0170 chunk 254 optimal weight: 0.6980 chunk 225 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 230 optimal weight: 0.6980 chunk 257 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 236 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 HIS ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.054774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.042931 restraints weight = 122462.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.044452 restraints weight = 67938.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.045516 restraints weight = 46031.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.046176 restraints weight = 34922.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.046718 restraints weight = 29034.138| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22459 Z= 0.097 Angle : 0.525 11.098 30292 Z= 0.257 Chirality : 0.039 0.249 3232 Planarity : 0.003 0.053 3864 Dihedral : 3.840 42.337 2910 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.77 % Allowed : 25.79 % Favored : 72.43 % 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: 0.52 (0.17), residues: 2630 helix: 1.33 (0.14), residues: 1478 sheet: -1.63 (0.47), residues: 99 loop : -0.85 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 72 TYR 0.018 0.001 TYR A 223 PHE 0.016 0.001 PHE D 19 TRP 0.035 0.001 TRP B 143 HIS 0.004 0.001 HIS B 503 Details of bonding type rmsd covalent geometry : bond 0.00218 (22459) covalent geometry : angle 0.52479 (30292) hydrogen bonds : bond 0.02756 ( 1028) hydrogen bonds : angle 3.94523 ( 2949) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8216 (mmt) cc_final: 0.7716 (mmm) REVERT: A 204 MET cc_start: 0.9154 (tmm) cc_final: 0.8869 (tmm) REVERT: A 227 MET cc_start: 0.8882 (ptp) cc_final: 0.8280 (ptp) REVERT: A 874 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7034 (tp) REVERT: A 902 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.6855 (pttt) REVERT: A 913 MET cc_start: 0.9251 (mtp) cc_final: 0.8328 (tpp) REVERT: A 936 MET cc_start: 0.6068 (mmm) cc_final: 0.5690 (tpt) REVERT: A 976 MET cc_start: 0.8491 (mmm) cc_final: 0.8119 (mmm) REVERT: B 10 ARG cc_start: 0.8359 (mmp-170) cc_final: 0.7948 (ttt180) REVERT: B 124 MET cc_start: 0.9379 (mmm) cc_final: 0.8505 (mmm) REVERT: B 227 MET cc_start: 0.8844 (ppp) cc_final: 0.8467 (tmm) REVERT: B 519 MET cc_start: 0.9060 (tpp) cc_final: 0.8751 (mmm) REVERT: B 662 ASP cc_start: 0.8578 (p0) cc_final: 0.7933 (t0) REVERT: B 704 MET cc_start: 0.6464 (tpt) cc_final: 0.6209 (tpt) REVERT: B 976 MET cc_start: 0.8843 (ptp) cc_final: 0.8452 (mpp) REVERT: B 977 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8260 (tptm) REVERT: C 12 HIS cc_start: 0.8543 (p-80) cc_final: 0.8275 (p-80) REVERT: C 26 ASP cc_start: 0.8561 (t0) cc_final: 0.8187 (p0) REVERT: C 29 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.8055 (p90) REVERT: C 41 LYS cc_start: 0.9077 (mtmm) cc_final: 0.8793 (mmtt) REVERT: C 51 TYR cc_start: 0.8100 (m-10) cc_final: 0.7805 (m-10) REVERT: C 74 LEU cc_start: 0.8694 (mp) cc_final: 0.7949 (tp) REVERT: C 76 GLU cc_start: 0.6730 (tt0) cc_final: 0.6306 (tp30) REVERT: C 88 HIS cc_start: 0.7175 (t-170) cc_final: 0.6484 (t70) REVERT: C 98 ILE cc_start: 0.9127 (mp) cc_final: 0.8549 (tp) REVERT: C 115 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7114 (tm-30) REVERT: C 120 ASP cc_start: 0.8020 (m-30) cc_final: 0.7362 (t0) REVERT: D 134 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.6281 (m-10) REVERT: E 82 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7755 (p0) REVERT: E 124 MET cc_start: 0.8825 (mmm) cc_final: 0.8620 (mmm) REVERT: E 145 ARG cc_start: 0.8400 (mtp-110) cc_final: 0.7790 (tmm-80) outliers start: 43 outliers final: 27 residues processed: 168 average time/residue: 0.1300 time to fit residues: 35.2138 Evaluate side-chains 159 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 902 LYS Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 977 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 190 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 124 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 236 optimal weight: 0.7980 chunk 230 optimal weight: 0.0040 chunk 166 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 248 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 HIS B 698 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.054690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.042829 restraints weight = 122514.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.044365 restraints weight = 67901.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.045415 restraints weight = 45978.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.046090 restraints weight = 35020.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.046625 restraints weight = 29008.188| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22459 Z= 0.098 Angle : 0.527 11.654 30292 Z= 0.258 Chirality : 0.040 0.246 3232 Planarity : 0.003 0.052 3864 Dihedral : 3.826 42.588 2910 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.57 % Allowed : 25.79 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.55 (0.17), residues: 2630 helix: 1.36 (0.14), residues: 1477 sheet: -1.58 (0.47), residues: 99 loop : -0.83 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 72 TYR 0.018 0.001 TYR B 912 PHE 0.016 0.001 PHE D 19 TRP 0.029 0.001 TRP B 143 HIS 0.003 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00220 (22459) covalent geometry : angle 0.52700 (30292) hydrogen bonds : bond 0.02736 ( 1028) hydrogen bonds : angle 3.93929 ( 2949) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8225 (mmt) cc_final: 0.7737 (mmm) REVERT: A 526 ASP cc_start: 0.9351 (t0) cc_final: 0.9033 (t0) REVERT: A 571 GLU cc_start: 0.8806 (tt0) cc_final: 0.8182 (mm-30) REVERT: A 902 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.6902 (pttt) REVERT: A 936 MET cc_start: 0.6089 (mmm) cc_final: 0.5715 (tpt) REVERT: A 976 MET cc_start: 0.8518 (mmm) cc_final: 0.8156 (mmm) REVERT: B 10 ARG cc_start: 0.8400 (mmp-170) cc_final: 0.7956 (ttt180) REVERT: B 124 MET cc_start: 0.9410 (mmm) cc_final: 0.8479 (mmm) REVERT: B 227 MET cc_start: 0.8872 (ppp) cc_final: 0.8471 (tmm) REVERT: B 662 ASP cc_start: 0.8572 (p0) cc_final: 0.7870 (t0) REVERT: B 704 MET cc_start: 0.6429 (tpt) cc_final: 0.6187 (tpt) REVERT: B 976 MET cc_start: 0.8848 (ptp) cc_final: 0.8454 (mpp) REVERT: B 977 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8251 (tptm) REVERT: C 12 HIS cc_start: 0.8661 (p-80) cc_final: 0.8346 (p-80) REVERT: C 26 ASP cc_start: 0.8591 (t0) cc_final: 0.8152 (p0) REVERT: C 29 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.8127 (p90) REVERT: C 41 LYS cc_start: 0.9118 (mtmm) cc_final: 0.8834 (mmtt) REVERT: C 51 TYR cc_start: 0.8162 (m-10) cc_final: 0.7871 (m-10) REVERT: C 74 LEU cc_start: 0.8739 (mp) cc_final: 0.8002 (tp) REVERT: C 76 GLU cc_start: 0.6702 (tt0) cc_final: 0.6307 (tp30) REVERT: C 88 HIS cc_start: 0.7281 (t-170) cc_final: 0.6664 (t70) REVERT: C 98 ILE cc_start: 0.9209 (mp) cc_final: 0.8689 (tp) REVERT: C 115 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7569 (tm-30) REVERT: C 120 ASP cc_start: 0.7982 (m-30) cc_final: 0.7362 (t0) REVERT: D 21 MET cc_start: 0.7362 (ppp) cc_final: 0.7096 (ppp) REVERT: E 21 MET cc_start: 0.8679 (ppp) cc_final: 0.8430 (ppp) REVERT: E 82 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7750 (p0) REVERT: E 145 ARG cc_start: 0.8386 (mtp-110) cc_final: 0.7813 (tmm-80) REVERT: E 187 GLU cc_start: 0.9083 (tp30) cc_final: 0.8792 (tp30) outliers start: 38 outliers final: 29 residues processed: 167 average time/residue: 0.1456 time to fit residues: 39.4019 Evaluate side-chains 163 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 902 LYS Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 977 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 190 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 151 optimal weight: 0.3980 chunk 111 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 106 optimal weight: 0.0170 chunk 179 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 HIS ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.054526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.042622 restraints weight = 123848.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.044134 restraints weight = 68911.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.045192 restraints weight = 46822.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.045905 restraints weight = 35681.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.046399 restraints weight = 29484.323| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22459 Z= 0.100 Angle : 0.540 12.222 30292 Z= 0.262 Chirality : 0.040 0.241 3232 Planarity : 0.003 0.052 3864 Dihedral : 3.789 42.933 2910 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.65 % Allowed : 25.84 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.62 (0.17), residues: 2630 helix: 1.41 (0.14), residues: 1480 sheet: -1.53 (0.47), residues: 99 loop : -0.81 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 72 TYR 0.017 0.001 TYR B 912 PHE 0.014 0.001 PHE D 19 TRP 0.031 0.001 TRP B 143 HIS 0.003 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00227 (22459) covalent geometry : angle 0.54005 (30292) hydrogen bonds : bond 0.02745 ( 1028) hydrogen bonds : angle 3.93647 ( 2949) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.9111 (ttm) cc_final: 0.8754 (tpp) REVERT: A 902 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.6907 (pttt) REVERT: A 913 MET cc_start: 0.9240 (mtp) cc_final: 0.8313 (ttt) REVERT: A 936 MET cc_start: 0.6213 (mmm) cc_final: 0.5712 (tpt) REVERT: A 976 MET cc_start: 0.8533 (mmm) cc_final: 0.8169 (mmm) REVERT: A 993 ASP cc_start: 0.8387 (t0) cc_final: 0.8055 (t0) REVERT: B 10 ARG cc_start: 0.8388 (mmp-170) cc_final: 0.7961 (ttt180) REVERT: B 124 MET cc_start: 0.9397 (mmm) cc_final: 0.8455 (mmm) REVERT: B 227 MET cc_start: 0.8896 (ppp) cc_final: 0.8499 (tmm) REVERT: B 662 ASP cc_start: 0.8596 (p0) cc_final: 0.7861 (t0) REVERT: B 704 MET cc_start: 0.6450 (tpt) cc_final: 0.6200 (tpt) REVERT: B 976 MET cc_start: 0.8866 (ptp) cc_final: 0.8466 (mpp) REVERT: B 977 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8256 (tptm) REVERT: C 12 HIS cc_start: 0.8687 (p-80) cc_final: 0.8368 (p-80) REVERT: C 26 ASP cc_start: 0.8620 (t0) cc_final: 0.8109 (p0) REVERT: C 41 LYS cc_start: 0.9152 (mtmm) cc_final: 0.8878 (mmtt) REVERT: C 51 TYR cc_start: 0.8189 (m-10) cc_final: 0.7911 (m-10) REVERT: C 74 LEU cc_start: 0.8765 (mp) cc_final: 0.8024 (tp) REVERT: C 76 GLU cc_start: 0.6734 (tt0) cc_final: 0.6323 (tp30) REVERT: C 98 ILE cc_start: 0.9311 (mp) cc_final: 0.8802 (tp) REVERT: C 115 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7570 (tm-30) REVERT: C 120 ASP cc_start: 0.8095 (m-30) cc_final: 0.7429 (t0) REVERT: D 21 MET cc_start: 0.7408 (ppp) cc_final: 0.7079 (ppp) REVERT: D 220 LEU cc_start: 0.7949 (tp) cc_final: 0.7591 (pp) REVERT: E 21 MET cc_start: 0.8680 (ppp) cc_final: 0.8457 (ppp) REVERT: E 82 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7738 (p0) REVERT: E 145 ARG cc_start: 0.8415 (mtp-110) cc_final: 0.7842 (tmm-80) REVERT: E 187 GLU cc_start: 0.9070 (tp30) cc_final: 0.8771 (tp30) outliers start: 40 outliers final: 32 residues processed: 175 average time/residue: 0.1580 time to fit residues: 44.4959 Evaluate side-chains 163 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 902 LYS Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 977 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 190 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 245 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 220 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 HIS ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.053764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.041858 restraints weight = 124818.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.043339 restraints weight = 70034.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.044371 restraints weight = 47786.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.045074 restraints weight = 36552.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.045563 restraints weight = 30290.038| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22459 Z= 0.116 Angle : 0.575 13.592 30292 Z= 0.279 Chirality : 0.040 0.234 3232 Planarity : 0.003 0.051 3864 Dihedral : 3.814 42.960 2910 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.57 % Allowed : 26.08 % Favored : 72.35 % 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: 0.66 (0.17), residues: 2630 helix: 1.43 (0.14), residues: 1488 sheet: -1.92 (0.45), residues: 101 loop : -0.74 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 72 TYR 0.026 0.001 TYR A 223 PHE 0.014 0.001 PHE D 19 TRP 0.032 0.001 TRP B 143 HIS 0.003 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00264 (22459) covalent geometry : angle 0.57472 (30292) hydrogen bonds : bond 0.02825 ( 1028) hydrogen bonds : angle 3.96780 ( 2949) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3161.67 seconds wall clock time: 55 minutes 58.86 seconds (3358.86 seconds total)