Starting phenix.real_space_refine on Wed May 21 21:22:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wkt_37607/05_2025/8wkt_37607.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wkt_37607/05_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_37607/05_2025/8wkt_37607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wkt_37607/05_2025/8wkt_37607.map" model { file = "/net/cci-nas-00/data/ceres_data/8wkt_37607/05_2025/8wkt_37607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wkt_37607/05_2025/8wkt_37607.cif" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.00, per 1000 atoms: 0.64 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: 5.40 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.69 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: 6.95 Time building geometry restraints manager: 6.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 11.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 48.860 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.650 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.002 TRP B 143 HIS 0.007 0.001 HIS B 118 PHE 0.036 0.001 PHE B 933 TYR 0.020 0.001 TYR B 625 ARG 0.008 0.000 ARG E 233 Details of bonding type rmsd hydrogen bonds : bond 0.16808 ( 1028) hydrogen bonds : angle 6.03659 ( 2949) covalent geometry : bond 0.00392 (22459) covalent geometry : angle 0.63216 (30292) *********************** 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 : 2.444 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: 0.3768 time to fit residues: 214.5584 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 : 2.486 ------------------------------------------------------------------------------- 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 222 optimal weight: 0.5980 chunk 199 optimal weight: 0.3980 chunk 110 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 206 optimal weight: 0.4980 chunk 79 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 153 optimal weight: 0.0040 chunk 238 optimal weight: 0.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.057155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.045121 restraints weight = 121847.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.046673 restraints weight = 68963.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.047765 restraints weight = 47011.437| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22459 Z= 0.120 Angle : 0.575 11.281 30292 Z= 0.295 Chirality : 0.041 0.194 3232 Planarity : 0.004 0.074 3864 Dihedral : 4.258 51.740 2914 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.10 % Allowed : 25.84 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2630 helix: 0.71 (0.14), residues: 1476 sheet: -1.76 (0.47), residues: 108 loop : -1.12 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 60 HIS 0.006 0.001 HIS A 658 PHE 0.014 0.001 PHE C 79 TYR 0.010 0.001 TYR B 962 ARG 0.009 0.001 ARG D 247 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 1028) hydrogen bonds : angle 4.56188 ( 2949) covalent geometry : bond 0.00261 (22459) covalent geometry : angle 0.57520 (30292) *********************** 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 245 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 194 time to evaluate : 2.754 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 208 ILE cc_start: 0.8970 (mt) cc_final: 0.8689 (mm) REVERT: A 421 MET cc_start: 0.9329 (ptp) cc_final: 0.9023 (ptp) REVERT: A 647 MET cc_start: 0.8597 (mtp) cc_final: 0.8370 (mtp) REVERT: A 913 MET cc_start: 0.8588 (tpp) cc_final: 0.8171 (tpp) REVERT: A 936 MET cc_start: 0.6034 (mmm) cc_final: 0.5563 (tpt) REVERT: A 976 MET cc_start: 0.8609 (mmm) cc_final: 0.8327 (mmm) REVERT: B 10 ARG cc_start: 0.8414 (mmp-170) cc_final: 0.7685 (ttt180) REVERT: B 14 LYS cc_start: 0.7743 (ttpt) cc_final: 0.7421 (mmtp) REVERT: B 124 MET cc_start: 0.8585 (mmt) cc_final: 0.8354 (mmm) REVERT: B 391 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8322 (t0) REVERT: B 531 MET cc_start: 0.9314 (mmm) cc_final: 0.8994 (mmm) REVERT: B 662 ASP cc_start: 0.8624 (p0) cc_final: 0.8048 (t0) REVERT: B 938 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7746 (p0) REVERT: B 1001 MET cc_start: 0.9230 (mtp) cc_final: 0.8932 (mpp) REVERT: C 12 HIS cc_start: 0.8216 (p-80) cc_final: 0.7943 (p-80) REVERT: C 26 ASP cc_start: 0.8494 (t70) cc_final: 0.8042 (p0) REVERT: C 29 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7777 (p90) REVERT: C 74 LEU cc_start: 0.8289 (mp) cc_final: 0.7679 (tp) REVERT: C 88 HIS cc_start: 0.7669 (t70) cc_final: 0.7085 (t70) REVERT: C 115 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7919 (tm-30) REVERT: C 120 ASP cc_start: 0.8383 (m-30) cc_final: 0.7537 (t0) REVERT: D 134 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.6578 (m-10) REVERT: E 85 LEU cc_start: 0.9164 (mt) cc_final: 0.8943 (mm) REVERT: E 145 ARG cc_start: 0.8408 (mtp-110) cc_final: 0.7657 (ttp-170) REVERT: E 268 ILE cc_start: 0.9160 (mm) cc_final: 0.8877 (tp) REVERT: E 290 MET cc_start: 0.9451 (mmm) cc_final: 0.9184 (mtm) REVERT: E 294 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8542 (mm) outliers start: 51 outliers final: 13 residues processed: 237 average time/residue: 0.3642 time to fit residues: 136.3903 Evaluate side-chains 166 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 2.640 ------------------------------------------------------------------------------- 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 744 PHE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 391 ASN 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 294 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 106 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 237 optimal weight: 5.9990 chunk 174 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 45 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 428 GLN ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS B 297 GLN B 563 ASN B 698 GLN ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN E 67 HIS E 115 ASN E 118 HIS E 171 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.052699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.040634 restraints weight = 125090.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.042104 restraints weight = 70943.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.043109 restraints weight = 48627.371| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22459 Z= 0.197 Angle : 0.596 10.178 30292 Z= 0.309 Chirality : 0.042 0.157 3232 Planarity : 0.004 0.060 3864 Dihedral : 4.257 40.828 2910 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.76 % Allowed : 23.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2630 helix: 0.80 (0.14), residues: 1495 sheet: -1.83 (0.50), residues: 92 loop : -1.07 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 231 HIS 0.007 0.001 HIS B 881 PHE 0.024 0.002 PHE B 301 TYR 0.017 0.002 TYR B 134 ARG 0.006 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 1028) hydrogen bonds : angle 4.35117 ( 2949) covalent geometry : bond 0.00423 (22459) covalent geometry : angle 0.59642 (30292) *********************** 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 236 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 145 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8434 (mmt) cc_final: 0.7992 (mmm) REVERT: A 204 MET cc_start: 0.9153 (tmm) cc_final: 0.8719 (tmm) REVERT: A 208 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8820 (mm) REVERT: A 229 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9445 (mm) REVERT: A 874 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7025 (tp) REVERT: A 913 MET cc_start: 0.8671 (tpp) cc_final: 0.8295 (tpp) REVERT: A 936 MET cc_start: 0.6327 (mmm) cc_final: 0.5924 (tpt) REVERT: B 10 ARG cc_start: 0.8386 (mmp-170) cc_final: 0.7612 (ttt180) REVERT: B 14 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7449 (mmtp) REVERT: B 391 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8486 (t0) REVERT: B 454 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9082 (tp) REVERT: B 662 ASP cc_start: 0.8594 (p0) cc_final: 0.8032 (t0) REVERT: B 704 MET cc_start: 0.6877 (tpt) cc_final: 0.6612 (tpt) REVERT: B 749 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9033 (mt) REVERT: B 977 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8301 (tptm) REVERT: C 12 HIS cc_start: 0.8398 (p-80) cc_final: 0.8135 (p-80) REVERT: C 26 ASP cc_start: 0.8765 (t70) cc_final: 0.8311 (p0) REVERT: C 29 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.8074 (p90) REVERT: C 74 LEU cc_start: 0.8571 (mp) cc_final: 0.7939 (tp) REVERT: C 76 GLU cc_start: 0.6917 (tt0) cc_final: 0.6459 (tp30) REVERT: C 98 ILE cc_start: 0.9021 (mp) cc_final: 0.8322 (tp) REVERT: C 115 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7618 (tm-30) REVERT: D 80 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8740 (p) REVERT: D 134 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.6857 (m-80) REVERT: E 82 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7823 (p0) REVERT: E 124 MET cc_start: 0.8913 (mmm) cc_final: 0.8671 (mmm) REVERT: E 145 ARG cc_start: 0.8303 (mtp-110) cc_final: 0.7842 (tmm-80) REVERT: E 268 ILE cc_start: 0.9234 (mm) cc_final: 0.8915 (tp) REVERT: E 297 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7481 (pm20) outliers start: 91 outliers final: 36 residues processed: 225 average time/residue: 0.3068 time to fit residues: 111.6633 Evaluate side-chains 176 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 2.335 ------------------------------------------------------------------------------- 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 229 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 756 VAL 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 B residue 142 CYS Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 194 ASP 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 702 ASN Chi-restraints excluded: chain B residue 724 LYS Chi-restraints excluded: chain B residue 749 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 22 THR 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 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 160 ASN Chi-restraints excluded: chain E residue 183 VAL 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 73 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 186 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 65 optimal weight: 0.1980 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS D 171 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 = 0.3250 r_free = 0.3250 target = 0.052199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.040233 restraints weight = 127039.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.041711 restraints weight = 71688.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.042726 restraints weight = 48921.909| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22459 Z= 0.169 Angle : 0.549 14.652 30292 Z= 0.281 Chirality : 0.041 0.234 3232 Planarity : 0.003 0.060 3864 Dihedral : 4.191 40.397 2910 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.89 % Allowed : 25.01 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2630 helix: 0.97 (0.14), residues: 1486 sheet: -2.10 (0.48), residues: 99 loop : -0.94 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 231 HIS 0.005 0.001 HIS A 658 PHE 0.017 0.001 PHE C 59 TYR 0.011 0.001 TYR E 286 ARG 0.004 0.000 ARG A 987 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 1028) hydrogen bonds : angle 4.22026 ( 2949) covalent geometry : bond 0.00372 (22459) covalent geometry : angle 0.54921 (30292) *********************** 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 213 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 143 time to evaluate : 2.308 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: 0.8317 (mmt) cc_final: 0.7888 (mmm) REVERT: A 204 MET cc_start: 0.9142 (tmm) cc_final: 0.8721 (tmm) REVERT: A 208 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8746 (mm) REVERT: A 421 MET cc_start: 0.9298 (ptp) cc_final: 0.8783 (ttp) REVERT: A 902 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7178 (pttt) REVERT: A 936 MET cc_start: 0.6265 (mmm) cc_final: 0.5419 (tpt) REVERT: A 976 MET cc_start: 0.8530 (mmm) cc_final: 0.8321 (mmm) REVERT: B 10 ARG cc_start: 0.8512 (mmp-170) cc_final: 0.7728 (ttt180) REVERT: B 14 LYS cc_start: 0.7816 (ttpt) cc_final: 0.7505 (mmtp) REVERT: B 124 MET cc_start: 0.9334 (mmm) cc_final: 0.8531 (mmm) REVERT: B 391 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8564 (t0) REVERT: B 647 MET cc_start: 0.9151 (mmm) cc_final: 0.8581 (mmm) REVERT: B 977 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8305 (tptm) REVERT: B 992 ASN cc_start: 0.8335 (m-40) cc_final: 0.8084 (t0) REVERT: C 12 HIS cc_start: 0.8608 (p-80) cc_final: 0.8327 (p-80) REVERT: C 26 ASP cc_start: 0.8731 (t70) cc_final: 0.8202 (p0) REVERT: C 51 TYR cc_start: 0.8317 (m-10) cc_final: 0.7999 (m-10) REVERT: C 72 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7351 (mmm160) REVERT: C 74 LEU cc_start: 0.8741 (mp) cc_final: 0.8020 (tp) REVERT: C 76 GLU cc_start: 0.6789 (tt0) cc_final: 0.6347 (tp30) REVERT: C 98 ILE cc_start: 0.9049 (mp) cc_final: 0.8430 (tp) REVERT: C 115 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7308 (tm-30) REVERT: C 120 ASP cc_start: 0.8233 (m-30) cc_final: 0.7606 (t0) REVERT: D 134 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.6793 (m-10) REVERT: E 82 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7789 (p0) REVERT: E 124 MET cc_start: 0.8855 (mmm) cc_final: 0.8616 (mmm) REVERT: E 145 ARG cc_start: 0.8393 (mtp-110) cc_final: 0.7874 (tmm-80) REVERT: E 187 GLU cc_start: 0.9210 (tp30) cc_final: 0.8883 (tp30) REVERT: E 297 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7495 (pt0) outliers start: 70 outliers final: 39 residues processed: 202 average time/residue: 0.3137 time to fit residues: 101.6102 Evaluate side-chains 174 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 128 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 615 SER 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 902 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 911 ASP 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 22 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 50 VAL 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 73 SER 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 160 ASN Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 297 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 192 optimal weight: 0.0070 chunk 117 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 211 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 237 optimal weight: 0.3980 chunk 159 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.6400 ------------------------------------------------------------------------------- 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 765 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 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 = 0.3270 r_free = 0.3270 target = 0.052940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.041069 restraints weight = 125376.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.042548 restraints weight = 69957.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.043585 restraints weight = 47537.933| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3719 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= 0.102 Angle : 0.506 8.381 30292 Z= 0.258 Chirality : 0.039 0.153 3232 Planarity : 0.003 0.059 3864 Dihedral : 4.048 41.313 2910 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.77 % Allowed : 25.46 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2630 helix: 1.12 (0.14), residues: 1487 sheet: -2.03 (0.48), residues: 99 loop : -0.87 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 231 HIS 0.003 0.001 HIS A 658 PHE 0.013 0.001 PHE C 59 TYR 0.013 0.001 TYR A 223 ARG 0.003 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 1028) hydrogen bonds : angle 4.06921 ( 2949) covalent geometry : bond 0.00226 (22459) covalent geometry : angle 0.50625 (30292) *********************** 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 210 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 143 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8198 (mmt) cc_final: 0.7768 (mmm) REVERT: A 208 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8694 (mm) REVERT: A 421 MET cc_start: 0.9285 (ptp) cc_final: 0.8786 (ttp) REVERT: A 526 ASP cc_start: 0.9406 (t0) cc_final: 0.9119 (t0) REVERT: A 634 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7831 (mt) REVERT: A 902 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.6954 (pttt) REVERT: A 913 MET cc_start: 0.9068 (mtp) cc_final: 0.8247 (tpp) REVERT: A 976 MET cc_start: 0.8596 (mmm) cc_final: 0.8333 (mmm) REVERT: B 10 ARG cc_start: 0.8415 (mmp-170) cc_final: 0.7973 (ttt180) REVERT: B 71 TYR cc_start: 0.9008 (m-10) cc_final: 0.8754 (m-10) REVERT: B 124 MET cc_start: 0.9323 (mmm) cc_final: 0.8340 (mmm) REVERT: B 391 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8556 (t0) REVERT: B 519 MET cc_start: 0.9012 (tpp) cc_final: 0.8802 (mmm) REVERT: B 647 MET cc_start: 0.9164 (mmm) cc_final: 0.8574 (mmm) REVERT: B 976 MET cc_start: 0.8926 (ptp) cc_final: 0.8526 (mpp) REVERT: B 992 ASN cc_start: 0.8424 (m-40) cc_final: 0.8053 (t0) REVERT: C 12 HIS cc_start: 0.8647 (p-80) cc_final: 0.8379 (p-80) REVERT: C 26 ASP cc_start: 0.8728 (t70) cc_final: 0.8227 (p0) REVERT: C 41 LYS cc_start: 0.9217 (mtmm) cc_final: 0.8921 (mmtt) REVERT: C 51 TYR cc_start: 0.8266 (m-10) cc_final: 0.7950 (m-10) REVERT: C 72 ARG cc_start: 0.7887 (mmm160) cc_final: 0.7304 (mmm160) REVERT: C 74 LEU cc_start: 0.8775 (mp) cc_final: 0.8039 (tp) REVERT: C 76 GLU cc_start: 0.6779 (tt0) cc_final: 0.6348 (tp30) REVERT: C 98 ILE cc_start: 0.9114 (mp) cc_final: 0.8538 (tp) REVERT: C 115 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7383 (tm-30) REVERT: C 120 ASP cc_start: 0.8169 (m-30) cc_final: 0.7506 (t0) REVERT: D 21 MET cc_start: 0.8393 (tpt) cc_final: 0.7572 (ptt) REVERT: D 165 ARG cc_start: 0.8249 (ptp90) cc_final: 0.8017 (ptp90) REVERT: D 173 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.7080 (m-30) REVERT: E 82 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7844 (p0) REVERT: E 124 MET cc_start: 0.8833 (mmm) cc_final: 0.8487 (mmm) REVERT: E 145 ARG cc_start: 0.8287 (mtp-110) cc_final: 0.7906 (tmm-80) REVERT: E 187 GLU cc_start: 0.9166 (tp30) cc_final: 0.8826 (tp30) REVERT: E 297 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7377 (pm20) outliers start: 67 outliers final: 29 residues processed: 203 average time/residue: 0.3119 time to fit residues: 103.0366 Evaluate side-chains 164 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 634 LEU 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 959 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 143 TRP 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 582 ILE Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 911 ASP 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 33 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 297 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 247 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 214 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 765 ASN B 990 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS E 133 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.052598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.040738 restraints weight = 125425.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.042201 restraints weight = 70659.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.043230 restraints weight = 48181.670| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22459 Z= 0.118 Angle : 0.520 9.455 30292 Z= 0.263 Chirality : 0.040 0.361 3232 Planarity : 0.003 0.057 3864 Dihedral : 4.018 42.476 2910 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.68 % Allowed : 25.75 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.17), residues: 2630 helix: 1.14 (0.14), residues: 1497 sheet: -1.87 (0.51), residues: 89 loop : -0.85 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 958 HIS 0.003 0.001 HIS A 658 PHE 0.024 0.001 PHE D 19 TYR 0.013 0.001 TYR D 261 ARG 0.002 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.02975 ( 1028) hydrogen bonds : angle 4.07003 ( 2949) covalent geometry : bond 0.00263 (22459) covalent geometry : angle 0.51973 (30292) *********************** 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 198 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 133 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8699 (mm) REVERT: A 421 MET cc_start: 0.9208 (ptp) cc_final: 0.8857 (ttp) REVERT: A 634 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7899 (mt) REVERT: A 647 MET cc_start: 0.9069 (tpp) cc_final: 0.8663 (mmm) REVERT: A 902 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.6966 (pttt) REVERT: A 913 MET cc_start: 0.9259 (mtp) cc_final: 0.8295 (tpp) REVERT: A 936 MET cc_start: 0.6107 (mmm) cc_final: 0.5703 (tpt) REVERT: A 976 MET cc_start: 0.8598 (mmm) cc_final: 0.8312 (mmm) REVERT: B 10 ARG cc_start: 0.8425 (mmp-170) cc_final: 0.7979 (ttt180) REVERT: B 71 TYR cc_start: 0.9019 (m-10) cc_final: 0.8756 (m-10) REVERT: B 124 MET cc_start: 0.9328 (mmm) cc_final: 0.8385 (mmm) REVERT: B 391 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8577 (t0) REVERT: B 647 MET cc_start: 0.9162 (mmm) cc_final: 0.8606 (mmm) REVERT: B 992 ASN cc_start: 0.8503 (m-40) cc_final: 0.8083 (t0) REVERT: B 1001 MET cc_start: 0.9179 (mpp) cc_final: 0.8969 (mpp) REVERT: C 12 HIS cc_start: 0.8671 (p-80) cc_final: 0.8410 (p-80) REVERT: C 26 ASP cc_start: 0.8708 (t70) cc_final: 0.8094 (p0) REVERT: C 41 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8907 (mmtt) REVERT: C 51 TYR cc_start: 0.8301 (m-10) cc_final: 0.8038 (m-10) REVERT: C 72 ARG cc_start: 0.7853 (mmm160) cc_final: 0.7274 (mmm160) REVERT: C 74 LEU cc_start: 0.8790 (mp) cc_final: 0.8067 (tp) REVERT: C 76 GLU cc_start: 0.6698 (tt0) cc_final: 0.6274 (tp30) REVERT: C 88 HIS cc_start: 0.7375 (t-170) cc_final: 0.6756 (t70) REVERT: C 115 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7349 (tm-30) REVERT: C 120 ASP cc_start: 0.8188 (m-30) cc_final: 0.7556 (t0) REVERT: D 21 MET cc_start: 0.8333 (tpt) cc_final: 0.7643 (ptm) REVERT: D 165 ARG cc_start: 0.8098 (ptp90) cc_final: 0.7892 (ptp90) REVERT: D 173 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.7087 (m-30) REVERT: E 82 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7753 (p0) REVERT: E 145 ARG cc_start: 0.8298 (mtp-110) cc_final: 0.7768 (tmm-80) REVERT: E 187 GLU cc_start: 0.9183 (tp30) cc_final: 0.8844 (tp30) REVERT: E 297 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7349 (pm20) outliers start: 65 outliers final: 44 residues processed: 188 average time/residue: 0.3174 time to fit residues: 97.3229 Evaluate side-chains 182 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 130 time to evaluate : 2.760 ------------------------------------------------------------------------------- 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 158 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 634 LEU 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 902 LYS 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 143 TRP Chi-restraints excluded: chain B residue 213 ILE 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 391 ASN Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 765 ASN 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 C residue 14 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 41 LYS 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 173 ASP Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 297 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 182 optimal weight: 0.1980 chunk 132 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 256 optimal weight: 0.7980 chunk 261 optimal weight: 0.0670 chunk 134 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.053211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.041336 restraints weight = 125299.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.042816 restraints weight = 71056.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.043833 restraints weight = 48626.539| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22459 Z= 0.098 Angle : 0.518 9.439 30292 Z= 0.259 Chirality : 0.039 0.292 3232 Planarity : 0.003 0.054 3864 Dihedral : 3.968 42.626 2910 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.52 % Allowed : 26.33 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2630 helix: 1.17 (0.14), residues: 1505 sheet: -1.85 (0.51), residues: 89 loop : -0.84 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 958 HIS 0.003 0.001 HIS D 211 PHE 0.018 0.001 PHE D 19 TYR 0.018 0.001 TYR A 223 ARG 0.002 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.02852 ( 1028) hydrogen bonds : angle 4.01336 ( 2949) covalent geometry : bond 0.00221 (22459) covalent geometry : angle 0.51828 (30292) *********************** 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 198 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 137 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8517 (mt0) REVERT: A 208 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8674 (mm) REVERT: A 421 MET cc_start: 0.9194 (ptp) cc_final: 0.8816 (ttp) REVERT: A 634 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7826 (mt) REVERT: A 647 MET cc_start: 0.9025 (tpp) cc_final: 0.8657 (mmm) REVERT: A 902 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7014 (pttt) REVERT: A 913 MET cc_start: 0.9233 (mtp) cc_final: 0.8234 (tpp) REVERT: A 936 MET cc_start: 0.6063 (mmm) cc_final: 0.5687 (tpt) REVERT: A 976 MET cc_start: 0.8553 (mmm) cc_final: 0.8290 (mmm) REVERT: B 10 ARG cc_start: 0.8384 (mmp-170) cc_final: 0.7976 (ttt180) REVERT: B 71 TYR cc_start: 0.8964 (m-10) cc_final: 0.8644 (m-10) REVERT: B 124 MET cc_start: 0.9241 (mmm) cc_final: 0.8341 (mmm) REVERT: B 391 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8575 (t0) REVERT: B 647 MET cc_start: 0.9056 (mmm) cc_final: 0.8470 (mmm) REVERT: B 704 MET cc_start: 0.7022 (tpt) cc_final: 0.6744 (tpt) REVERT: B 976 MET cc_start: 0.8943 (ptp) cc_final: 0.8558 (mpp) REVERT: B 977 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8269 (tptm) REVERT: B 992 ASN cc_start: 0.8495 (m-40) cc_final: 0.8063 (t0) REVERT: B 997 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.8871 (tt) REVERT: B 1001 MET cc_start: 0.9112 (mpp) cc_final: 0.8850 (mpp) REVERT: C 12 HIS cc_start: 0.8668 (p-80) cc_final: 0.8381 (p-80) REVERT: C 26 ASP cc_start: 0.8637 (t70) cc_final: 0.8098 (p0) REVERT: C 51 TYR cc_start: 0.8262 (m-10) cc_final: 0.8001 (m-10) REVERT: C 72 ARG cc_start: 0.7640 (mmm160) cc_final: 0.7003 (mmm160) REVERT: C 74 LEU cc_start: 0.8804 (mp) cc_final: 0.8069 (tp) REVERT: C 76 GLU cc_start: 0.6726 (tt0) cc_final: 0.6279 (tp30) REVERT: C 98 ILE cc_start: 0.9222 (mp) cc_final: 0.8617 (tp) REVERT: C 115 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7741 (tm-30) REVERT: C 120 ASP cc_start: 0.8219 (m-30) cc_final: 0.7604 (t0) REVERT: D 21 MET cc_start: 0.8245 (tpt) cc_final: 0.7607 (ptm) REVERT: D 165 ARG cc_start: 0.8126 (ptp90) cc_final: 0.7912 (ptp90) REVERT: D 173 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6966 (m-30) REVERT: D 220 LEU cc_start: 0.8142 (tp) cc_final: 0.7661 (pp) REVERT: D 222 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7698 (p0) REVERT: E 82 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7804 (p0) REVERT: E 145 ARG cc_start: 0.8238 (mtp-110) cc_final: 0.7677 (tmm-80) REVERT: E 187 GLU cc_start: 0.9126 (tp30) cc_final: 0.8795 (tp30) REVERT: E 297 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7385 (pm20) outliers start: 61 outliers final: 42 residues processed: 191 average time/residue: 0.3114 time to fit residues: 97.6405 Evaluate side-chains 178 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 125 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 634 LEU 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 902 LYS Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 391 ASN 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 765 ASN Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LYS Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 248 THR 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 160 ASN Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 297 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 48 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 139 optimal weight: 0.0980 chunk 145 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 187 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 208 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 297 GLN ** B 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.052815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.041017 restraints weight = 125923.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.042453 restraints weight = 71077.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.043461 restraints weight = 48681.734| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22459 Z= 0.115 Angle : 0.537 10.985 30292 Z= 0.265 Chirality : 0.039 0.150 3232 Planarity : 0.003 0.067 3864 Dihedral : 3.959 42.827 2910 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.77 % Allowed : 25.84 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2630 helix: 1.25 (0.14), residues: 1501 sheet: -1.71 (0.48), residues: 99 loop : -0.86 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 958 HIS 0.003 0.001 HIS A 658 PHE 0.015 0.001 PHE D 19 TYR 0.015 0.001 TYR B 912 ARG 0.002 0.000 ARG E 285 Details of bonding type rmsd hydrogen bonds : bond 0.02836 ( 1028) hydrogen bonds : angle 3.98501 ( 2949) covalent geometry : bond 0.00254 (22459) covalent geometry : angle 0.53715 (30292) *********************** 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 199 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 132 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8499 (mt0) REVERT: A 124 MET cc_start: 0.8685 (mmm) cc_final: 0.7884 (mmm) REVERT: A 208 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8689 (mm) REVERT: A 421 MET cc_start: 0.9213 (ptp) cc_final: 0.8808 (ttp) REVERT: A 634 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7916 (mt) REVERT: A 647 MET cc_start: 0.9057 (tpp) cc_final: 0.8684 (mmm) REVERT: A 902 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.6843 (pttt) REVERT: A 913 MET cc_start: 0.9248 (mtp) cc_final: 0.9004 (mtp) REVERT: A 936 MET cc_start: 0.6127 (mmm) cc_final: 0.5547 (tpt) REVERT: A 976 MET cc_start: 0.8569 (mmm) cc_final: 0.8284 (mmm) REVERT: B 10 ARG cc_start: 0.8371 (mmp-170) cc_final: 0.7975 (ttt180) REVERT: B 71 TYR cc_start: 0.8980 (m-10) cc_final: 0.8690 (m-10) REVERT: B 124 MET cc_start: 0.9260 (mmm) cc_final: 0.8367 (mmm) REVERT: B 391 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8597 (t0) REVERT: B 647 MET cc_start: 0.9006 (mmm) cc_final: 0.8630 (mmm) REVERT: B 933 PHE cc_start: 0.7144 (OUTLIER) cc_final: 0.6064 (t80) REVERT: B 976 MET cc_start: 0.8936 (ptp) cc_final: 0.8504 (mpp) REVERT: B 977 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8276 (tptm) REVERT: B 992 ASN cc_start: 0.8691 (m-40) cc_final: 0.8224 (t0) REVERT: B 997 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.8859 (tt) REVERT: B 1001 MET cc_start: 0.9089 (mpp) cc_final: 0.8829 (mpp) REVERT: C 12 HIS cc_start: 0.8809 (p-80) cc_final: 0.8542 (p-80) REVERT: C 26 ASP cc_start: 0.8661 (t70) cc_final: 0.8106 (p0) REVERT: C 72 ARG cc_start: 0.7715 (mmm160) cc_final: 0.7112 (mmm160) REVERT: C 74 LEU cc_start: 0.8808 (mp) cc_final: 0.8095 (tp) REVERT: C 76 GLU cc_start: 0.6760 (tt0) cc_final: 0.6277 (tp30) REVERT: C 98 ILE cc_start: 0.9268 (mp) cc_final: 0.8713 (tp) REVERT: C 115 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7757 (tm-30) REVERT: D 21 MET cc_start: 0.8220 (tpt) cc_final: 0.7651 (ptm) REVERT: D 173 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6880 (m-30) REVERT: D 220 LEU cc_start: 0.8173 (tp) cc_final: 0.7741 (pp) REVERT: D 222 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7684 (p0) REVERT: E 82 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7694 (p0) REVERT: E 145 ARG cc_start: 0.8261 (mtp-110) cc_final: 0.7691 (tmm-80) outliers start: 67 outliers final: 44 residues processed: 193 average time/residue: 0.3164 time to fit residues: 99.9615 Evaluate side-chains 179 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 124 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 664 ILE 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 902 LYS Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 213 ILE 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 411 SER Chi-restraints excluded: chain B residue 463 ILE 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 933 PHE 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 B residue 997 LEU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 27 VAL 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 163 SER Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 248 THR 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 160 ASN Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 297 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 166 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 48 optimal weight: 0.0670 chunk 206 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 259 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.052853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.041122 restraints weight = 126115.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.042581 restraints weight = 71005.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.043588 restraints weight = 48479.819| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22459 Z= 0.104 Angle : 0.540 12.627 30292 Z= 0.264 Chirality : 0.040 0.235 3232 Planarity : 0.003 0.060 3864 Dihedral : 3.938 42.650 2910 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.52 % Allowed : 26.29 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.17), residues: 2630 helix: 1.26 (0.14), residues: 1505 sheet: -1.67 (0.48), residues: 99 loop : -0.87 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 958 HIS 0.003 0.001 HIS D 211 PHE 0.014 0.001 PHE D 19 TYR 0.020 0.001 TYR B 912 ARG 0.002 0.000 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.02797 ( 1028) hydrogen bonds : angle 3.97938 ( 2949) covalent geometry : bond 0.00233 (22459) covalent geometry : angle 0.53956 (30292) *********************** 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 194 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 133 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8678 (mmm) cc_final: 0.8018 (mmm) REVERT: A 208 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8680 (mm) REVERT: A 421 MET cc_start: 0.9205 (ptp) cc_final: 0.8817 (ttp) REVERT: A 526 ASP cc_start: 0.9394 (t0) cc_final: 0.9059 (t0) REVERT: A 634 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7906 (mt) REVERT: A 647 MET cc_start: 0.9048 (tpp) cc_final: 0.8668 (mmm) REVERT: A 902 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6750 (pttt) REVERT: A 913 MET cc_start: 0.9249 (mtp) cc_final: 0.9023 (mtp) REVERT: A 936 MET cc_start: 0.6147 (mmm) cc_final: 0.5526 (tpt) REVERT: A 976 MET cc_start: 0.8538 (mmm) cc_final: 0.8278 (mmm) REVERT: B 10 ARG cc_start: 0.8344 (mmp-170) cc_final: 0.7960 (ttt180) REVERT: B 71 TYR cc_start: 0.8965 (m-10) cc_final: 0.8700 (m-10) REVERT: B 124 MET cc_start: 0.9256 (mmm) cc_final: 0.8322 (mmm) REVERT: B 391 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8598 (t0) REVERT: B 647 MET cc_start: 0.8914 (mmm) cc_final: 0.8657 (mmm) REVERT: B 704 MET cc_start: 0.6794 (tpt) cc_final: 0.6563 (tpt) REVERT: B 933 PHE cc_start: 0.7032 (OUTLIER) cc_final: 0.6076 (t80) REVERT: B 940 TYR cc_start: 0.9087 (t80) cc_final: 0.8863 (t80) REVERT: B 976 MET cc_start: 0.8900 (ptp) cc_final: 0.8485 (mpp) REVERT: B 977 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8265 (tptm) REVERT: B 992 ASN cc_start: 0.8709 (m-40) cc_final: 0.8247 (t0) REVERT: B 997 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.8857 (tt) REVERT: B 1001 MET cc_start: 0.8983 (mpp) cc_final: 0.8769 (mpp) REVERT: C 12 HIS cc_start: 0.8900 (p-80) cc_final: 0.8593 (p-80) REVERT: C 26 ASP cc_start: 0.8672 (t70) cc_final: 0.8128 (p0) REVERT: C 72 ARG cc_start: 0.7683 (mmm160) cc_final: 0.7048 (mmm160) REVERT: C 74 LEU cc_start: 0.8832 (mp) cc_final: 0.8151 (tp) REVERT: C 76 GLU cc_start: 0.6783 (tt0) cc_final: 0.6282 (tp30) REVERT: C 98 ILE cc_start: 0.9227 (mp) cc_final: 0.8710 (tp) REVERT: C 115 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7763 (tm-30) REVERT: C 120 ASP cc_start: 0.7738 (p0) cc_final: 0.7306 (t0) REVERT: D 21 MET cc_start: 0.8189 (tpt) cc_final: 0.7702 (ptm) REVERT: D 165 ARG cc_start: 0.7974 (ptp90) cc_final: 0.7750 (ptt-90) REVERT: D 220 LEU cc_start: 0.8114 (tp) cc_final: 0.7716 (pp) REVERT: E 21 MET cc_start: 0.8714 (ppp) cc_final: 0.8510 (ppp) REVERT: E 82 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7682 (p0) REVERT: E 145 ARG cc_start: 0.8304 (mtp-110) cc_final: 0.7734 (tmm-80) outliers start: 61 outliers final: 43 residues processed: 188 average time/residue: 0.3083 time to fit residues: 95.3492 Evaluate side-chains 179 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 128 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 664 ILE 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 902 LYS Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 213 ILE 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 411 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 977 LYS Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 27 VAL 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 228 LEU Chi-restraints excluded: chain D residue 248 THR 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 160 ASN Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 297 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 30 optimal weight: 0.0470 chunk 262 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 0.2980 chunk 205 optimal weight: 0.6980 chunk 171 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 219 optimal weight: 7.9990 chunk 226 optimal weight: 0.9980 chunk 190 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.053068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.041185 restraints weight = 126545.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.042649 restraints weight = 71403.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.043663 restraints weight = 48946.158| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4374 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= 0.098 Angle : 0.540 12.274 30292 Z= 0.265 Chirality : 0.040 0.281 3232 Planarity : 0.003 0.064 3864 Dihedral : 3.833 41.540 2908 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.94 % Allowed : 26.62 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2630 helix: 1.29 (0.14), residues: 1508 sheet: -1.67 (0.48), residues: 99 loop : -0.86 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 958 HIS 0.003 0.001 HIS D 211 PHE 0.013 0.001 PHE D 19 TYR 0.018 0.001 TYR B 912 ARG 0.002 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.02762 ( 1028) hydrogen bonds : angle 3.95826 ( 2949) covalent geometry : bond 0.00224 (22459) covalent geometry : angle 0.54027 (30292) ********************** 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 176 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 129 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8644 (mmm) cc_final: 0.8075 (mmm) REVERT: A 208 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8671 (mm) REVERT: A 634 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7843 (mt) REVERT: A 647 MET cc_start: 0.9076 (tpp) cc_final: 0.8715 (mmm) REVERT: A 902 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.6824 (pttt) REVERT: A 913 MET cc_start: 0.9256 (mtp) cc_final: 0.9036 (mtp) REVERT: A 936 MET cc_start: 0.6126 (mmm) cc_final: 0.5537 (tpt) REVERT: A 976 MET cc_start: 0.8603 (mmm) cc_final: 0.8340 (mmm) REVERT: B 10 ARG cc_start: 0.8365 (mmp-170) cc_final: 0.7981 (ttt180) REVERT: B 71 TYR cc_start: 0.8956 (m-10) cc_final: 0.8692 (m-10) REVERT: B 124 MET cc_start: 0.9256 (mmm) cc_final: 0.8345 (mmm) REVERT: B 291 ASP cc_start: 0.9112 (m-30) cc_final: 0.8553 (m-30) REVERT: B 391 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8586 (t0) REVERT: B 704 MET cc_start: 0.6786 (tpt) cc_final: 0.6584 (tpt) REVERT: B 933 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.6330 (t80) REVERT: B 976 MET cc_start: 0.8898 (ptp) cc_final: 0.8483 (mpp) REVERT: B 977 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8243 (tptm) REVERT: B 992 ASN cc_start: 0.8761 (m-40) cc_final: 0.8334 (t0) REVERT: B 997 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.8843 (tt) REVERT: C 26 ASP cc_start: 0.8677 (t70) cc_final: 0.8132 (p0) REVERT: C 72 ARG cc_start: 0.7714 (mmm160) cc_final: 0.7032 (mmm160) REVERT: C 74 LEU cc_start: 0.8841 (mp) cc_final: 0.8148 (tp) REVERT: C 76 GLU cc_start: 0.6768 (tt0) cc_final: 0.6283 (tp30) REVERT: C 98 ILE cc_start: 0.9208 (mp) cc_final: 0.8708 (tp) REVERT: C 115 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7743 (tm-30) REVERT: C 120 ASP cc_start: 0.7758 (p0) cc_final: 0.7299 (t0) REVERT: D 21 MET cc_start: 0.8184 (tpt) cc_final: 0.7722 (ptm) REVERT: D 220 LEU cc_start: 0.8107 (tp) cc_final: 0.7778 (pp) REVERT: E 82 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7747 (p0) REVERT: E 124 MET cc_start: 0.8558 (mmm) cc_final: 0.8325 (mmm) REVERT: E 145 ARG cc_start: 0.8323 (mtp-110) cc_final: 0.7747 (tmm-80) outliers start: 47 outliers final: 37 residues processed: 170 average time/residue: 0.3212 time to fit residues: 89.7858 Evaluate side-chains 171 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 634 LEU 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 959 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 213 ILE 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 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 933 PHE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 977 LYS Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 27 VAL 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 228 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 297 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 79 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 190 optimal weight: 0.0980 chunk 75 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.053048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.041263 restraints weight = 125618.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.042716 restraints weight = 70703.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.043726 restraints weight = 48372.069| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4467 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= 0.101 Angle : 0.547 12.168 30292 Z= 0.267 Chirality : 0.040 0.270 3232 Planarity : 0.003 0.060 3864 Dihedral : 3.802 41.908 2908 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.02 % Allowed : 26.83 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2630 helix: 1.35 (0.14), residues: 1498 sheet: -1.68 (0.47), residues: 99 loop : -0.84 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 958 HIS 0.003 0.001 HIS D 211 PHE 0.012 0.001 PHE D 19 TYR 0.024 0.001 TYR A 223 ARG 0.003 0.000 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.02760 ( 1028) hydrogen bonds : angle 3.96367 ( 2949) covalent geometry : bond 0.00227 (22459) covalent geometry : angle 0.54719 (30292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6175.87 seconds wall clock time: 110 minutes 29.46 seconds (6629.46 seconds total)