Starting phenix.real_space_refine on Fri Jun 13 06:57:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5nd1_3619/06_2025/5nd1_3619.cif Found real_map, /net/cci-nas-00/data/ceres_data/5nd1_3619/06_2025/5nd1_3619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5nd1_3619/06_2025/5nd1_3619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5nd1_3619/06_2025/5nd1_3619.map" model { file = "/net/cci-nas-00/data/ceres_data/5nd1_3619/06_2025/5nd1_3619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5nd1_3619/06_2025/5nd1_3619.cif" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.090 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 103 5.16 5 C 9278 2.51 5 N 2702 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14963 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7371 Classifications: {'peptide': 972} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 34, 'TRANS': 934} Chain: "B" Number of atoms: 7592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7592 Classifications: {'peptide': 1005} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 974} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.86, per 1000 atoms: 0.59 Number of scatterers: 14963 At special positions: 0 Unit cell: (140.7, 116.58, 107.2, 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 103 16.00 O 2880 8.00 N 2702 7.00 C 9278 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 1.9 seconds 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 17 sheets defined 35.5% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.957A pdb=" N LYS A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.590A pdb=" N ASP A 45 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 46 " --> pdb=" O GLY A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 46' Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.522A pdb=" N ALA A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 144 through 152 removed outlier: 4.079A pdb=" N ARG A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 175 removed outlier: 3.806A pdb=" N MET A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 203 removed outlier: 3.506A pdb=" N MET A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 removed outlier: 4.059A pdb=" N LEU A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 254' Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.552A pdb=" N VAL A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 327 removed outlier: 4.089A pdb=" N SER A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 4.063A pdb=" N TYR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 346 through 350' Processing helix chain 'A' and resid 377 through 385 Processing helix chain 'A' and resid 398 through 411 removed outlier: 3.563A pdb=" N ALA A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 440 through 447 removed outlier: 3.555A pdb=" N MET A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.747A pdb=" N PHE A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 498 removed outlier: 4.183A pdb=" N PHE A 497 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 540 removed outlier: 3.833A pdb=" N GLY A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 527 " --> pdb=" O TYR A 523 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 564 removed outlier: 3.573A pdb=" N THR A 560 " --> pdb=" O HIS A 556 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 592 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 599 through 603 removed outlier: 4.057A pdb=" N GLU A 603 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 removed outlier: 3.739A pdb=" N ASN A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 648 removed outlier: 3.603A pdb=" N ILE A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 707 Processing helix chain 'A' and resid 738 through 748 removed outlier: 4.059A pdb=" N MET A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 747 " --> pdb=" O ALA A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 761 Processing helix chain 'A' and resid 766 through 782 removed outlier: 3.661A pdb=" N ASN A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A 772 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 782 " --> pdb=" O GLY A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 removed outlier: 3.541A pdb=" N MET A 812 " --> pdb=" O ALA A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 removed outlier: 3.832A pdb=" N HIS A 841 " --> pdb=" O SER A 837 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 846 " --> pdb=" O ARG A 842 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 847 " --> pdb=" O ARG A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 896 Processing helix chain 'A' and resid 898 through 904 removed outlier: 4.052A pdb=" N MET A 902 " --> pdb=" O THR A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 943 removed outlier: 4.283A pdb=" N LEU A 942 " --> pdb=" O ASN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 971 removed outlier: 3.621A pdb=" N GLN A 967 " --> pdb=" O ASP A 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 22 through 26 Processing helix chain 'B' and resid 67 through 78 removed outlier: 3.652A pdb=" N LEU B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 108 removed outlier: 3.848A pdb=" N ASN B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA B 108 " --> pdb=" O CYS B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.788A pdb=" N ARG B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 237 removed outlier: 3.830A pdb=" N THR B 225 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 253 Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.557A pdb=" N GLN B 308 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 309' Processing helix chain 'B' and resid 335 through 346 removed outlier: 3.663A pdb=" N ALA B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 367 removed outlier: 3.612A pdb=" N THR B 361 " --> pdb=" O HIS B 357 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N MET B 364 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 404 removed outlier: 3.521A pdb=" N LEU B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 402 " --> pdb=" O GLY B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 Processing helix chain 'B' and resid 410 through 422 removed outlier: 3.814A pdb=" N LEU B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B 417 " --> pdb=" O ARG B 413 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN B 418 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 422 " --> pdb=" O GLN B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 458 Processing helix chain 'B' and resid 470 through 505 removed outlier: 4.111A pdb=" N LEU B 474 " --> pdb=" O ASP B 470 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL B 489 " --> pdb=" O GLN B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 527 removed outlier: 3.624A pdb=" N ASP B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 544 removed outlier: 3.532A pdb=" N GLN B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 562 removed outlier: 3.782A pdb=" N LEU B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B 558 " --> pdb=" O VAL B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 618 removed outlier: 3.745A pdb=" N TYR B 612 " --> pdb=" O SER B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 681 removed outlier: 3.656A pdb=" N HIS B 677 " --> pdb=" O TRP B 673 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS B 680 " --> pdb=" O TRP B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 704 removed outlier: 3.767A pdb=" N VAL B 695 " --> pdb=" O GLY B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 716 Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 770 through 785 Processing helix chain 'B' and resid 787 through 794 removed outlier: 3.520A pdb=" N SER B 792 " --> pdb=" O LEU B 788 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 793 " --> pdb=" O MET B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 831 removed outlier: 3.793A pdb=" N VAL B 831 " --> pdb=" O CYS B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 873 removed outlier: 4.084A pdb=" N VAL B 863 " --> pdb=" O PRO B 859 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS B 872 " --> pdb=" O THR B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 929 removed outlier: 3.916A pdb=" N ASP B 928 " --> pdb=" O GLU B 924 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR B 929 " --> pdb=" O ALA B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 962 removed outlier: 3.925A pdb=" N THR B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.581A pdb=" N GLY A 100 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 79 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 97 removed outlier: 3.843A pdb=" N VAL A 83 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 82 " --> pdb=" O ASP A 853 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP A 853 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 851 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 217 removed outlier: 4.170A pdb=" N ARG A 206 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 340 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 331 " --> pdb=" O THR A 343 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 283 " --> pdb=" O TYR A 330 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS A 280 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 303 " --> pdb=" O CYS A 280 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 245 removed outlier: 3.633A pdb=" N ARG A 728 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA A 725 " --> pdb=" O PHE A 691 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 691 " --> pdb=" O ALA A 725 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 370 removed outlier: 6.407A pdb=" N ILE A 367 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA A 420 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR A 369 " --> pdb=" O ALA A 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 547 through 549 removed outlier: 3.971A pdb=" N VAL A 549 " --> pdb=" O HIS A 679 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS A 679 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 652 through 657 removed outlier: 3.565A pdb=" N TRP A 657 " --> pdb=" O ARG A 802 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 669 through 670 removed outlier: 3.971A pdb=" N GLY A 686 " --> pdb=" O ILE A 669 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 928 through 929 removed outlier: 3.693A pdb=" N GLN A 929 " --> pdb=" O VAL B 599 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 952 through 953 removed outlier: 3.605A pdb=" N THR A 953 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA B 293 " --> pdb=" O THR A 953 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.743A pdb=" N LYS B 979 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 137 through 140 Processing sheet with id=AB4, first strand: chain 'B' and resid 137 through 140 Processing sheet with id=AB5, first strand: chain 'B' and resid 160 through 163 removed outlier: 6.568A pdb=" N THR B 160 " --> pdb=" O MET B 441 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 263 through 264 Processing sheet with id=AB7, first strand: chain 'B' and resid 641 through 644 removed outlier: 3.655A pdb=" N ILE B 813 " --> pdb=" O GLY B 641 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 886 through 889 removed outlier: 4.174A pdb=" N GLU B 910 " --> pdb=" O ASN B 878 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL B 880 " --> pdb=" O VAL B 908 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL B 908 " --> pdb=" O VAL B 880 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1227 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: 4.76 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2523 1.29 - 1.42: 3935 1.42 - 1.55: 8554 1.55 - 1.68: 59 1.68 - 1.82: 179 Bond restraints: 15250 Sorted by residual: bond pdb=" C ALA A 235 " pdb=" N CYS A 236 " ideal model delta sigma weight residual 1.330 1.605 -0.275 1.26e-02 6.30e+03 4.78e+02 bond pdb=" C ALA B 196 " pdb=" N PRO B 197 " ideal model delta sigma weight residual 1.333 1.407 -0.075 1.17e-02 7.31e+03 4.06e+01 bond pdb=" C MET B 364 " pdb=" O MET B 364 " ideal model delta sigma weight residual 1.236 1.165 0.072 1.15e-02 7.56e+03 3.92e+01 bond pdb=" CA THR A 440 " pdb=" C THR A 440 " ideal model delta sigma weight residual 1.519 1.438 0.081 1.32e-02 5.74e+03 3.77e+01 bond pdb=" C ILE A 685 " pdb=" O ILE A 685 " ideal model delta sigma weight residual 1.236 1.173 0.063 1.02e-02 9.61e+03 3.77e+01 ... (remaining 15245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 19354 4.15 - 8.31: 1093 8.31 - 12.46: 185 12.46 - 16.62: 58 16.62 - 20.77: 13 Bond angle restraints: 20703 Sorted by residual: angle pdb=" N VAL A 621 " pdb=" CA VAL A 621 " pdb=" C VAL A 621 " ideal model delta sigma weight residual 113.10 128.65 -15.55 9.70e-01 1.06e+00 2.57e+02 angle pdb=" N GLY A 476 " pdb=" CA GLY A 476 " pdb=" C GLY A 476 " ideal model delta sigma weight residual 112.73 131.77 -19.04 1.20e+00 6.94e-01 2.52e+02 angle pdb=" N LYS A 433 " pdb=" CA LYS A 433 " pdb=" C LYS A 433 " ideal model delta sigma weight residual 111.82 93.45 18.37 1.16e+00 7.43e-01 2.51e+02 angle pdb=" C ILE A 747 " pdb=" CA ILE A 747 " pdb=" CB ILE A 747 " ideal model delta sigma weight residual 111.06 99.30 11.76 8.80e-01 1.29e+00 1.78e+02 angle pdb=" N TYR A 229 " pdb=" CA TYR A 229 " pdb=" C TYR A 229 " ideal model delta sigma weight residual 110.20 89.43 20.77 1.58e+00 4.01e-01 1.73e+02 ... (remaining 20698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 7263 17.54 - 35.07: 1064 35.07 - 52.61: 546 52.61 - 70.15: 206 70.15 - 87.68: 17 Dihedral angle restraints: 9096 sinusoidal: 3444 harmonic: 5652 Sorted by residual: dihedral pdb=" C LEU A 623 " pdb=" N LEU A 623 " pdb=" CA LEU A 623 " pdb=" CB LEU A 623 " ideal model delta harmonic sigma weight residual -122.60 -148.83 26.23 0 2.50e+00 1.60e-01 1.10e+02 dihedral pdb=" CA THR A 953 " pdb=" C THR A 953 " pdb=" N ALA A 954 " pdb=" CA ALA A 954 " ideal model delta harmonic sigma weight residual -180.00 -128.94 -51.06 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" C CYS B 679 " pdb=" N CYS B 679 " pdb=" CA CYS B 679 " pdb=" CB CYS B 679 " ideal model delta harmonic sigma weight residual -122.60 -147.43 24.83 0 2.50e+00 1.60e-01 9.87e+01 ... (remaining 9093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.239: 2121 0.239 - 0.478: 203 0.478 - 0.717: 25 0.717 - 0.956: 3 0.956 - 1.195: 4 Chirality restraints: 2356 Sorted by residual: chirality pdb=" CA LEU A 623 " pdb=" N LEU A 623 " pdb=" C LEU A 623 " pdb=" CB LEU A 623 " both_signs ideal model delta sigma weight residual False 2.51 1.32 1.19 2.00e-01 2.50e+01 3.57e+01 chirality pdb=" CA MET A 307 " pdb=" N MET A 307 " pdb=" C MET A 307 " pdb=" CB MET A 307 " both_signs ideal model delta sigma weight residual False 2.51 1.40 1.11 2.00e-01 2.50e+01 3.07e+01 chirality pdb=" CA LEU A 671 " pdb=" N LEU A 671 " pdb=" C LEU A 671 " pdb=" CB LEU A 671 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 2353 not shown) Planarity restraints: 2702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 752 " 0.114 5.00e-02 4.00e+02 1.76e-01 4.97e+01 pdb=" N PRO B 753 " -0.305 5.00e-02 4.00e+02 pdb=" CA PRO B 753 " 0.101 5.00e-02 4.00e+02 pdb=" CD PRO B 753 " 0.091 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 264 " 0.105 5.00e-02 4.00e+02 1.63e-01 4.27e+01 pdb=" N PRO B 265 " -0.283 5.00e-02 4.00e+02 pdb=" CA PRO B 265 " 0.091 5.00e-02 4.00e+02 pdb=" CD PRO B 265 " 0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 381 " -0.098 5.00e-02 4.00e+02 1.52e-01 3.68e+01 pdb=" N PRO B 382 " 0.262 5.00e-02 4.00e+02 pdb=" CA PRO B 382 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO B 382 " -0.072 5.00e-02 4.00e+02 ... (remaining 2699 not shown) Histogram of nonbonded interaction distances: 0.20 - 1.14: 22 1.14 - 2.08: 175 2.08 - 3.02: 10944 3.02 - 3.96: 37570 3.96 - 4.90: 71458 Warning: very small nonbonded interaction distances. Nonbonded interactions: 120169 Sorted by model distance: nonbonded pdb=" NZ LYS A 918 " pdb=" ND2 ASN A 922 " model vdw 0.204 3.200 nonbonded pdb=" O GLY B 377 " pdb=" OG SER B 464 " model vdw 0.248 3.040 nonbonded pdb=" NH2 ARG A 324 " pdb=" OE1 GLN A 413 " model vdw 0.412 3.120 nonbonded pdb=" O GLY B 44 " pdb=" CD1 ILE B 53 " model vdw 0.485 3.460 nonbonded pdb=" CD1 LEU A 55 " pdb=" CE MET A 528 " model vdw 0.485 3.880 ... (remaining 120164 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.570 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 : 0.019 0.706 15257 Z= 1.438 Angle : 2.274 20.773 20703 Z= 1.540 Chirality : 0.152 1.195 2356 Planarity : 0.015 0.176 2702 Dihedral : 22.442 87.682 5472 Min Nonbonded Distance : 0.204 Molprobity Statistics. All-atom Clashscore : 100.40 Ramachandran Plot: Outliers : 2.49 % Allowed : 7.81 % Favored : 89.70 % Rotamer: Outliers : 32.66 % Allowed : 17.03 % Favored : 50.32 % Cbeta Deviations : 2.98 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % Twisted Proline : 3.03 % Twisted General : 0.68 % 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: -2.95 (0.16), residues: 1971 helix: -1.04 (0.20), residues: 566 sheet: -1.12 (0.31), residues: 229 loop : -2.75 (0.15), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 690 HIS 0.014 0.002 HIS A 202 PHE 0.033 0.002 PHE A 191 TYR 0.084 0.003 TYR B 295 ARG 0.009 0.001 ARG A 607 Details of bonding type rmsd hydrogen bonds : bond 0.28160 ( 433) hydrogen bonds : angle 10.41722 ( 1227) covalent geometry : bond 0.01696 (15250) covalent geometry : angle 2.27373 (20703) Misc. bond : bond 0.37973 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 514 poor density : 300 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: A 9 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.7136 (p0) REVERT: A 12 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8304 (tm-30) REVERT: A 23 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.5991 (mmt180) REVERT: A 49 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8741 (tt) REVERT: A 70 HIS cc_start: 0.7048 (OUTLIER) cc_final: 0.6276 (t-90) REVERT: A 79 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7515 (pm20) REVERT: A 93 SER cc_start: 0.8075 (OUTLIER) cc_final: 0.7671 (t) REVERT: A 120 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7981 (ptt90) REVERT: A 177 MET cc_start: 0.7343 (tpp) cc_final: 0.7070 (tpp) REVERT: A 218 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8280 (mt) REVERT: A 258 GLN cc_start: 0.7734 (tt0) cc_final: 0.7351 (tt0) REVERT: A 342 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8145 (tt) REVERT: A 389 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8915 (ttt180) REVERT: A 414 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8626 (p0) REVERT: A 425 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6330 (mtt90) REVERT: A 446 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7641 (mtt-85) REVERT: A 486 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8348 (p0) REVERT: A 490 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8108 (t80) REVERT: A 564 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8027 (ptt90) REVERT: A 575 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7277 (tptt) REVERT: A 579 SER cc_start: 0.8127 (m) cc_final: 0.7824 (p) REVERT: A 623 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8065 (mt) REVERT: A 640 MET cc_start: 0.6616 (mtt) cc_final: 0.6401 (ttm) REVERT: A 648 LYS cc_start: 0.6505 (OUTLIER) cc_final: 0.4837 (mttt) REVERT: A 688 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: A 689 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7947 (tpp-160) REVERT: A 708 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8259 (mmt180) REVERT: A 801 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8024 (pp) REVERT: A 802 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7759 (ttm-80) REVERT: A 826 ASP cc_start: 0.7593 (t0) cc_final: 0.7252 (p0) REVERT: A 843 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.6513 (mtt180) REVERT: A 846 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.6907 (mp) REVERT: A 865 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7315 (mmt90) REVERT: A 879 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8182 (mmt180) REVERT: A 886 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7074 (mtm110) REVERT: A 927 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8115 (t0) REVERT: A 928 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7775 (mtt180) REVERT: A 932 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7349 (mtm-85) REVERT: A 938 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8191 (ptt90) REVERT: B 7 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8450 (mt0) REVERT: B 58 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: B 91 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.7657 (mttt) REVERT: B 246 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7738 (m) REVERT: B 310 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8625 (tt) REVERT: B 327 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.5996 (m-80) REVERT: B 381 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8465 (t) REVERT: B 395 TYR cc_start: 0.8457 (m-10) cc_final: 0.8218 (m-10) REVERT: B 403 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7851 (t70) REVERT: B 434 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7036 (ttt) REVERT: B 435 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7504 (m-40) REVERT: B 448 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.5943 (pp-130) REVERT: B 503 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8585 (tm) REVERT: B 666 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8114 (tp) REVERT: B 795 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: B 799 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8514 (tpt-90) REVERT: B 801 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7639 (tp40) REVERT: B 806 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.5260 (p90) REVERT: B 807 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8288 (p90) REVERT: B 813 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8749 (mt) REVERT: B 866 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8004 (tm) REVERT: B 880 VAL cc_start: 0.8574 (t) cc_final: 0.8179 (p) REVERT: B 889 ILE cc_start: 0.8381 (mp) cc_final: 0.8150 (pt) REVERT: B 930 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.7284 (p0) REVERT: B 970 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.7253 (m-80) REVERT: B 979 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8450 (tttm) REVERT: B 992 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.7723 (m-80) REVERT: B 993 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8456 (tptt) REVERT: B 999 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7970 (mp) REVERT: B 1005 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.5645 (pptt) outliers start: 514 outliers final: 277 residues processed: 713 average time/residue: 0.3360 time to fit residues: 331.6483 Evaluate side-chains 590 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 339 poor density : 251 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 309 TRP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 445 ARG Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 454 CYS Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 TYR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 627 ARG Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 689 ARG Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 708 ARG Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 828 ARG Chi-restraints excluded: chain A residue 830 ARG Chi-restraints excluded: chain A residue 834 MET Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 879 ARG Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 886 ARG Chi-restraints excluded: chain A residue 889 GLU Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 928 ARG Chi-restraints excluded: chain A residue 929 GLN Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 938 ARG Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 141 TYR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 ARG Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 403 HIS Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 468 MET Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 588 PHE Chi-restraints excluded: chain B residue 589 TYR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 735 HIS Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 795 GLU Chi-restraints excluded: chain B residue 799 ARG Chi-restraints excluded: chain B residue 801 GLN Chi-restraints excluded: chain B residue 806 TYR Chi-restraints excluded: chain B residue 807 PHE Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 835 ARG Chi-restraints excluded: chain B residue 838 ARG Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 844 THR Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain B residue 930 ASN Chi-restraints excluded: chain B residue 943 GLU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 970 TYR Chi-restraints excluded: chain B residue 979 LYS Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1005 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 93 optimal weight: 0.0010 chunk 114 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 17 ASN A 20 HIS A 40 GLN ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 ASN A 290 GLN A 299 HIS A 341 HIS A 387 ASN A 393 HIS A 414 ASN A 455 HIS ** A 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN A 714 ASN A 757 HIS ** A 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 ASN A 939 ASN ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN B 26 GLN B 100 ASN B 110 GLN B 169 GLN B 184 GLN B 204 GLN B 220 HIS ** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 HIS B 383 HIS B 414 ASN B 431 HIS B 437 HIS ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN B 555 ASN B 636 ASN B 744 ASN B 769 ASN B 801 GLN ** B 805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 854 ASN B 865 GLN B 881 ASN ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 982 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.146084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.134499 restraints weight = 17180.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.137284 restraints weight = 10433.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.139119 restraints weight = 7075.584| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15257 Z= 0.210 Angle : 0.954 16.927 20703 Z= 0.500 Chirality : 0.051 0.288 2356 Planarity : 0.007 0.101 2702 Dihedral : 18.317 104.486 2938 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.81 % Favored : 91.37 % Rotamer: Outliers : 17.66 % Allowed : 23.51 % Favored : 58.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % Twisted Proline : 1.52 % Twisted General : 0.26 % 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: -2.74 (0.16), residues: 1971 helix: -0.66 (0.20), residues: 608 sheet: -0.94 (0.29), residues: 258 loop : -2.85 (0.15), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 186 HIS 0.021 0.003 HIS B 523 PHE 0.028 0.003 PHE B 399 TYR 0.043 0.003 TYR B 754 ARG 0.008 0.001 ARG A 352 Details of bonding type rmsd hydrogen bonds : bond 0.05571 ( 433) hydrogen bonds : angle 6.29775 ( 1227) covalent geometry : bond 0.00457 (15250) covalent geometry : angle 0.95442 (20703) Misc. bond : bond 0.00108 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 278 poor density : 292 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.8483 (mp) cc_final: 0.8125 (mm) REVERT: A 40 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7078 (tt0) REVERT: A 66 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8461 (pt) REVERT: A 95 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8141 (pt0) REVERT: A 112 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8922 (mtm) REVERT: A 120 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7799 (ptt90) REVERT: A 163 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6727 (tp30) REVERT: A 170 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8218 (tt) REVERT: A 176 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7510 (mpt180) REVERT: A 177 MET cc_start: 0.7591 (tpp) cc_final: 0.7256 (mtt) REVERT: A 201 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8207 (mmt) REVERT: A 217 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: A 262 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.5950 (mtt180) REVERT: A 290 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7783 (pp30) REVERT: A 305 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7089 (p0) REVERT: A 317 SER cc_start: 0.7429 (OUTLIER) cc_final: 0.6998 (p) REVERT: A 329 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.7623 (p-80) REVERT: A 375 GLU cc_start: 0.7599 (tp30) cc_final: 0.6938 (pt0) REVERT: A 388 SER cc_start: 0.8087 (OUTLIER) cc_final: 0.7655 (m) REVERT: A 499 ASP cc_start: 0.7249 (t0) cc_final: 0.7007 (t0) REVERT: A 623 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8320 (mt) REVERT: A 625 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7833 (tpt-90) REVERT: A 641 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8168 (ttm) REVERT: A 685 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.7701 (pt) REVERT: A 745 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.6548 (mpp) REVERT: A 801 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7698 (pp) REVERT: A 826 ASP cc_start: 0.7850 (t0) cc_final: 0.7618 (p0) REVERT: A 834 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8592 (tmm) REVERT: A 843 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.6160 (mtm180) REVERT: A 863 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8539 (m) REVERT: A 879 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.8017 (mtt-85) REVERT: A 890 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8102 (mtm180) REVERT: A 938 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7643 (ptt180) REVERT: B 1 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7517 (tmm) REVERT: B 51 LEU cc_start: 0.7936 (tp) cc_final: 0.7667 (tp) REVERT: B 58 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7574 (tm-30) REVERT: B 112 THR cc_start: 0.8978 (m) cc_final: 0.8745 (m) REVERT: B 224 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8173 (tp) REVERT: B 253 HIS cc_start: 0.8657 (OUTLIER) cc_final: 0.7535 (t70) REVERT: B 266 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.8316 (p-80) REVERT: B 273 TRP cc_start: 0.8228 (OUTLIER) cc_final: 0.8027 (t-100) REVERT: B 299 MET cc_start: 0.8337 (mmm) cc_final: 0.7814 (ttt) REVERT: B 327 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.5752 (m-80) REVERT: B 347 TRP cc_start: 0.7716 (t60) cc_final: 0.5360 (t60) REVERT: B 391 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6990 (tt0) REVERT: B 603 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7049 (t0) REVERT: B 622 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8564 (pp) REVERT: B 653 VAL cc_start: 0.7637 (t) cc_final: 0.7429 (t) REVERT: B 795 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6954 (tt0) REVERT: B 838 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8397 (ttp-110) REVERT: B 860 MET cc_start: 0.8204 (ptp) cc_final: 0.7702 (ptp) REVERT: B 866 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7479 (tm) REVERT: B 930 ASN cc_start: 0.7475 (p0) cc_final: 0.7261 (p0) REVERT: B 941 MET cc_start: 0.7774 (mmt) cc_final: 0.7193 (mmt) REVERT: B 945 ARG cc_start: 0.7409 (mmm-85) cc_final: 0.4676 (ttm170) REVERT: B 970 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: B 979 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8076 (tttm) REVERT: B 993 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8421 (tptt) REVERT: B 1005 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.6426 (pttt) outliers start: 278 outliers final: 128 residues processed: 508 average time/residue: 0.3205 time to fit residues: 229.5416 Evaluate side-chains 415 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 242 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 309 TRP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 590 PHE Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 TYR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 627 ARG Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 757 HIS Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 834 MET Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 879 ARG Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 890 ARG Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 929 GLN Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 938 ARG Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 273 TRP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 710 HIS Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 795 GLU Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 ARG Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain B residue 943 GLU Chi-restraints excluded: chain B residue 970 TYR Chi-restraints excluded: chain B residue 979 LYS Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1005 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 44 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 GLN A 208 HIS A 393 HIS ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 HIS A 612 ASN ** A 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN A 800 HIS A 900 HIS A 922 ASN ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 467 GLN B 490 ASN B 677 HIS B 705 ASN B 805 HIS B 885 ASN B 902 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.138754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.131174 restraints weight = 17046.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.132130 restraints weight = 12914.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.133640 restraints weight = 10272.604| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15257 Z= 0.170 Angle : 0.802 14.009 20703 Z= 0.414 Chirality : 0.047 0.236 2356 Planarity : 0.005 0.063 2702 Dihedral : 14.024 102.760 2464 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.12 % Favored : 91.22 % Rotamer: Outliers : 12.33 % Allowed : 25.79 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % 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: -2.45 (0.17), residues: 1971 helix: -0.40 (0.20), residues: 616 sheet: -0.67 (0.29), residues: 274 loop : -2.76 (0.16), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 333 HIS 0.025 0.002 HIS A 757 PHE 0.016 0.002 PHE B 399 TYR 0.025 0.002 TYR B 754 ARG 0.007 0.001 ARG B 390 Details of bonding type rmsd hydrogen bonds : bond 0.04351 ( 433) hydrogen bonds : angle 5.56182 ( 1227) covalent geometry : bond 0.00381 (15250) covalent geometry : angle 0.80236 (20703) Misc. bond : bond 0.00178 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 295 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6947 (tt0) REVERT: A 95 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8417 (pt0) REVERT: A 163 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6609 (tp30) REVERT: A 170 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8464 (tt) REVERT: A 174 ARG cc_start: 0.8497 (mtm-85) cc_final: 0.8260 (mtm-85) REVERT: A 177 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7269 (mtt) REVERT: A 217 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7494 (mm-30) REVERT: A 262 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6082 (mtp180) REVERT: A 272 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6872 (ttm110) REVERT: A 328 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: A 380 CYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7824 (t) REVERT: A 446 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7594 (mtt-85) REVERT: A 487 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8464 (mt) REVERT: A 708 ARG cc_start: 0.7994 (mmt90) cc_final: 0.7719 (mmt180) REVERT: A 801 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7702 (pp) REVERT: A 890 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8070 (mtm180) REVERT: A 915 GLU cc_start: 0.7879 (tp30) cc_final: 0.7589 (tp30) REVERT: A 938 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7605 (ptt90) REVERT: A 943 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7136 (tmt90) REVERT: B 38 LYS cc_start: 0.7937 (tptp) cc_final: 0.7430 (mmtm) REVERT: B 58 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: B 65 GLU cc_start: 0.7825 (pt0) cc_final: 0.7536 (pt0) REVERT: B 69 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: B 74 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7612 (mtm) REVERT: B 225 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.7991 (m) REVERT: B 253 HIS cc_start: 0.8588 (OUTLIER) cc_final: 0.8210 (t70) REVERT: B 327 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.5685 (m-80) REVERT: B 437 HIS cc_start: 0.6543 (OUTLIER) cc_final: 0.6279 (t-170) REVERT: B 481 ARG cc_start: 0.8190 (tmm160) cc_final: 0.7571 (ttp80) REVERT: B 509 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7980 (tt) REVERT: B 603 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7195 (t0) REVERT: B 613 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8415 (tt) REVERT: B 622 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8542 (pp) REVERT: B 656 TYR cc_start: 0.8651 (m-10) cc_final: 0.8310 (m-10) REVERT: B 813 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8516 (mt) REVERT: B 866 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7628 (tm) REVERT: B 893 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7912 (pt) REVERT: B 941 MET cc_start: 0.7870 (mmt) cc_final: 0.7161 (mmt) REVERT: B 945 ARG cc_start: 0.7504 (mmm-85) cc_final: 0.4774 (ttm170) REVERT: B 970 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: B 979 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8045 (tttt) REVERT: B 993 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8240 (tptp) REVERT: B 1005 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.6253 (pttt) outliers start: 194 outliers final: 102 residues processed: 453 average time/residue: 0.3162 time to fit residues: 208.7498 Evaluate side-chains 391 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 255 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 309 TRP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 590 PHE Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 TYR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 649 HIS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 890 ARG Chi-restraints excluded: chain A residue 929 GLN Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 938 ARG Chi-restraints excluded: chain A residue 943 ARG Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 903 THR Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain B residue 943 GLU Chi-restraints excluded: chain B residue 970 TYR Chi-restraints excluded: chain B residue 979 LYS Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1005 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 172 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 144 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 128 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 GLN A 407 HIS A 612 ASN ** A 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 ASN A 722 HIS ** A 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 811 ASN B 100 ASN ** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.136953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.127029 restraints weight = 16954.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.128954 restraints weight = 11355.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.130485 restraints weight = 8243.499| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15257 Z= 0.166 Angle : 0.752 10.671 20703 Z= 0.385 Chirality : 0.045 0.296 2356 Planarity : 0.004 0.046 2702 Dihedral : 11.764 90.058 2345 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.61 % Favored : 91.73 % Rotamer: Outliers : 11.82 % Allowed : 27.13 % Favored : 61.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % 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: -2.30 (0.17), residues: 1971 helix: -0.24 (0.20), residues: 614 sheet: -0.59 (0.29), residues: 278 loop : -2.69 (0.16), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 333 HIS 0.013 0.002 HIS A 20 PHE 0.014 0.002 PHE B 399 TYR 0.013 0.002 TYR B1003 ARG 0.010 0.001 ARG A 879 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 433) hydrogen bonds : angle 5.22610 ( 1227) covalent geometry : bond 0.00380 (15250) covalent geometry : angle 0.75245 (20703) Misc. bond : bond 0.00118 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 287 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: A 95 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8537 (pt0) REVERT: A 150 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7274 (ttm110) REVERT: A 163 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6614 (tp30) REVERT: A 164 MET cc_start: 0.7878 (mmt) cc_final: 0.7544 (mmm) REVERT: A 170 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8448 (tt) REVERT: A 199 MET cc_start: 0.7745 (tmm) cc_final: 0.7042 (ttt) REVERT: A 217 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: A 262 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6325 (mtt180) REVERT: A 328 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: A 380 CYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7695 (t) REVERT: A 411 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7728 (p90) REVERT: A 446 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7533 (mtt-85) REVERT: A 512 MET cc_start: 0.8708 (mmm) cc_final: 0.8358 (mmt) REVERT: A 603 GLU cc_start: 0.6844 (pp20) cc_final: 0.6588 (pp20) REVERT: A 623 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8476 (mt) REVERT: A 745 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.6403 (mpp) REVERT: A 783 ASP cc_start: 0.7417 (p0) cc_final: 0.7042 (p0) REVERT: A 801 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7885 (pp) REVERT: A 821 ASP cc_start: 0.7167 (m-30) cc_final: 0.6915 (m-30) REVERT: A 878 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: A 915 GLU cc_start: 0.7888 (tp30) cc_final: 0.7615 (tp30) REVERT: A 943 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7137 (tmt90) REVERT: B 69 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6975 (mt-10) REVERT: B 225 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8054 (m) REVERT: B 253 HIS cc_start: 0.8434 (OUTLIER) cc_final: 0.8035 (t70) REVERT: B 437 HIS cc_start: 0.6415 (OUTLIER) cc_final: 0.6118 (t-170) REVERT: B 481 ARG cc_start: 0.8149 (tmm160) cc_final: 0.7435 (ttp80) REVERT: B 509 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7921 (tt) REVERT: B 603 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7429 (t0) REVERT: B 751 ARG cc_start: 0.7665 (mtp85) cc_final: 0.7213 (mtp85) REVERT: B 813 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8656 (mt) REVERT: B 866 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7656 (tm) REVERT: B 941 MET cc_start: 0.7968 (mmt) cc_final: 0.7207 (mmt) REVERT: B 943 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8039 (mm-30) REVERT: B 945 ARG cc_start: 0.7472 (mmm-85) cc_final: 0.4636 (ttm170) REVERT: B 970 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.7302 (m-80) REVERT: B 979 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7915 (tttm) REVERT: B 993 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8290 (tptp) REVERT: B 1005 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6215 (pttt) outliers start: 186 outliers final: 100 residues processed: 427 average time/residue: 0.3078 time to fit residues: 192.1635 Evaluate side-chains 388 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 259 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 309 TRP Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 590 PHE Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 TYR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 929 GLN Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 943 ARG Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 735 HIS Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 903 THR Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain B residue 943 GLU Chi-restraints excluded: chain B residue 970 TYR Chi-restraints excluded: chain B residue 979 LYS Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1005 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 34 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 194 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS A 38 ASN A 612 ASN ** A 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 HIS B 100 ASN B 220 HIS ** B 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.132409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.123871 restraints weight = 17321.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.125002 restraints weight = 13303.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.126644 restraints weight = 10266.564| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15257 Z= 0.185 Angle : 0.741 11.417 20703 Z= 0.380 Chirality : 0.045 0.312 2356 Planarity : 0.004 0.038 2702 Dihedral : 10.933 90.203 2300 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.97 % Favored : 91.37 % Rotamer: Outliers : 10.86 % Allowed : 28.40 % Favored : 60.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % 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: -2.23 (0.17), residues: 1971 helix: -0.24 (0.20), residues: 620 sheet: -0.65 (0.30), residues: 280 loop : -2.58 (0.16), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 333 HIS 0.013 0.002 HIS B 523 PHE 0.014 0.002 PHE A 431 TYR 0.016 0.002 TYR A 850 ARG 0.006 0.001 ARG A 879 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 433) hydrogen bonds : angle 5.09077 ( 1227) covalent geometry : bond 0.00430 (15250) covalent geometry : angle 0.74052 (20703) Misc. bond : bond 0.00100 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 272 time to evaluate : 1.702 Fit side-chains revert: symmetry clash REVERT: A 95 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8457 (pt0) REVERT: A 162 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6777 (ttp80) REVERT: A 163 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6761 (tp30) REVERT: A 199 MET cc_start: 0.7978 (tmm) cc_final: 0.7280 (ttt) REVERT: A 217 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: A 262 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6382 (mtt180) REVERT: A 329 HIS cc_start: 0.8087 (OUTLIER) cc_final: 0.7580 (p-80) REVERT: A 380 CYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7682 (t) REVERT: A 411 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8158 (p90) REVERT: A 444 MET cc_start: 0.7945 (mtm) cc_final: 0.7662 (mtm) REVERT: A 512 MET cc_start: 0.8848 (mmm) cc_final: 0.8389 (mmt) REVERT: A 592 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7702 (mt0) REVERT: A 623 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8518 (mt) REVERT: A 632 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8099 (ptp90) REVERT: A 745 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.6474 (mpp) REVERT: A 783 ASP cc_start: 0.7397 (p0) cc_final: 0.7138 (p0) REVERT: A 801 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8099 (pp) REVERT: A 821 ASP cc_start: 0.7306 (m-30) cc_final: 0.7004 (m-30) REVERT: A 890 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8113 (mtm180) REVERT: A 943 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7086 (tmt90) REVERT: B 69 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6851 (mt-10) REVERT: B 74 MET cc_start: 0.8208 (mtt) cc_final: 0.7799 (mtm) REVERT: B 111 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8045 (mmt) REVERT: B 225 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8077 (m) REVERT: B 437 HIS cc_start: 0.6575 (OUTLIER) cc_final: 0.6373 (t-170) REVERT: B 467 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.6055 (pp30) REVERT: B 481 ARG cc_start: 0.7988 (tmm160) cc_final: 0.7322 (ttp80) REVERT: B 509 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8021 (tt) REVERT: B 603 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7360 (t0) REVERT: B 609 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.7781 (t) REVERT: B 613 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8485 (tt) REVERT: B 656 TYR cc_start: 0.8681 (m-10) cc_final: 0.8465 (m-10) REVERT: B 941 MET cc_start: 0.8042 (mmt) cc_final: 0.7392 (mmt) REVERT: B 943 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8085 (mm-30) REVERT: B 945 ARG cc_start: 0.7598 (mmm-85) cc_final: 0.4883 (ttm170) REVERT: B 970 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.7358 (m-80) REVERT: B 979 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7959 (tttt) REVERT: B 993 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8310 (tptt) REVERT: B 1005 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.6116 (pttt) outliers start: 171 outliers final: 105 residues processed: 399 average time/residue: 0.2948 time to fit residues: 171.5731 Evaluate side-chains 384 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 250 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 309 TRP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 TYR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 890 ARG Chi-restraints excluded: chain A residue 929 GLN Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 943 ARG Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 735 HIS Chi-restraints excluded: chain B residue 757 ARG Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 903 THR Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 943 GLU Chi-restraints excluded: chain B residue 970 TYR Chi-restraints excluded: chain B residue 979 LYS Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1005 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 26 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 184 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 136 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS A 387 ASN A 612 ASN ** A 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS B 449 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.134896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.126170 restraints weight = 17023.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.127818 restraints weight = 11922.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.129124 restraints weight = 8920.711| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15257 Z= 0.151 Angle : 0.710 10.546 20703 Z= 0.362 Chirality : 0.044 0.314 2356 Planarity : 0.004 0.038 2702 Dihedral : 10.448 91.137 2287 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.81 % Favored : 91.58 % Rotamer: Outliers : 9.34 % Allowed : 30.30 % Favored : 60.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % 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: -2.13 (0.18), residues: 1971 helix: -0.10 (0.21), residues: 625 sheet: -0.62 (0.30), residues: 280 loop : -2.57 (0.17), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 333 HIS 0.023 0.001 HIS B 220 PHE 0.013 0.001 PHE A 431 TYR 0.014 0.002 TYR B 327 ARG 0.006 0.000 ARG A 879 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 433) hydrogen bonds : angle 4.96177 ( 1227) covalent geometry : bond 0.00348 (15250) covalent geometry : angle 0.71045 (20703) Misc. bond : bond 0.00079 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 270 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8495 (pt0) REVERT: A 162 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6678 (ttp80) REVERT: A 163 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6743 (tp30) REVERT: A 199 MET cc_start: 0.7839 (tmm) cc_final: 0.7115 (ttt) REVERT: A 217 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: A 262 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6388 (mtt180) REVERT: A 329 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7437 (p-80) REVERT: A 411 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8179 (p90) REVERT: A 444 MET cc_start: 0.7900 (mtm) cc_final: 0.7590 (mtm) REVERT: A 472 ASP cc_start: 0.7201 (t0) cc_final: 0.6960 (m-30) REVERT: A 512 MET cc_start: 0.8815 (mmm) cc_final: 0.8328 (mmt) REVERT: A 545 SER cc_start: 0.8047 (m) cc_final: 0.7281 (p) REVERT: A 552 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7119 (m-80) REVERT: A 623 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8441 (mt) REVERT: A 632 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7606 (ptp90) REVERT: A 671 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7311 (tm) REVERT: A 742 MET cc_start: 0.8363 (mmm) cc_final: 0.7942 (tpp) REVERT: A 745 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.6281 (mpp) REVERT: A 783 ASP cc_start: 0.7392 (p0) cc_final: 0.7099 (p0) REVERT: A 801 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7897 (pp) REVERT: A 821 ASP cc_start: 0.7284 (m-30) cc_final: 0.6943 (m-30) REVERT: A 890 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8145 (mtm180) REVERT: A 943 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7173 (tmt90) REVERT: B 111 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8067 (mmt) REVERT: B 437 HIS cc_start: 0.6541 (OUTLIER) cc_final: 0.6254 (t-170) REVERT: B 449 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8571 (m-40) REVERT: B 467 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.6227 (pp30) REVERT: B 500 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7862 (mm-40) REVERT: B 509 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7840 (tt) REVERT: B 511 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.7002 (t0) REVERT: B 521 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7396 (tt) REVERT: B 603 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7324 (t0) REVERT: B 613 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8486 (tt) REVERT: B 653 VAL cc_start: 0.7993 (t) cc_final: 0.7680 (t) REVERT: B 866 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.7919 (tm) REVERT: B 941 MET cc_start: 0.8201 (mmt) cc_final: 0.7378 (mmt) REVERT: B 943 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8130 (mm-30) REVERT: B 945 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.4805 (ttm170) REVERT: B 970 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.7320 (m-80) REVERT: B 979 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8088 (ttpp) REVERT: B 993 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8303 (tptt) REVERT: B 1005 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.6165 (pttt) outliers start: 147 outliers final: 98 residues processed: 379 average time/residue: 0.3447 time to fit residues: 192.0667 Evaluate side-chains 384 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 255 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 309 TRP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 TYR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 890 ARG Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 929 GLN Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 943 ARG Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 757 ARG Chi-restraints excluded: chain B residue 784 MET Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 850 LYS Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain B residue 943 GLU Chi-restraints excluded: chain B residue 970 TYR Chi-restraints excluded: chain B residue 979 LYS Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1005 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 180 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 91 optimal weight: 0.0370 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS A 612 ASN A 722 HIS B 220 HIS B 449 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.132247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.123721 restraints weight = 17199.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.125229 restraints weight = 12201.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.126446 restraints weight = 9271.268| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15257 Z= 0.182 Angle : 0.724 11.573 20703 Z= 0.371 Chirality : 0.045 0.325 2356 Planarity : 0.004 0.036 2702 Dihedral : 10.217 91.100 2280 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.37 % Favored : 91.02 % Rotamer: Outliers : 9.85 % Allowed : 29.54 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % 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: -2.11 (0.18), residues: 1971 helix: -0.10 (0.21), residues: 625 sheet: -0.72 (0.30), residues: 285 loop : -2.51 (0.17), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 333 HIS 0.012 0.001 HIS B 523 PHE 0.014 0.002 PHE A 431 TYR 0.017 0.002 TYR A 850 ARG 0.005 0.000 ARG A 879 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 433) hydrogen bonds : angle 4.94488 ( 1227) covalent geometry : bond 0.00429 (15250) covalent geometry : angle 0.72363 (20703) Misc. bond : bond 0.00085 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 267 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8386 (pt0) REVERT: A 163 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6754 (tp30) REVERT: A 199 MET cc_start: 0.7943 (tmm) cc_final: 0.7045 (ttt) REVERT: A 217 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: A 258 GLN cc_start: 0.7414 (tt0) cc_final: 0.7147 (tt0) REVERT: A 262 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6380 (mtt180) REVERT: A 329 HIS cc_start: 0.8202 (OUTLIER) cc_final: 0.7556 (p-80) REVERT: A 380 CYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7134 (t) REVERT: A 411 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.8319 (p90) REVERT: A 444 MET cc_start: 0.7911 (mtm) cc_final: 0.7667 (mtm) REVERT: A 472 ASP cc_start: 0.7241 (t0) cc_final: 0.6956 (m-30) REVERT: A 545 SER cc_start: 0.8018 (m) cc_final: 0.7327 (p) REVERT: A 552 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: A 615 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.8143 (m-80) REVERT: A 623 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8450 (mt) REVERT: A 671 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7290 (tm) REVERT: A 706 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: A 742 MET cc_start: 0.8210 (mmm) cc_final: 0.7872 (tpp) REVERT: A 745 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.6390 (mpp) REVERT: A 783 ASP cc_start: 0.7406 (p0) cc_final: 0.7134 (p0) REVERT: A 801 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8015 (pp) REVERT: A 821 ASP cc_start: 0.7333 (m-30) cc_final: 0.6962 (m-30) REVERT: A 890 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8219 (mtm180) REVERT: A 943 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7398 (tmt90) REVERT: B 38 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7576 (mmtm) REVERT: B 69 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.7055 (mt-10) REVERT: B 74 MET cc_start: 0.8146 (mtt) cc_final: 0.7757 (mtm) REVERT: B 111 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8061 (mmt) REVERT: B 351 LYS cc_start: 0.8363 (mmmm) cc_final: 0.7938 (mmtm) REVERT: B 437 HIS cc_start: 0.6471 (OUTLIER) cc_final: 0.6166 (t-170) REVERT: B 467 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.6450 (pp30) REVERT: B 500 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7878 (mm-40) REVERT: B 509 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7911 (tt) REVERT: B 511 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.7019 (t0) REVERT: B 546 MET cc_start: 0.8355 (mmp) cc_final: 0.8059 (mmm) REVERT: B 566 MET cc_start: 0.8937 (tpt) cc_final: 0.8513 (tpt) REVERT: B 603 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7329 (t0) REVERT: B 613 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8461 (tt) REVERT: B 653 VAL cc_start: 0.8226 (t) cc_final: 0.7867 (t) REVERT: B 941 MET cc_start: 0.8029 (mmt) cc_final: 0.7341 (mmt) REVERT: B 943 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8147 (mm-30) REVERT: B 945 ARG cc_start: 0.7637 (mmm-85) cc_final: 0.5025 (ttm170) REVERT: B 970 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.7270 (m-80) REVERT: B 993 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8316 (tmtp) REVERT: B 1005 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.6283 (pttt) outliers start: 155 outliers final: 102 residues processed: 384 average time/residue: 0.2770 time to fit residues: 154.9598 Evaluate side-chains 385 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 253 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 309 TRP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 TYR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 890 ARG Chi-restraints excluded: chain A residue 929 GLN Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 943 ARG Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 757 ARG Chi-restraints excluded: chain B residue 784 MET Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 943 GLU Chi-restraints excluded: chain B residue 970 TYR Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 997 THR Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1005 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 21 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN A 722 HIS B 220 HIS B 449 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.132288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.123630 restraints weight = 17224.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.125200 restraints weight = 12076.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.126443 restraints weight = 9077.454| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15257 Z= 0.163 Angle : 0.706 11.754 20703 Z= 0.359 Chirality : 0.044 0.319 2356 Planarity : 0.004 0.035 2702 Dihedral : 9.976 91.931 2274 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.12 % Favored : 91.32 % Rotamer: Outliers : 9.40 % Allowed : 29.86 % Favored : 60.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % 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: -2.05 (0.18), residues: 1971 helix: -0.07 (0.21), residues: 628 sheet: -0.67 (0.30), residues: 286 loop : -2.47 (0.17), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 333 HIS 0.013 0.001 HIS B 606 PHE 0.014 0.001 PHE A 431 TYR 0.017 0.002 TYR A 850 ARG 0.006 0.000 ARG B 668 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 433) hydrogen bonds : angle 4.87838 ( 1227) covalent geometry : bond 0.00379 (15250) covalent geometry : angle 0.70649 (20703) Misc. bond : bond 0.00067 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 273 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8369 (pt0) REVERT: A 163 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6869 (tp30) REVERT: A 199 MET cc_start: 0.7958 (tmm) cc_final: 0.7048 (ttt) REVERT: A 217 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: A 258 GLN cc_start: 0.7603 (tt0) cc_final: 0.7399 (tt0) REVERT: A 262 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.6593 (mtt180) REVERT: A 329 HIS cc_start: 0.8031 (OUTLIER) cc_final: 0.7326 (p-80) REVERT: A 375 GLU cc_start: 0.7555 (tp30) cc_final: 0.6921 (pt0) REVERT: A 380 CYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7136 (t) REVERT: A 411 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8283 (p90) REVERT: A 472 ASP cc_start: 0.7186 (t0) cc_final: 0.6915 (m-30) REVERT: A 512 MET cc_start: 0.8871 (mmm) cc_final: 0.8468 (mmt) REVERT: A 545 SER cc_start: 0.8039 (m) cc_final: 0.7295 (p) REVERT: A 552 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7192 (m-80) REVERT: A 615 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: A 623 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8415 (mt) REVERT: A 671 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7243 (tm) REVERT: A 706 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: A 730 THR cc_start: 0.9407 (OUTLIER) cc_final: 0.9190 (t) REVERT: A 742 MET cc_start: 0.8142 (mmm) cc_final: 0.7783 (tpp) REVERT: A 745 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6340 (mpp) REVERT: A 783 ASP cc_start: 0.7418 (p0) cc_final: 0.7194 (p0) REVERT: A 801 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.7992 (pp) REVERT: A 821 ASP cc_start: 0.7307 (m-30) cc_final: 0.6930 (m-30) REVERT: A 890 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8271 (mtm180) REVERT: A 943 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7421 (tmt90) REVERT: B 38 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7411 (mmtm) REVERT: B 69 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7037 (mt-10) REVERT: B 74 MET cc_start: 0.8096 (mtt) cc_final: 0.7700 (mtm) REVERT: B 111 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8075 (mmt) REVERT: B 437 HIS cc_start: 0.6519 (OUTLIER) cc_final: 0.6225 (t-170) REVERT: B 467 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.6523 (pp30) REVERT: B 500 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7846 (mm-40) REVERT: B 509 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8061 (tt) REVERT: B 511 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6970 (t0) REVERT: B 521 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7434 (tt) REVERT: B 543 ASN cc_start: 0.8204 (t0) cc_final: 0.7878 (t0) REVERT: B 603 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7273 (t0) REVERT: B 609 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7741 (t) REVERT: B 613 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8547 (tt) REVERT: B 653 VAL cc_start: 0.8177 (t) cc_final: 0.7844 (t) REVERT: B 941 MET cc_start: 0.7836 (mmt) cc_final: 0.7072 (mmt) REVERT: B 943 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8160 (mm-30) REVERT: B 945 ARG cc_start: 0.7632 (mmm-85) cc_final: 0.5031 (ttm170) REVERT: B 966 ARG cc_start: 0.7517 (ttm-80) cc_final: 0.7286 (ttm-80) REVERT: B 970 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.7242 (m-80) REVERT: B 993 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8472 (tmtp) REVERT: B 1005 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.6280 (pttt) outliers start: 148 outliers final: 101 residues processed: 380 average time/residue: 0.3326 time to fit residues: 190.6979 Evaluate side-chains 394 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 260 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 309 TRP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 TYR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 890 ARG Chi-restraints excluded: chain A residue 929 GLN Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 943 ARG Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 757 ARG Chi-restraints excluded: chain B residue 784 MET Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 943 GLU Chi-restraints excluded: chain B residue 970 TYR Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 997 THR Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1005 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 114 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN A 722 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.134731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.126206 restraints weight = 16990.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.127641 restraints weight = 11874.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.128905 restraints weight = 9035.073| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15257 Z= 0.144 Angle : 0.691 11.852 20703 Z= 0.351 Chirality : 0.043 0.335 2356 Planarity : 0.004 0.035 2702 Dihedral : 9.713 92.210 2268 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.17 % Favored : 91.27 % Rotamer: Outliers : 8.45 % Allowed : 31.13 % Favored : 60.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % 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: -1.93 (0.18), residues: 1971 helix: 0.04 (0.21), residues: 624 sheet: -0.61 (0.30), residues: 288 loop : -2.40 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 333 HIS 0.014 0.001 HIS B 606 PHE 0.014 0.001 PHE A 431 TYR 0.015 0.001 TYR A 850 ARG 0.005 0.000 ARG A 103 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 433) hydrogen bonds : angle 4.74137 ( 1227) covalent geometry : bond 0.00329 (15250) covalent geometry : angle 0.69142 (20703) Misc. bond : bond 0.00113 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 275 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8488 (pt0) REVERT: A 163 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6830 (tp30) REVERT: A 199 MET cc_start: 0.7735 (tmm) cc_final: 0.6990 (ttt) REVERT: A 217 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: A 258 GLN cc_start: 0.7602 (tt0) cc_final: 0.7362 (tt0) REVERT: A 262 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6625 (mtt180) REVERT: A 329 HIS cc_start: 0.8033 (OUTLIER) cc_final: 0.7247 (p-80) REVERT: A 375 GLU cc_start: 0.7514 (tp30) cc_final: 0.6909 (pt0) REVERT: A 380 CYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7155 (t) REVERT: A 411 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.8032 (p90) REVERT: A 444 MET cc_start: 0.7761 (mtm) cc_final: 0.7519 (mtp) REVERT: A 512 MET cc_start: 0.8862 (mmm) cc_final: 0.8480 (mmt) REVERT: A 545 SER cc_start: 0.7954 (m) cc_final: 0.7241 (p) REVERT: A 552 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: A 613 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: A 615 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: A 623 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8383 (mt) REVERT: A 706 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: A 742 MET cc_start: 0.7949 (mmm) cc_final: 0.7579 (tpp) REVERT: A 745 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6125 (mpp) REVERT: A 783 ASP cc_start: 0.7509 (p0) cc_final: 0.7176 (p0) REVERT: A 801 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8003 (pp) REVERT: A 821 ASP cc_start: 0.7288 (m-30) cc_final: 0.6892 (m-30) REVERT: A 834 MET cc_start: 0.9143 (ttp) cc_final: 0.8867 (ttp) REVERT: A 878 GLU cc_start: 0.8172 (pp20) cc_final: 0.7565 (pp20) REVERT: A 890 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8246 (mtm180) REVERT: A 943 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7492 (tmt90) REVERT: B 38 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7452 (mmtm) REVERT: B 56 ARG cc_start: 0.7751 (ptt180) cc_final: 0.7319 (ptt180) REVERT: B 65 GLU cc_start: 0.8004 (pt0) cc_final: 0.7722 (pt0) REVERT: B 69 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7046 (mt-10) REVERT: B 89 ASP cc_start: 0.6917 (m-30) cc_final: 0.6534 (m-30) REVERT: B 111 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8100 (mmt) REVERT: B 347 TRP cc_start: 0.8841 (OUTLIER) cc_final: 0.7236 (t60) REVERT: B 351 LYS cc_start: 0.8473 (mmmm) cc_final: 0.8220 (mmmm) REVERT: B 437 HIS cc_start: 0.6444 (OUTLIER) cc_final: 0.6110 (t-170) REVERT: B 467 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.6496 (pp30) REVERT: B 500 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7861 (mm-40) REVERT: B 509 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7969 (tt) REVERT: B 511 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6995 (t0) REVERT: B 521 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7453 (tt) REVERT: B 543 ASN cc_start: 0.8373 (t0) cc_final: 0.7978 (t0) REVERT: B 566 MET cc_start: 0.8810 (tpt) cc_final: 0.8578 (tpt) REVERT: B 603 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7196 (t0) REVERT: B 609 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7715 (t) REVERT: B 613 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8470 (tt) REVERT: B 653 VAL cc_start: 0.8303 (t) cc_final: 0.8015 (t) REVERT: B 866 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8036 (tm) REVERT: B 932 SER cc_start: 0.8872 (p) cc_final: 0.8659 (p) REVERT: B 941 MET cc_start: 0.8014 (mmt) cc_final: 0.7221 (mmt) REVERT: B 943 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8120 (mm-30) REVERT: B 945 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.4891 (ttm170) REVERT: B 970 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.7263 (m-80) REVERT: B 993 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8521 (tmtp) REVERT: B 1005 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.6427 (pttt) outliers start: 133 outliers final: 91 residues processed: 372 average time/residue: 0.2839 time to fit residues: 156.3541 Evaluate side-chains 385 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 261 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 309 TRP Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 TYR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 890 ARG Chi-restraints excluded: chain A residue 929 GLN Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 943 ARG Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 347 TRP Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 757 ARG Chi-restraints excluded: chain B residue 784 MET Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 943 GLU Chi-restraints excluded: chain B residue 970 TYR Chi-restraints excluded: chain B residue 993 LYS Chi-restraints excluded: chain B residue 997 THR Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1005 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 67 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 162 optimal weight: 0.2980 chunk 102 optimal weight: 0.0670 chunk 99 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.136285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.127704 restraints weight = 17025.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.129318 restraints weight = 11909.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.130592 restraints weight = 8947.188| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15257 Z= 0.133 Angle : 0.689 11.659 20703 Z= 0.347 Chirality : 0.043 0.345 2356 Planarity : 0.004 0.036 2702 Dihedral : 9.246 91.500 2259 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.86 % Favored : 91.68 % Rotamer: Outliers : 7.75 % Allowed : 31.70 % Favored : 60.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % 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: -1.82 (0.18), residues: 1971 helix: 0.17 (0.21), residues: 619 sheet: -0.53 (0.31), residues: 288 loop : -2.35 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 333 HIS 0.014 0.001 HIS B 606 PHE 0.013 0.001 PHE A 431 TYR 0.014 0.001 TYR A 850 ARG 0.005 0.000 ARG A 879 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 433) hydrogen bonds : angle 4.66319 ( 1227) covalent geometry : bond 0.00300 (15250) covalent geometry : angle 0.68926 (20703) Misc. bond : bond 0.00087 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 273 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6843 (tp30) REVERT: A 164 MET cc_start: 0.8244 (mmm) cc_final: 0.7946 (mmm) REVERT: A 199 MET cc_start: 0.7691 (tmm) cc_final: 0.6989 (ttt) REVERT: A 217 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: A 258 GLN cc_start: 0.7638 (tt0) cc_final: 0.7401 (tt0) REVERT: A 262 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6605 (mtt180) REVERT: A 329 HIS cc_start: 0.7990 (OUTLIER) cc_final: 0.7205 (p-80) REVERT: A 375 GLU cc_start: 0.7505 (tp30) cc_final: 0.6870 (pt0) REVERT: A 411 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.7981 (p90) REVERT: A 444 MET cc_start: 0.7683 (mtm) cc_final: 0.7394 (mtp) REVERT: A 512 MET cc_start: 0.8748 (mmm) cc_final: 0.8331 (mmt) REVERT: A 545 SER cc_start: 0.7895 (m) cc_final: 0.7155 (p) REVERT: A 552 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7129 (m-80) REVERT: A 615 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: A 633 ASP cc_start: 0.7658 (t0) cc_final: 0.7447 (t0) REVERT: A 706 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: A 742 MET cc_start: 0.7965 (mmm) cc_final: 0.7420 (tpp) REVERT: A 745 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6134 (mpp) REVERT: A 783 ASP cc_start: 0.7439 (p0) cc_final: 0.7150 (p0) REVERT: A 801 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7899 (pp) REVERT: A 810 MET cc_start: 0.8710 (ppp) cc_final: 0.8232 (ppp) REVERT: A 821 ASP cc_start: 0.7375 (m-30) cc_final: 0.6944 (m-30) REVERT: A 830 ARG cc_start: 0.7933 (pmt-80) cc_final: 0.7714 (pmt-80) REVERT: A 834 MET cc_start: 0.9091 (ttp) cc_final: 0.8859 (ttp) REVERT: A 890 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8245 (mtm180) REVERT: A 943 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7384 (tmt90) REVERT: B 38 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7484 (mmtm) REVERT: B 56 ARG cc_start: 0.7724 (ptt180) cc_final: 0.7297 (ptt180) REVERT: B 58 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: B 65 GLU cc_start: 0.7942 (pt0) cc_final: 0.7686 (pt0) REVERT: B 69 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6962 (mt-10) REVERT: B 89 ASP cc_start: 0.6947 (m-30) cc_final: 0.6742 (m-30) REVERT: B 92 LEU cc_start: 0.8368 (pt) cc_final: 0.8066 (tp) REVERT: B 351 LYS cc_start: 0.8226 (mmmm) cc_final: 0.7836 (mmmm) REVERT: B 437 HIS cc_start: 0.6581 (OUTLIER) cc_final: 0.6315 (t-170) REVERT: B 467 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.6470 (pp30) REVERT: B 500 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7940 (mm-40) REVERT: B 509 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7879 (tt) REVERT: B 511 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6930 (t0) REVERT: B 521 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7434 (tt) REVERT: B 543 ASN cc_start: 0.8113 (t0) cc_final: 0.7798 (t0) REVERT: B 550 MET cc_start: 0.5861 (mmp) cc_final: 0.5618 (mmm) REVERT: B 603 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7149 (t0) REVERT: B 609 SER cc_start: 0.8122 (OUTLIER) cc_final: 0.7680 (t) REVERT: B 613 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8457 (tt) REVERT: B 653 VAL cc_start: 0.8360 (t) cc_final: 0.8072 (t) REVERT: B 861 MET cc_start: 0.7903 (mmt) cc_final: 0.7366 (mmt) REVERT: B 866 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.7931 (tm) REVERT: B 941 MET cc_start: 0.7955 (mmt) cc_final: 0.7136 (mmt) REVERT: B 945 ARG cc_start: 0.7579 (mmm-85) cc_final: 0.4893 (ttm170) REVERT: B 966 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.7284 (ttm-80) REVERT: B 970 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.7216 (m-80) REVERT: B 1005 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.6392 (pttt) outliers start: 122 outliers final: 82 residues processed: 364 average time/residue: 0.3012 time to fit residues: 162.6511 Evaluate side-chains 367 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 258 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 309 TRP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 615 TYR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 890 ARG Chi-restraints excluded: chain A residue 929 GLN Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 943 ARG Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 500 GLN Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 757 ARG Chi-restraints excluded: chain B residue 784 MET Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 970 TYR Chi-restraints excluded: chain B residue 997 THR Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1005 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 177 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 12 optimal weight: 0.1980 chunk 21 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 125 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.139698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.129706 restraints weight = 16812.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.131870 restraints weight = 12180.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.133775 restraints weight = 8070.695| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15257 Z= 0.121 Angle : 0.675 14.000 20703 Z= 0.338 Chirality : 0.042 0.339 2356 Planarity : 0.004 0.036 2702 Dihedral : 8.529 92.580 2238 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.91 % Favored : 91.63 % Rotamer: Outliers : 7.05 % Allowed : 32.53 % Favored : 60.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.05 % 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: -1.71 (0.18), residues: 1971 helix: 0.28 (0.21), residues: 623 sheet: -0.39 (0.31), residues: 286 loop : -2.32 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 186 HIS 0.014 0.001 HIS B 606 PHE 0.013 0.001 PHE A 431 TYR 0.013 0.001 TYR A 850 ARG 0.005 0.000 ARG A 103 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 433) hydrogen bonds : angle 4.59027 ( 1227) covalent geometry : bond 0.00267 (15250) covalent geometry : angle 0.67483 (20703) Misc. bond : bond 0.00067 ( 7) =============================================================================== Job complete usr+sys time: 5809.64 seconds wall clock time: 104 minutes 4.13 seconds (6244.13 seconds total)