Starting phenix.real_space_refine on Fri Sep 19 04:53:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygc_39243/09_2025/8ygc_39243.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygc_39243/09_2025/8ygc_39243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ygc_39243/09_2025/8ygc_39243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygc_39243/09_2025/8ygc_39243.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygc_39243/09_2025/8ygc_39243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygc_39243/09_2025/8ygc_39243.cif" } resolution = 4.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 85 5.16 5 C 14987 2.51 5 N 3749 2.21 5 O 4421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23242 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 8183 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 963} Chain: "B" Number of atoms: 8183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 8183 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 963} Chain: "C" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 1 Chain: "D" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 1 Chain: "E" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2260 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain: "F" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2220 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Time building chain proxies: 5.87, per 1000 atoms: 0.25 Number of scatterers: 23242 At special positions: 0 Unit cell: (107.07, 133.63, 181.77, 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 85 16.00 O 4421 8.00 N 3749 7.00 C 14987 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5354 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 12 sheets defined 62.7% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 47 through 52 removed outlier: 4.011A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.561A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 95 removed outlier: 4.028A pdb=" N LEU A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.615A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.761A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 removed outlier: 3.515A pdb=" N ARG A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 removed outlier: 4.198A pdb=" N ASN A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 removed outlier: 3.563A pdb=" N VAL A 183 " --> pdb=" O GLY A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.501A pdb=" N TYR A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 222 through 237 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.966A pdb=" N GLY A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 removed outlier: 4.098A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.966A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 366 removed outlier: 3.788A pdb=" N PHE A 361 " --> pdb=" O MET A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 374 through 391 removed outlier: 3.515A pdb=" N LYS A 390 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.570A pdb=" N MET A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 removed outlier: 4.438A pdb=" N ALA A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 462 removed outlier: 3.835A pdb=" N ASP A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 495 removed outlier: 4.369A pdb=" N TYR A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.578A pdb=" N MET A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 546 removed outlier: 5.532A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 572 removed outlier: 3.543A pdb=" N THR A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A 557 " --> pdb=" O ASP A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.820A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 4.248A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.753A pdb=" N LEU A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 648 through 659 removed outlier: 3.532A pdb=" N ASN A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 669 removed outlier: 3.569A pdb=" N ARG A 669 " --> pdb=" O LYS A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 701 removed outlier: 3.552A pdb=" N ILE A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 711 removed outlier: 3.998A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.633A pdb=" N PHE A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 761 removed outlier: 3.659A pdb=" N TYR A 755 " --> pdb=" O ILE A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 799 through 812 removed outlier: 4.296A pdb=" N ASP A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 808 " --> pdb=" O TYR A 804 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.633A pdb=" N CYS A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 838 removed outlier: 3.586A pdb=" N LEU A 838 " --> pdb=" O GLN A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 846 through 855 removed outlier: 3.577A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 878 through 903 Processing helix chain 'A' and resid 912 through 922 removed outlier: 3.727A pdb=" N PHE A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY A 917 " --> pdb=" O MET A 913 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 918 " --> pdb=" O SER A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 934 removed outlier: 4.008A pdb=" N GLU A 931 " --> pdb=" O SER A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 removed outlier: 3.713A pdb=" N PHE A 943 " --> pdb=" O GLN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 955 through 962 removed outlier: 3.551A pdb=" N LEU A 959 " --> pdb=" O PRO A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'A' and resid 973 through 977 removed outlier: 3.592A pdb=" N MET A 976 " --> pdb=" O ASN A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 991 removed outlier: 3.570A pdb=" N LYS A 989 " --> pdb=" O LYS A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1003 removed outlier: 3.899A pdb=" N TYR A1003 " --> pdb=" O ILE A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 39 Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.923A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 58 through 72 Processing helix chain 'B' and resid 80 through 109 removed outlier: 4.045A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 7.293A pdb=" N GLU B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N MET B 98 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA B 99 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 125 removed outlier: 3.964A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B 125 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 removed outlier: 3.528A pdb=" N TRP B 143 " --> pdb=" O ASP B 139 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 237 Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.688A pdb=" N VAL B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.845A pdb=" N ILE B 302 " --> pdb=" O ASN B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 removed outlier: 3.618A pdb=" N VAL B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 4.017A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.780A pdb=" N VAL B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 removed outlier: 3.866A pdb=" N GLU B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 396 through 400 Processing helix chain 'B' and resid 417 through 427 removed outlier: 3.583A pdb=" N GLU B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 427 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.802A pdb=" N SER B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR B 452 " --> pdb=" O TRP B 448 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 466 Processing helix chain 'B' and resid 468 through 495 removed outlier: 3.618A pdb=" N TYR B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 526 through 531 removed outlier: 3.863A pdb=" N MET B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 540 through 544 removed outlier: 4.387A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 570 removed outlier: 4.355A pdb=" N ASP B 554 " --> pdb=" O PHE B 550 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 570 " --> pdb=" O ARG B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 598 removed outlier: 3.785A pdb=" N ASN B 598 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 604 removed outlier: 3.639A pdb=" N SER B 604 " --> pdb=" O TRP B 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 601 through 604' Processing helix chain 'B' and resid 605 through 628 removed outlier: 3.727A pdb=" N TYR B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 612 " --> pdb=" O PHE B 608 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 618 " --> pdb=" O ASN B 614 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR B 628 " --> pdb=" O GLU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 660 through 671 removed outlier: 3.701A pdb=" N ASN B 666 " --> pdb=" O ASP B 662 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 667 " --> pdb=" O ASP B 663 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 670 " --> pdb=" O ASN B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 682 through 701 removed outlier: 3.587A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 3.674A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B 713 " --> pdb=" O TYR B 709 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 720 " --> pdb=" O ALA B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 750 through 761 removed outlier: 3.693A pdb=" N TYR B 755 " --> pdb=" O ILE B 751 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 756 " --> pdb=" O GLY B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.827A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 827 removed outlier: 3.545A pdb=" N LEU B 827 " --> pdb=" O ILE B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 841 removed outlier: 4.568A pdb=" N PHE B 837 " --> pdb=" O LYS B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 856 Processing helix chain 'B' and resid 861 through 871 removed outlier: 3.679A pdb=" N ILE B 871 " --> pdb=" O ASN B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 903 removed outlier: 4.136A pdb=" N VAL B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 922 removed outlier: 3.639A pdb=" N THR B 915 " --> pdb=" O ASP B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 934 removed outlier: 3.704A pdb=" N GLU B 931 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 934 " --> pdb=" O GLU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 957 through 962 removed outlier: 3.973A pdb=" N TYR B 962 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 976 through 990 removed outlier: 3.777A pdb=" N ARG B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1003 removed outlier: 3.502A pdb=" N LEU B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 removed outlier: 3.755A pdb=" N GLY C 78 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.573A pdb=" N GLY D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 Processing helix chain 'E' and resid 47 through 54 removed outlier: 3.721A pdb=" N SER E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 72 removed outlier: 3.720A pdb=" N LEU E 62 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 96 removed outlier: 3.598A pdb=" N LEU E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 115 through 124 removed outlier: 3.855A pdb=" N ASP E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 146 Processing helix chain 'E' and resid 154 through 160 removed outlier: 3.681A pdb=" N VAL E 158 " --> pdb=" O ALA E 154 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 186 through 197 removed outlier: 3.503A pdb=" N TYR E 190 " --> pdb=" O LYS E 186 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASP E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLN E 195 " --> pdb=" O LEU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 254 through 264 Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.524A pdb=" N ARG E 285 " --> pdb=" O ASP E 281 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 39 Processing helix chain 'F' and resid 48 through 53 Processing helix chain 'F' and resid 58 through 72 removed outlier: 3.918A pdb=" N LEU F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 96 removed outlier: 3.915A pdb=" N LEU F 85 " --> pdb=" O SER F 81 " (cutoff:3.500A) Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 115 through 124 removed outlier: 3.814A pdb=" N ASP F 119 " --> pdb=" O ASN F 115 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET F 124 " --> pdb=" O LYS F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 146 Processing helix chain 'F' and resid 154 through 160 removed outlier: 3.982A pdb=" N VAL F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 177 removed outlier: 4.500A pdb=" N LYS F 176 " --> pdb=" O ASP F 173 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY F 177 " --> pdb=" O PHE F 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 173 through 177' Processing helix chain 'F' and resid 179 through 183 removed outlier: 3.868A pdb=" N ASN F 182 " --> pdb=" O LYS F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 192 Processing helix chain 'F' and resid 192 through 197 Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 222 through 237 Processing helix chain 'F' and resid 238 through 240 No H-bonds generated for 'chain 'F' and resid 238 through 240' Processing helix chain 'F' and resid 254 through 264 Processing helix chain 'F' and resid 272 through 274 No H-bonds generated for 'chain 'F' and resid 272 through 274' Processing helix chain 'F' and resid 281 through 296 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.518A pdb=" N LEU A 167 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU A 42 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ILE A 130 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 43 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE A 216 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE A 45 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'A' and resid 904 through 907 removed outlier: 6.746A pdb=" N VAL D 187 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN D 181 " --> pdb=" O VAL D 187 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.422A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE B 44 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B 43 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE B 216 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE B 45 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 245 through 247 Processing sheet with id=AA6, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA7, first strand: chain 'B' and resid 574 through 575 removed outlier: 3.928A pdb=" N SER D 31 " --> pdb=" O THR D 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 20 through 24 removed outlier: 3.925A pdb=" N LYS C 20 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG C 15 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL C 22 " --> pdb=" O PHE C 13 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR C 12 " --> pdb=" O GLU C 174 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 173 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 33 through 35 removed outlier: 4.841A pdb=" N ILE C 59 " --> pdb=" O ALA C 222 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 150 through 152 removed outlier: 6.362A pdb=" N SER E 150 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS E 169 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE E 152 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL E 129 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N HIS E 128 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE E 245 " --> pdb=" O ILE E 269 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 150 through 152 removed outlier: 5.965A pdb=" N SER F 150 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS F 169 " --> pdb=" O SER F 150 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE F 152 " --> pdb=" O LYS F 169 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE F 44 " --> pdb=" O HIS F 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 244 through 247 removed outlier: 6.853A pdb=" N PHE F 245 " --> pdb=" O ILE F 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 1103 hydrogen bonds defined for protein. 3153 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: 4.42 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4413 1.32 - 1.45: 6277 1.45 - 1.57: 12936 1.57 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 23772 Sorted by residual: bond pdb=" N ILE B 294 " pdb=" CA ILE B 294 " ideal model delta sigma weight residual 1.462 1.413 0.049 1.14e-02 7.69e+03 1.84e+01 bond pdb=" N PHE A 301 " pdb=" CA PHE A 301 " ideal model delta sigma weight residual 1.457 1.414 0.043 1.29e-02 6.01e+03 1.12e+01 bond pdb=" CA GLN B 297 " pdb=" C GLN B 297 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.34e-02 5.57e+03 9.84e+00 bond pdb=" CA ASN B 299 " pdb=" C ASN B 299 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.34e-02 5.57e+03 9.07e+00 bond pdb=" N ILE A 294 " pdb=" CA ILE A 294 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.30e+00 ... (remaining 23767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 31731 3.19 - 6.38: 296 6.38 - 9.56: 39 9.56 - 12.75: 5 12.75 - 15.94: 1 Bond angle restraints: 32072 Sorted by residual: angle pdb=" C LYS B 300 " pdb=" N PHE B 301 " pdb=" CA PHE B 301 " ideal model delta sigma weight residual 122.65 113.28 9.37 1.60e+00 3.91e-01 3.43e+01 angle pdb=" N VAL A 430 " pdb=" CA VAL A 430 " pdb=" C VAL A 430 " ideal model delta sigma weight residual 112.43 107.05 5.38 9.20e-01 1.18e+00 3.42e+01 angle pdb=" N GLN A 297 " pdb=" CA GLN A 297 " pdb=" C GLN A 297 " ideal model delta sigma weight residual 112.94 105.56 7.38 1.41e+00 5.03e-01 2.74e+01 angle pdb=" C HIS F 241 " pdb=" CA HIS F 241 " pdb=" CB HIS F 241 " ideal model delta sigma weight residual 109.53 117.27 -7.74 1.65e+00 3.67e-01 2.20e+01 angle pdb=" CB LYS A 717 " pdb=" CG LYS A 717 " pdb=" CD LYS A 717 " ideal model delta sigma weight residual 111.30 100.52 10.78 2.30e+00 1.89e-01 2.20e+01 ... (remaining 32067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 11998 17.78 - 35.55: 1671 35.55 - 53.33: 425 53.33 - 71.11: 69 71.11 - 88.89: 25 Dihedral angle restraints: 14188 sinusoidal: 5847 harmonic: 8341 Sorted by residual: dihedral pdb=" CA GLN A 297 " pdb=" C GLN A 297 " pdb=" N GLU A 298 " pdb=" CA GLU A 298 " ideal model delta harmonic sigma weight residual 180.00 91.57 88.43 0 5.00e+00 4.00e-02 3.13e+02 dihedral pdb=" CA ASP C 69 " pdb=" C ASP C 69 " pdb=" N LEU C 70 " pdb=" CA LEU C 70 " ideal model delta harmonic sigma weight residual 180.00 -143.77 -36.23 0 5.00e+00 4.00e-02 5.25e+01 dihedral pdb=" CA THR D 3 " pdb=" C THR D 3 " pdb=" N VAL D 4 " pdb=" CA VAL D 4 " ideal model delta harmonic sigma weight residual 180.00 148.90 31.10 0 5.00e+00 4.00e-02 3.87e+01 ... (remaining 14185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2992 0.072 - 0.144: 400 0.144 - 0.215: 23 0.215 - 0.287: 4 0.287 - 0.359: 3 Chirality restraints: 3422 Sorted by residual: chirality pdb=" CB ILE A 673 " pdb=" CA ILE A 673 " pdb=" CG1 ILE A 673 " pdb=" CG2 ILE A 673 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CB ILE B 904 " pdb=" CA ILE B 904 " pdb=" CG1 ILE B 904 " pdb=" CG2 ILE B 904 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB THR D 29 " pdb=" CA THR D 29 " pdb=" OG1 THR D 29 " pdb=" CG2 THR D 29 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 3419 not shown) Planarity restraints: 4114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 958 " 0.047 2.00e-02 2.50e+03 3.82e-02 3.65e+01 pdb=" CG TRP A 958 " -0.103 2.00e-02 2.50e+03 pdb=" CD1 TRP A 958 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP A 958 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 958 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 958 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 958 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 958 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 958 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 958 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 72 " 0.032 2.00e-02 2.50e+03 2.27e-02 1.29e+01 pdb=" CG TRP C 72 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP C 72 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP C 72 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 72 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 72 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 72 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 72 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 72 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 72 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 293 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C LEU A 293 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU A 293 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE A 294 " -0.020 2.00e-02 2.50e+03 ... (remaining 4111 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.42: 124 2.42 - 3.04: 15581 3.04 - 3.66: 35209 3.66 - 4.28: 50955 4.28 - 4.90: 81922 Nonbonded interactions: 183791 Sorted by model distance: nonbonded pdb=" OD1 ASP B 950 " pdb=" NZ LYS B 953 " model vdw 1.806 3.120 nonbonded pdb=" NZ LYS A 965 " pdb=" OH TYR D 51 " model vdw 1.807 2.496 nonbonded pdb=" CE3 TRP B 919 " pdb=" OE1 GLU B 924 " model vdw 2.003 3.340 nonbonded pdb=" CE LYS A 965 " pdb=" OH TYR D 51 " model vdw 2.036 3.440 nonbonded pdb=" O LEU D 50 " pdb=" CD1 TYR D 51 " model vdw 2.044 3.340 ... (remaining 183786 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 26 through 297) selection = chain 'F' } 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: 6.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.510 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.007 0.241 23773 Z= 0.351 Angle : 0.801 15.941 32072 Z= 0.443 Chirality : 0.049 0.359 3422 Planarity : 0.005 0.075 4114 Dihedral : 17.327 88.886 8834 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.93 % Allowed : 7.18 % Favored : 91.90 % Rotamer: Outliers : 0.63 % Allowed : 26.69 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.16), residues: 2801 helix: 0.18 (0.14), residues: 1454 sheet: -1.03 (0.37), residues: 202 loop : -1.75 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 380 TYR 0.031 0.002 TYR A 912 PHE 0.036 0.002 PHE B 678 TRP 0.103 0.004 TRP A 958 HIS 0.013 0.001 HIS A 349 Details of bonding type rmsd covalent geometry : bond 0.00662 (23772) covalent geometry : angle 0.80112 (32072) hydrogen bonds : bond 0.18970 ( 1103) hydrogen bonds : angle 6.88058 ( 3153) Misc. bond : bond 0.24134 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 604 time to evaluate : 0.964 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: symmetry clash REVERT: A 46 VAL cc_start: 0.8590 (t) cc_final: 0.8342 (t) REVERT: A 240 PHE cc_start: 0.7614 (t80) cc_final: 0.7403 (t80) REVERT: A 300 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8804 (tttt) REVERT: A 588 LEU cc_start: 0.9348 (tp) cc_final: 0.9086 (tt) REVERT: A 895 ASN cc_start: 0.8675 (m-40) cc_final: 0.8451 (m110) REVERT: B 24 ASN cc_start: 0.8251 (m-40) cc_final: 0.7325 (p0) REVERT: B 357 MET cc_start: 0.8739 (mmt) cc_final: 0.8496 (tpp) REVERT: B 437 LYS cc_start: 0.9346 (mttt) cc_final: 0.9047 (mtpt) REVERT: B 519 MET cc_start: 0.8111 (mmm) cc_final: 0.7843 (mmm) REVERT: C 61 LEU cc_start: 0.9226 (mp) cc_final: 0.9001 (mp) REVERT: C 188 TYR cc_start: 0.3757 (p90) cc_final: 0.2448 (p90) REVERT: C 191 ILE cc_start: 0.8787 (mt) cc_final: 0.8378 (mp) REVERT: C 193 ILE cc_start: 0.9257 (mt) cc_final: 0.9043 (mp) REVERT: D 1 MET cc_start: 0.0957 (pp-130) cc_final: 0.0095 (pp-130) REVERT: D 239 ARG cc_start: 0.6420 (ptm-80) cc_final: 0.5741 (mmt180) REVERT: E 21 MET cc_start: 0.3693 (mtt) cc_final: 0.2932 (ptt) REVERT: E 109 GLN cc_start: 0.8357 (tt0) cc_final: 0.8095 (mt0) REVERT: E 111 ASP cc_start: 0.7918 (m-30) cc_final: 0.7675 (m-30) REVERT: E 189 ASP cc_start: 0.9113 (m-30) cc_final: 0.8747 (m-30) REVERT: E 197 TYR cc_start: 0.8040 (m-80) cc_final: 0.7504 (m-10) REVERT: E 202 ASN cc_start: 0.8864 (m-40) cc_final: 0.8030 (t0) REVERT: E 203 LEU cc_start: 0.9550 (tp) cc_final: 0.9201 (tp) REVERT: E 204 MET cc_start: 0.9484 (mtp) cc_final: 0.9209 (tmm) REVERT: E 205 LYS cc_start: 0.9505 (mttt) cc_final: 0.9103 (pttp) REVERT: E 223 TYR cc_start: 0.6669 (t80) cc_final: 0.6448 (t80) REVERT: E 227 MET cc_start: 0.8177 (mtp) cc_final: 0.7460 (mtp) REVERT: E 280 TYR cc_start: 0.8260 (m-80) cc_final: 0.8013 (m-80) REVERT: F 111 ASP cc_start: 0.5747 (m-30) cc_final: 0.4971 (t0) REVERT: F 124 MET cc_start: 0.7380 (mmm) cc_final: 0.6881 (mmp) outliers start: 16 outliers final: 2 residues processed: 616 average time/residue: 0.1846 time to fit residues: 171.9226 Evaluate side-chains 287 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 284 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 133 ASN A 241 HIS ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS B 391 ASN B 548 ASN B 863 ASN B 881 HIS ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN D 6 GLN D 60 ASN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN F 195 GLN ** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.072701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.054717 restraints weight = 132145.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.056444 restraints weight = 78415.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.057621 restraints weight = 54147.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.058414 restraints weight = 41110.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.058888 restraints weight = 33912.930| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 23773 Z= 0.166 Angle : 0.729 11.007 32072 Z= 0.385 Chirality : 0.046 0.266 3422 Planarity : 0.005 0.066 4114 Dihedral : 5.174 49.754 3097 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.71 % Favored : 93.72 % Rotamer: Outliers : 0.51 % Allowed : 4.23 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.15), residues: 2801 helix: 0.21 (0.13), residues: 1511 sheet: -0.91 (0.37), residues: 202 loop : -1.76 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 61 TYR 0.020 0.002 TYR B 218 PHE 0.043 0.002 PHE B 907 TRP 0.036 0.003 TRP A 143 HIS 0.011 0.001 HIS B 852 Details of bonding type rmsd covalent geometry : bond 0.00355 (23772) covalent geometry : angle 0.72920 (32072) hydrogen bonds : bond 0.05024 ( 1103) hydrogen bonds : angle 5.29557 ( 3153) Misc. bond : bond 0.00286 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 417 time to evaluate : 0.973 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: A 179 LYS cc_start: 0.9441 (mttt) cc_final: 0.9230 (mtmm) REVERT: A 227 MET cc_start: 0.9212 (tpt) cc_final: 0.8983 (tpp) REVERT: A 240 PHE cc_start: 0.8371 (t80) cc_final: 0.7938 (t80) REVERT: A 396 MET cc_start: 0.7794 (tmm) cc_final: 0.7246 (tmm) REVERT: A 607 GLU cc_start: 0.8616 (mp0) cc_final: 0.8330 (mp0) REVERT: A 610 GLN cc_start: 0.8960 (mm110) cc_final: 0.8730 (mm110) REVERT: A 774 ILE cc_start: 0.9661 (OUTLIER) cc_final: 0.9419 (tp) REVERT: A 895 ASN cc_start: 0.8843 (m-40) cc_final: 0.8595 (m110) REVERT: B 24 ASN cc_start: 0.8449 (m-40) cc_final: 0.7516 (p0) REVERT: B 134 TYR cc_start: 0.7891 (m-10) cc_final: 0.7461 (m-10) REVERT: B 375 LYS cc_start: 0.8313 (pptt) cc_final: 0.7764 (pptt) REVERT: B 379 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8655 (mm-30) REVERT: B 437 LYS cc_start: 0.9470 (mttt) cc_final: 0.9131 (mtpt) REVERT: B 509 ASP cc_start: 0.9062 (p0) cc_final: 0.8781 (p0) REVERT: B 531 MET cc_start: 0.8878 (mmp) cc_final: 0.8617 (mmp) REVERT: B 784 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8504 (mm-30) REVERT: C 193 ILE cc_start: 0.8998 (mt) cc_final: 0.8768 (mm) REVERT: D 50 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7796 (pp) REVERT: D 54 LYS cc_start: 0.8452 (pttp) cc_final: 0.8101 (pptt) REVERT: D 239 ARG cc_start: 0.7411 (ptt90) cc_final: 0.6286 (mmt180) REVERT: E 21 MET cc_start: 0.3016 (mtt) cc_final: 0.2101 (ptt) REVERT: E 109 GLN cc_start: 0.8926 (tt0) cc_final: 0.8597 (mt0) REVERT: E 202 ASN cc_start: 0.9102 (m-40) cc_final: 0.8629 (t0) REVERT: E 204 MET cc_start: 0.9481 (mtp) cc_final: 0.9186 (tmm) REVERT: E 205 LYS cc_start: 0.9380 (mttt) cc_final: 0.8903 (mmmm) REVERT: E 223 TYR cc_start: 0.7420 (t80) cc_final: 0.7161 (t80) REVERT: E 227 MET cc_start: 0.8601 (mtp) cc_final: 0.8388 (mtp) REVERT: E 233 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7789 (ptp90) REVERT: F 44 PHE cc_start: 0.7910 (m-10) cc_final: 0.7560 (m-10) REVERT: F 168 LEU cc_start: 0.8530 (mm) cc_final: 0.8261 (mt) REVERT: F 203 LEU cc_start: 0.9620 (tp) cc_final: 0.9274 (tp) REVERT: F 215 PHE cc_start: 0.9106 (m-80) cc_final: 0.8566 (m-10) REVERT: F 218 TYR cc_start: 0.4945 (t80) cc_final: 0.4654 (t80) outliers start: 13 outliers final: 1 residues processed: 429 average time/residue: 0.1808 time to fit residues: 118.9024 Evaluate side-chains 258 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 255 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 174 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 233 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 208 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 391 ASN B 467 ASN B 681 GLN D 181 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.070799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.052757 restraints weight = 133316.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.054446 restraints weight = 78416.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.055520 restraints weight = 53925.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.056322 restraints weight = 41578.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.056803 restraints weight = 34283.495| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23773 Z= 0.172 Angle : 0.667 8.894 32072 Z= 0.352 Chirality : 0.044 0.203 3422 Planarity : 0.004 0.062 4114 Dihedral : 5.064 31.257 3097 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.89 % Favored : 93.57 % Rotamer: Outliers : 0.20 % Allowed : 2.94 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.16), residues: 2801 helix: 0.42 (0.13), residues: 1516 sheet: -0.98 (0.35), residues: 220 loop : -1.62 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 61 TYR 0.025 0.002 TYR A 804 PHE 0.026 0.002 PHE B 301 TRP 0.023 0.002 TRP E 60 HIS 0.004 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00379 (23772) covalent geometry : angle 0.66679 (32072) hydrogen bonds : bond 0.04439 ( 1103) hydrogen bonds : angle 4.99071 ( 3153) Misc. bond : bond 0.00169 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 337 time to evaluate : 1.008 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: A 179 LYS cc_start: 0.9499 (mttt) cc_final: 0.9274 (mtmm) REVERT: A 240 PHE cc_start: 0.8520 (t80) cc_final: 0.8191 (t80) REVERT: A 421 MET cc_start: 0.8863 (mtm) cc_final: 0.8569 (mtm) REVERT: A 436 TYR cc_start: 0.8016 (t80) cc_final: 0.7617 (t80) REVERT: A 895 ASN cc_start: 0.8942 (m-40) cc_final: 0.8696 (m110) REVERT: A 913 MET cc_start: 0.8725 (tpp) cc_final: 0.8339 (tpp) REVERT: B 24 ASN cc_start: 0.8483 (m-40) cc_final: 0.7531 (p0) REVERT: B 167 LEU cc_start: 0.8716 (tt) cc_final: 0.8471 (pp) REVERT: B 375 LYS cc_start: 0.8407 (pptt) cc_final: 0.7868 (pttp) REVERT: B 379 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8651 (mm-30) REVERT: B 437 LYS cc_start: 0.9508 (mttt) cc_final: 0.9162 (mtmt) REVERT: B 509 ASP cc_start: 0.9074 (p0) cc_final: 0.8757 (p0) REVERT: B 519 MET cc_start: 0.9004 (mmm) cc_final: 0.8731 (mmm) REVERT: B 784 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8596 (mm-30) REVERT: C 180 TYR cc_start: 0.6028 (m-80) cc_final: 0.5805 (m-80) REVERT: C 193 ILE cc_start: 0.8988 (mt) cc_final: 0.8620 (mm) REVERT: C 219 LYS cc_start: 0.9089 (mppt) cc_final: 0.8811 (mmtm) REVERT: D 239 ARG cc_start: 0.7353 (ptt90) cc_final: 0.6145 (mmt180) REVERT: E 21 MET cc_start: 0.2991 (mtt) cc_final: 0.2170 (ptt) REVERT: E 197 TYR cc_start: 0.8547 (m-10) cc_final: 0.8082 (m-10) REVERT: E 199 LEU cc_start: 0.9090 (mm) cc_final: 0.8771 (mm) REVERT: E 202 ASN cc_start: 0.9123 (m-40) cc_final: 0.8653 (t0) REVERT: E 204 MET cc_start: 0.9510 (mtp) cc_final: 0.9202 (tmm) REVERT: E 205 LYS cc_start: 0.9360 (mttt) cc_final: 0.8990 (mmmt) REVERT: E 223 TYR cc_start: 0.7430 (t80) cc_final: 0.7220 (t80) REVERT: E 227 MET cc_start: 0.8611 (mtp) cc_final: 0.8297 (mtp) REVERT: F 44 PHE cc_start: 0.8168 (m-10) cc_final: 0.7754 (m-10) REVERT: F 89 GLN cc_start: 0.9523 (mm110) cc_final: 0.9126 (mm-40) REVERT: F 168 LEU cc_start: 0.8228 (mm) cc_final: 0.7881 (mt) REVERT: F 215 PHE cc_start: 0.9102 (m-80) cc_final: 0.8624 (m-10) REVERT: F 290 MET cc_start: 0.9154 (mtp) cc_final: 0.8609 (tpp) outliers start: 5 outliers final: 1 residues processed: 342 average time/residue: 0.1837 time to fit residues: 96.0150 Evaluate side-chains 236 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 100 optimal weight: 0.8980 chunk 217 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 273 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN A 610 GLN A 765 ASN ** A 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN B 483 GLN B 790 ASN D 197 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.070775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.052711 restraints weight = 133732.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.054436 restraints weight = 79168.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.055579 restraints weight = 54372.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.056350 restraints weight = 41468.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.056825 restraints weight = 34117.752| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 23773 Z= 0.134 Angle : 0.630 10.487 32072 Z= 0.332 Chirality : 0.044 0.280 3422 Planarity : 0.004 0.057 4114 Dihedral : 4.911 35.340 3097 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.64 % Favored : 93.93 % Rotamer: Outliers : 0.12 % Allowed : 3.09 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.16), residues: 2801 helix: 0.63 (0.13), residues: 1508 sheet: -1.05 (0.34), residues: 228 loop : -1.44 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 38 TYR 0.031 0.001 TYR E 134 PHE 0.022 0.002 PHE B 301 TRP 0.032 0.002 TRP D 72 HIS 0.003 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00288 (23772) covalent geometry : angle 0.63028 (32072) hydrogen bonds : bond 0.03991 ( 1103) hydrogen bonds : angle 4.71053 ( 3153) Misc. bond : bond 0.00578 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 339 time to evaluate : 0.975 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: A 35 GLU cc_start: 0.9610 (mm-30) cc_final: 0.9295 (mm-30) REVERT: A 227 MET cc_start: 0.9121 (tpt) cc_final: 0.8910 (tpp) REVERT: A 519 MET cc_start: 0.8830 (mmt) cc_final: 0.8616 (mmm) REVERT: A 895 ASN cc_start: 0.8907 (m-40) cc_final: 0.8665 (m110) REVERT: A 907 PHE cc_start: 0.8804 (m-80) cc_final: 0.8587 (m-80) REVERT: A 913 MET cc_start: 0.8706 (tpp) cc_final: 0.8430 (tpp) REVERT: B 24 ASN cc_start: 0.8491 (m-40) cc_final: 0.7572 (p0) REVERT: B 168 LEU cc_start: 0.8983 (tt) cc_final: 0.8359 (tt) REVERT: B 179 LYS cc_start: 0.9170 (mmtm) cc_final: 0.8933 (mmtt) REVERT: B 375 LYS cc_start: 0.8463 (pptt) cc_final: 0.8013 (pptt) REVERT: B 379 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8659 (mm-30) REVERT: B 421 MET cc_start: 0.8794 (mtm) cc_final: 0.8045 (ptp) REVERT: B 437 LYS cc_start: 0.9504 (mttt) cc_final: 0.9150 (mtmt) REVERT: B 509 ASP cc_start: 0.9080 (p0) cc_final: 0.8773 (p0) REVERT: B 519 MET cc_start: 0.9029 (mmm) cc_final: 0.8738 (mmm) REVERT: B 531 MET cc_start: 0.8818 (mmp) cc_final: 0.8555 (mmp) REVERT: B 913 MET cc_start: 0.8245 (tmm) cc_final: 0.8033 (tmm) REVERT: C 7 ASP cc_start: 0.7411 (m-30) cc_final: 0.6632 (t70) REVERT: C 180 TYR cc_start: 0.6015 (m-80) cc_final: 0.5786 (m-80) REVERT: C 193 ILE cc_start: 0.8951 (mt) cc_final: 0.8574 (mm) REVERT: D 239 ARG cc_start: 0.7331 (ptt90) cc_final: 0.6032 (mmt180) REVERT: E 21 MET cc_start: 0.2927 (mtt) cc_final: 0.2119 (ptt) REVERT: E 197 TYR cc_start: 0.8602 (m-10) cc_final: 0.8157 (m-10) REVERT: E 199 LEU cc_start: 0.9087 (mm) cc_final: 0.8766 (mm) REVERT: E 202 ASN cc_start: 0.9148 (m-40) cc_final: 0.8610 (t0) REVERT: E 204 MET cc_start: 0.9510 (mtp) cc_final: 0.9211 (tmm) REVERT: E 205 LYS cc_start: 0.9346 (mttt) cc_final: 0.9021 (mmmt) REVERT: E 223 TYR cc_start: 0.7354 (t80) cc_final: 0.7140 (t80) REVERT: E 227 MET cc_start: 0.8603 (mtp) cc_final: 0.8352 (mtp) REVERT: F 44 PHE cc_start: 0.8299 (m-10) cc_final: 0.7935 (m-10) REVERT: F 89 GLN cc_start: 0.9485 (mm110) cc_final: 0.9208 (mm-40) REVERT: F 169 LYS cc_start: 0.8163 (mttt) cc_final: 0.7358 (tttt) REVERT: F 202 ASN cc_start: 0.9749 (m110) cc_final: 0.9408 (t0) REVERT: F 203 LEU cc_start: 0.9504 (tp) cc_final: 0.9278 (tp) REVERT: F 290 MET cc_start: 0.9161 (mtp) cc_final: 0.8717 (tpp) outliers start: 3 outliers final: 0 residues processed: 342 average time/residue: 0.1833 time to fit residues: 95.2800 Evaluate side-chains 235 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 240 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 165 optimal weight: 0.0010 chunk 30 optimal weight: 0.9990 chunk 271 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 275 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN B 483 GLN B 961 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 ASN F 195 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.069156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.050937 restraints weight = 132659.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.052559 restraints weight = 78638.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.053671 restraints weight = 54326.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.054359 restraints weight = 41709.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.054864 restraints weight = 34840.236| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 23773 Z= 0.160 Angle : 0.637 10.196 32072 Z= 0.334 Chirality : 0.044 0.221 3422 Planarity : 0.004 0.049 4114 Dihedral : 4.922 33.345 3097 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.89 % Favored : 93.65 % Rotamer: Outliers : 0.08 % Allowed : 2.70 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.16), residues: 2801 helix: 0.68 (0.13), residues: 1523 sheet: -0.79 (0.34), residues: 219 loop : -1.42 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 61 TYR 0.025 0.001 TYR D 175 PHE 0.035 0.002 PHE B 45 TRP 0.027 0.002 TRP D 72 HIS 0.003 0.001 HIS B 503 Details of bonding type rmsd covalent geometry : bond 0.00352 (23772) covalent geometry : angle 0.63695 (32072) hydrogen bonds : bond 0.03948 ( 1103) hydrogen bonds : angle 4.71655 ( 3153) Misc. bond : bond 0.00886 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 315 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9609 (mm-30) cc_final: 0.9287 (mm-30) REVERT: A 140 THR cc_start: 0.9411 (m) cc_final: 0.9207 (p) REVERT: A 421 MET cc_start: 0.8899 (mtm) cc_final: 0.8652 (mtm) REVERT: A 519 MET cc_start: 0.8881 (mmt) cc_final: 0.8585 (mmm) REVERT: A 907 PHE cc_start: 0.8806 (m-80) cc_final: 0.8506 (m-80) REVERT: A 913 MET cc_start: 0.8756 (tpp) cc_final: 0.8530 (tpp) REVERT: B 24 ASN cc_start: 0.8538 (m-40) cc_final: 0.7627 (p0) REVERT: B 185 LEU cc_start: 0.8856 (tp) cc_final: 0.7964 (pt) REVERT: B 375 LYS cc_start: 0.8536 (pptt) cc_final: 0.8090 (pptt) REVERT: B 379 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8649 (mm-30) REVERT: B 421 MET cc_start: 0.8884 (mtm) cc_final: 0.8081 (ptp) REVERT: B 437 LYS cc_start: 0.9515 (mttt) cc_final: 0.9159 (mtmt) REVERT: B 509 ASP cc_start: 0.9079 (p0) cc_final: 0.8778 (p0) REVERT: B 519 MET cc_start: 0.9105 (mmm) cc_final: 0.8760 (mmm) REVERT: B 651 ASP cc_start: 0.9001 (m-30) cc_final: 0.8321 (t0) REVERT: B 908 SER cc_start: 0.8698 (p) cc_final: 0.8478 (p) REVERT: C 7 ASP cc_start: 0.7385 (m-30) cc_final: 0.6551 (t70) REVERT: C 193 ILE cc_start: 0.8976 (mt) cc_final: 0.8619 (mm) REVERT: C 206 MET cc_start: 0.8618 (tpp) cc_final: 0.8175 (tpp) REVERT: C 231 MET cc_start: 0.8806 (mmp) cc_final: 0.8334 (mmm) REVERT: D 239 ARG cc_start: 0.7317 (ptt90) cc_final: 0.5964 (mmt180) REVERT: E 21 MET cc_start: 0.3024 (mtt) cc_final: 0.2353 (ttp) REVERT: E 61 ARG cc_start: 0.9027 (mpp80) cc_final: 0.8734 (mpt-90) REVERT: E 197 TYR cc_start: 0.8584 (m-10) cc_final: 0.8177 (m-10) REVERT: E 199 LEU cc_start: 0.9101 (mm) cc_final: 0.8795 (mm) REVERT: E 202 ASN cc_start: 0.9180 (m-40) cc_final: 0.8641 (t0) REVERT: E 204 MET cc_start: 0.9490 (mtp) cc_final: 0.9171 (tmm) REVERT: E 205 LYS cc_start: 0.9334 (mttt) cc_final: 0.8987 (mmmm) REVERT: E 227 MET cc_start: 0.8630 (mtp) cc_final: 0.8342 (mtp) REVERT: F 202 ASN cc_start: 0.9753 (m110) cc_final: 0.9347 (t0) REVERT: F 290 MET cc_start: 0.9182 (mtp) cc_final: 0.8737 (tpp) outliers start: 2 outliers final: 0 residues processed: 317 average time/residue: 0.1777 time to fit residues: 86.3681 Evaluate side-chains 222 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 80 optimal weight: 0.0010 chunk 236 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 70 optimal weight: 0.0060 chunk 170 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 248 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.070194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.052073 restraints weight = 131551.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.053821 restraints weight = 76945.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.054966 restraints weight = 52254.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.055734 restraints weight = 39780.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.056226 restraints weight = 32809.681| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23773 Z= 0.124 Angle : 0.616 9.159 32072 Z= 0.322 Chirality : 0.043 0.345 3422 Planarity : 0.004 0.066 4114 Dihedral : 4.798 27.562 3097 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.57 % Favored : 93.97 % Rotamer: Outliers : 0.08 % Allowed : 1.72 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.16), residues: 2801 helix: 0.79 (0.13), residues: 1521 sheet: -0.62 (0.35), residues: 213 loop : -1.37 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 233 TYR 0.018 0.001 TYR B 324 PHE 0.025 0.002 PHE B 550 TRP 0.028 0.002 TRP D 72 HIS 0.006 0.001 HIS B 503 Details of bonding type rmsd covalent geometry : bond 0.00273 (23772) covalent geometry : angle 0.61626 (32072) hydrogen bonds : bond 0.03789 ( 1103) hydrogen bonds : angle 4.57851 ( 3153) Misc. bond : bond 0.00341 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 326 time to evaluate : 0.944 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: A 35 GLU cc_start: 0.9607 (mm-30) cc_final: 0.9297 (mm-30) REVERT: A 227 MET cc_start: 0.9131 (tpt) cc_final: 0.8836 (mmm) REVERT: A 436 TYR cc_start: 0.7918 (t80) cc_final: 0.7664 (t80) REVERT: A 519 MET cc_start: 0.8864 (mmt) cc_final: 0.8597 (mmm) REVERT: A 737 VAL cc_start: 0.9783 (t) cc_final: 0.9577 (m) REVERT: A 749 LEU cc_start: 0.9381 (tp) cc_final: 0.8984 (mt) REVERT: A 895 ASN cc_start: 0.8811 (m110) cc_final: 0.8491 (m-40) REVERT: A 907 PHE cc_start: 0.8855 (m-80) cc_final: 0.8405 (m-80) REVERT: A 913 MET cc_start: 0.8764 (tpp) cc_final: 0.8542 (tpp) REVERT: A 1001 MET cc_start: 0.9495 (tmm) cc_final: 0.9281 (tmm) REVERT: B 24 ASN cc_start: 0.8562 (m-40) cc_final: 0.7657 (p0) REVERT: B 59 TRP cc_start: 0.7492 (t60) cc_final: 0.7192 (t60) REVERT: B 185 LEU cc_start: 0.8573 (tp) cc_final: 0.7990 (pp) REVERT: B 375 LYS cc_start: 0.8381 (pptt) cc_final: 0.7980 (pptt) REVERT: B 379 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8662 (mm-30) REVERT: B 421 MET cc_start: 0.8910 (mtm) cc_final: 0.8021 (ptp) REVERT: B 437 LYS cc_start: 0.9481 (mttt) cc_final: 0.9121 (mtmt) REVERT: B 509 ASP cc_start: 0.9076 (p0) cc_final: 0.8783 (p0) REVERT: B 519 MET cc_start: 0.9081 (mmm) cc_final: 0.8742 (mmm) REVERT: B 749 LEU cc_start: 0.8264 (tp) cc_final: 0.8055 (tp) REVERT: B 784 GLU cc_start: 0.8378 (mp0) cc_final: 0.8144 (mm-30) REVERT: B 908 SER cc_start: 0.8648 (p) cc_final: 0.8443 (p) REVERT: C 6 GLN cc_start: 0.7566 (pm20) cc_final: 0.7300 (pm20) REVERT: C 7 ASP cc_start: 0.7384 (m-30) cc_final: 0.6480 (t70) REVERT: C 23 PHE cc_start: 0.7641 (p90) cc_final: 0.7407 (p90) REVERT: C 193 ILE cc_start: 0.8946 (mt) cc_final: 0.8588 (mm) REVERT: C 206 MET cc_start: 0.8718 (tpp) cc_final: 0.8197 (tpp) REVERT: D 239 ARG cc_start: 0.7222 (ptt90) cc_final: 0.5853 (mmt180) REVERT: E 21 MET cc_start: 0.3028 (mtt) cc_final: 0.2334 (ttp) REVERT: E 61 ARG cc_start: 0.9073 (mpp80) cc_final: 0.8766 (mpt-90) REVERT: E 197 TYR cc_start: 0.8581 (m-10) cc_final: 0.8242 (m-10) REVERT: E 202 ASN cc_start: 0.9178 (m-40) cc_final: 0.8709 (p0) REVERT: E 204 MET cc_start: 0.9480 (mtp) cc_final: 0.9258 (ppp) REVERT: E 205 LYS cc_start: 0.9310 (mttt) cc_final: 0.9004 (tppt) REVERT: E 233 ARG cc_start: 0.7903 (mtm180) cc_final: 0.7692 (ptp90) REVERT: F 44 PHE cc_start: 0.7954 (m-10) cc_final: 0.7313 (m-10) REVERT: F 202 ASN cc_start: 0.9752 (m110) cc_final: 0.9504 (t0) REVERT: F 203 LEU cc_start: 0.9621 (tp) cc_final: 0.9392 (tp) REVERT: F 215 PHE cc_start: 0.9269 (m-80) cc_final: 0.9037 (m-80) outliers start: 2 outliers final: 0 residues processed: 328 average time/residue: 0.1726 time to fit residues: 86.9055 Evaluate side-chains 235 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 57 optimal weight: 3.9990 chunk 168 optimal weight: 0.0980 chunk 134 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 249 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 257 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 905 GLN ** A 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN B 343 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.068292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.050216 restraints weight = 133239.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.051813 restraints weight = 78061.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.052910 restraints weight = 54072.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.053651 restraints weight = 41323.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.054103 restraints weight = 34239.055| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 23773 Z= 0.167 Angle : 0.640 11.025 32072 Z= 0.333 Chirality : 0.044 0.325 3422 Planarity : 0.004 0.056 4114 Dihedral : 4.814 28.497 3097 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.82 % Favored : 93.75 % Rotamer: Outliers : 0.04 % Allowed : 1.72 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.16), residues: 2801 helix: 0.80 (0.13), residues: 1517 sheet: -0.48 (0.34), residues: 227 loop : -1.39 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 267 TYR 0.026 0.001 TYR A 589 PHE 0.042 0.002 PHE B 45 TRP 0.023 0.002 TRP D 72 HIS 0.005 0.001 HIS B 503 Details of bonding type rmsd covalent geometry : bond 0.00368 (23772) covalent geometry : angle 0.63960 (32072) hydrogen bonds : bond 0.03817 ( 1103) hydrogen bonds : angle 4.63781 ( 3153) Misc. bond : bond 0.00153 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.962 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: A 35 GLU cc_start: 0.9626 (mm-30) cc_final: 0.9285 (mm-30) REVERT: A 341 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8635 (mm-30) REVERT: A 421 MET cc_start: 0.8934 (mtm) cc_final: 0.8637 (mtm) REVERT: A 519 MET cc_start: 0.8931 (mmt) cc_final: 0.8642 (mmt) REVERT: A 913 MET cc_start: 0.8849 (tpp) cc_final: 0.8600 (tpp) REVERT: A 1001 MET cc_start: 0.9547 (tmm) cc_final: 0.9338 (tmm) REVERT: B 24 ASN cc_start: 0.8549 (m-40) cc_final: 0.7650 (p0) REVERT: B 59 TRP cc_start: 0.7649 (t60) cc_final: 0.7215 (t60) REVERT: B 185 LEU cc_start: 0.8644 (tp) cc_final: 0.8071 (pp) REVERT: B 375 LYS cc_start: 0.8509 (pptt) cc_final: 0.8114 (pptt) REVERT: B 379 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8697 (mm-30) REVERT: B 437 LYS cc_start: 0.9517 (mttt) cc_final: 0.9161 (mtmt) REVERT: B 509 ASP cc_start: 0.9075 (p0) cc_final: 0.8777 (p0) REVERT: B 519 MET cc_start: 0.9129 (mmm) cc_final: 0.8717 (mmm) REVERT: B 651 ASP cc_start: 0.9009 (m-30) cc_final: 0.8393 (t0) REVERT: B 908 SER cc_start: 0.8622 (p) cc_final: 0.8188 (p) REVERT: B 936 MET cc_start: 0.8335 (mpp) cc_final: 0.8006 (mpp) REVERT: C 6 GLN cc_start: 0.7482 (pm20) cc_final: 0.7273 (pm20) REVERT: C 7 ASP cc_start: 0.7279 (m-30) cc_final: 0.6475 (t70) REVERT: C 193 ILE cc_start: 0.8923 (mt) cc_final: 0.8479 (mm) REVERT: C 219 LYS cc_start: 0.9268 (mtmm) cc_final: 0.8760 (mppt) REVERT: C 231 MET cc_start: 0.8848 (mmp) cc_final: 0.8557 (mmp) REVERT: D 239 ARG cc_start: 0.7268 (ptt90) cc_final: 0.5868 (mmt180) REVERT: E 21 MET cc_start: 0.3100 (mtt) cc_final: 0.2366 (ttp) REVERT: E 197 TYR cc_start: 0.8586 (m-10) cc_final: 0.8176 (m-10) REVERT: E 199 LEU cc_start: 0.9118 (mp) cc_final: 0.8881 (mp) REVERT: E 202 ASN cc_start: 0.9198 (m-40) cc_final: 0.8819 (t0) REVERT: E 204 MET cc_start: 0.9500 (mtp) cc_final: 0.9174 (tmm) REVERT: F 44 PHE cc_start: 0.8075 (m-10) cc_final: 0.7427 (m-10) REVERT: F 169 LYS cc_start: 0.8319 (mttt) cc_final: 0.7177 (tttt) REVERT: F 202 ASN cc_start: 0.9750 (m110) cc_final: 0.9374 (t0) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.1679 time to fit residues: 77.1078 Evaluate side-chains 209 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 25 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 8 optimal weight: 0.4980 chunk 250 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN B 343 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.068406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.050143 restraints weight = 133670.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.051818 restraints weight = 78762.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.052925 restraints weight = 53824.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.053674 restraints weight = 41289.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.054146 restraints weight = 34072.009| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 23773 Z= 0.138 Angle : 0.620 10.536 32072 Z= 0.322 Chirality : 0.043 0.292 3422 Planarity : 0.004 0.078 4114 Dihedral : 4.738 25.291 3097 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.64 % Favored : 93.93 % Rotamer: Outliers : 0.04 % Allowed : 0.74 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.16), residues: 2801 helix: 0.82 (0.13), residues: 1525 sheet: -0.33 (0.33), residues: 235 loop : -1.39 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 38 TYR 0.017 0.001 TYR B 596 PHE 0.046 0.002 PHE F 178 TRP 0.027 0.002 TRP D 72 HIS 0.003 0.001 HIS A 503 Details of bonding type rmsd covalent geometry : bond 0.00308 (23772) covalent geometry : angle 0.62000 (32072) hydrogen bonds : bond 0.03683 ( 1103) hydrogen bonds : angle 4.55690 ( 3153) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9622 (mm-30) cc_final: 0.9315 (mm-30) REVERT: A 125 ASN cc_start: 0.9518 (t0) cc_final: 0.9282 (t0) REVERT: A 227 MET cc_start: 0.9026 (tpt) cc_final: 0.8720 (tpp) REVERT: A 519 MET cc_start: 0.8905 (mmt) cc_final: 0.8603 (mmt) REVERT: A 578 MET cc_start: 0.8439 (tpp) cc_final: 0.8223 (tpp) REVERT: A 735 LYS cc_start: 0.9215 (mttp) cc_final: 0.8816 (mmtp) REVERT: A 907 PHE cc_start: 0.9158 (m-80) cc_final: 0.8926 (m-80) REVERT: A 913 MET cc_start: 0.8874 (tpp) cc_final: 0.8591 (tpp) REVERT: B 24 ASN cc_start: 0.8545 (m-40) cc_final: 0.7673 (p0) REVERT: B 185 LEU cc_start: 0.8667 (tp) cc_final: 0.8194 (pp) REVERT: B 375 LYS cc_start: 0.8534 (pptt) cc_final: 0.8127 (pptt) REVERT: B 379 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8715 (mm-30) REVERT: B 437 LYS cc_start: 0.9505 (mttt) cc_final: 0.9149 (mtmt) REVERT: B 509 ASP cc_start: 0.9065 (p0) cc_final: 0.8780 (p0) REVERT: B 519 MET cc_start: 0.9164 (mmm) cc_final: 0.8832 (mmm) REVERT: B 651 ASP cc_start: 0.9004 (m-30) cc_final: 0.8358 (t0) REVERT: C 6 GLN cc_start: 0.7505 (pm20) cc_final: 0.7220 (pm20) REVERT: C 7 ASP cc_start: 0.7284 (m-30) cc_final: 0.6498 (t70) REVERT: C 193 ILE cc_start: 0.8932 (mt) cc_final: 0.8559 (mm) REVERT: C 231 MET cc_start: 0.8794 (mmp) cc_final: 0.8476 (mmp) REVERT: D 208 LEU cc_start: 0.9012 (tp) cc_final: 0.8803 (tp) REVERT: D 239 ARG cc_start: 0.7244 (ptt90) cc_final: 0.5766 (mmt180) REVERT: E 21 MET cc_start: 0.2982 (mtt) cc_final: 0.2323 (ttp) REVERT: E 56 TYR cc_start: 0.7876 (t80) cc_final: 0.7185 (t80) REVERT: E 197 TYR cc_start: 0.8633 (m-10) cc_final: 0.8273 (m-10) REVERT: E 202 ASN cc_start: 0.9205 (m-40) cc_final: 0.8859 (p0) REVERT: E 204 MET cc_start: 0.9488 (mtp) cc_final: 0.9170 (tmm) REVERT: F 44 PHE cc_start: 0.8159 (m-10) cc_final: 0.7519 (m-10) REVERT: F 89 GLN cc_start: 0.9481 (mm-40) cc_final: 0.9227 (mm-40) REVERT: F 169 LYS cc_start: 0.8252 (mttt) cc_final: 0.7084 (tttt) REVERT: F 202 ASN cc_start: 0.9751 (m110) cc_final: 0.9497 (t0) REVERT: F 290 MET cc_start: 0.8794 (tpt) cc_final: 0.8269 (tpp) outliers start: 1 outliers final: 0 residues processed: 294 average time/residue: 0.1748 time to fit residues: 78.9958 Evaluate side-chains 210 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 134 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 HIS A 975 HIS ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.068621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.050496 restraints weight = 133971.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.052127 restraints weight = 78245.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.053229 restraints weight = 53677.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.053969 restraints weight = 41173.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.054418 restraints weight = 34108.095| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23773 Z= 0.121 Angle : 0.620 10.123 32072 Z= 0.321 Chirality : 0.044 0.348 3422 Planarity : 0.004 0.050 4114 Dihedral : 4.673 25.590 3097 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.46 % Favored : 94.07 % Rotamer: Outliers : 0.04 % Allowed : 0.47 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.16), residues: 2801 helix: 0.89 (0.14), residues: 1523 sheet: -0.22 (0.34), residues: 222 loop : -1.29 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 86 TYR 0.015 0.001 TYR C 171 PHE 0.043 0.002 PHE B 45 TRP 0.029 0.002 TRP D 72 HIS 0.004 0.001 HIS B 503 Details of bonding type rmsd covalent geometry : bond 0.00272 (23772) covalent geometry : angle 0.62005 (32072) hydrogen bonds : bond 0.03552 ( 1103) hydrogen bonds : angle 4.49195 ( 3153) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9621 (mm-30) cc_final: 0.9305 (mm-30) REVERT: A 235 LEU cc_start: 0.8307 (mp) cc_final: 0.8103 (mp) REVERT: A 519 MET cc_start: 0.8911 (mmt) cc_final: 0.8576 (mmt) REVERT: A 907 PHE cc_start: 0.9099 (m-80) cc_final: 0.8847 (m-80) REVERT: A 913 MET cc_start: 0.8890 (tpp) cc_final: 0.8608 (tpp) REVERT: B 24 ASN cc_start: 0.8526 (m-40) cc_final: 0.7642 (p0) REVERT: B 122 LEU cc_start: 0.9099 (pp) cc_final: 0.8831 (mt) REVERT: B 185 LEU cc_start: 0.8565 (tp) cc_final: 0.8206 (pp) REVERT: B 375 LYS cc_start: 0.8544 (pptt) cc_final: 0.8099 (pptt) REVERT: B 379 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8708 (mm-30) REVERT: B 437 LYS cc_start: 0.9489 (mttt) cc_final: 0.9125 (mtmt) REVERT: B 509 ASP cc_start: 0.9017 (p0) cc_final: 0.8733 (p0) REVERT: B 519 MET cc_start: 0.9203 (mmm) cc_final: 0.8791 (mmm) REVERT: B 651 ASP cc_start: 0.8970 (m-30) cc_final: 0.8309 (t0) REVERT: C 6 GLN cc_start: 0.7475 (pm20) cc_final: 0.7049 (pm20) REVERT: C 7 ASP cc_start: 0.7281 (m-30) cc_final: 0.6513 (t70) REVERT: C 193 ILE cc_start: 0.8908 (mt) cc_final: 0.8504 (mm) REVERT: C 227 ASP cc_start: 0.8434 (m-30) cc_final: 0.8140 (m-30) REVERT: C 231 MET cc_start: 0.8797 (mmp) cc_final: 0.8479 (mmp) REVERT: D 239 ARG cc_start: 0.7281 (ptt90) cc_final: 0.5688 (mmt180) REVERT: E 21 MET cc_start: 0.2986 (mtt) cc_final: 0.2317 (ttp) REVERT: E 56 TYR cc_start: 0.7854 (t80) cc_final: 0.7323 (t80) REVERT: E 197 TYR cc_start: 0.8627 (m-10) cc_final: 0.8314 (m-10) REVERT: E 202 ASN cc_start: 0.9139 (m-40) cc_final: 0.8715 (p0) REVERT: E 204 MET cc_start: 0.9452 (mtp) cc_final: 0.9238 (ppp) REVERT: E 205 LYS cc_start: 0.9310 (mttt) cc_final: 0.8964 (tptt) REVERT: E 233 ARG cc_start: 0.8194 (mtm180) cc_final: 0.7662 (ptp-110) REVERT: F 44 PHE cc_start: 0.8183 (m-10) cc_final: 0.7531 (m-10) REVERT: F 89 GLN cc_start: 0.9443 (mm-40) cc_final: 0.9080 (mm-40) REVERT: F 169 LYS cc_start: 0.8220 (mttt) cc_final: 0.7126 (tttt) REVERT: F 202 ASN cc_start: 0.9728 (m110) cc_final: 0.9331 (t0) REVERT: F 290 MET cc_start: 0.8843 (tpt) cc_final: 0.8562 (tpp) outliers start: 1 outliers final: 0 residues processed: 286 average time/residue: 0.1741 time to fit residues: 76.5317 Evaluate side-chains 208 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 124 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 chunk 191 optimal weight: 0.1980 chunk 279 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** 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 = 0.3632 r_free = 0.3632 target = 0.068310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.050356 restraints weight = 134140.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.051978 restraints weight = 78139.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.053071 restraints weight = 53447.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.053812 restraints weight = 40867.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.054325 restraints weight = 33636.589| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 23773 Z= 0.129 Angle : 0.627 10.441 32072 Z= 0.322 Chirality : 0.043 0.346 3422 Planarity : 0.004 0.050 4114 Dihedral : 4.649 25.791 3097 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.46 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.16), residues: 2801 helix: 0.90 (0.14), residues: 1529 sheet: -0.23 (0.33), residues: 241 loop : -1.29 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 38 TYR 0.022 0.001 TYR A 589 PHE 0.047 0.002 PHE D 220 TRP 0.027 0.002 TRP D 72 HIS 0.003 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00289 (23772) covalent geometry : angle 0.62693 (32072) hydrogen bonds : bond 0.03552 ( 1103) hydrogen bonds : angle 4.48494 ( 3153) Misc. bond : bond 0.00059 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5602 Ramachandran restraints generated. 2801 Oldfield, 0 Emsley, 2801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9616 (mm-30) cc_final: 0.9356 (mm-30) REVERT: A 124 MET cc_start: 0.9605 (mmm) cc_final: 0.9262 (mmt) REVERT: A 227 MET cc_start: 0.9012 (tpt) cc_final: 0.8594 (tpp) REVERT: A 235 LEU cc_start: 0.8350 (mp) cc_final: 0.8098 (mp) REVERT: A 519 MET cc_start: 0.8870 (mmt) cc_final: 0.8581 (mmt) REVERT: A 735 LYS cc_start: 0.9231 (mttp) cc_final: 0.8836 (mmtp) REVERT: A 913 MET cc_start: 0.8899 (tpp) cc_final: 0.8632 (tpp) REVERT: A 1001 MET cc_start: 0.9585 (tmm) cc_final: 0.9382 (tmm) REVERT: B 24 ASN cc_start: 0.8518 (m-40) cc_final: 0.7610 (p0) REVERT: B 122 LEU cc_start: 0.9081 (pp) cc_final: 0.8776 (mt) REVERT: B 185 LEU cc_start: 0.8584 (tp) cc_final: 0.8306 (pp) REVERT: B 375 LYS cc_start: 0.8615 (pptt) cc_final: 0.8193 (pptt) REVERT: B 379 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8687 (mm-30) REVERT: B 437 LYS cc_start: 0.9491 (mttt) cc_final: 0.9119 (mtmt) REVERT: B 509 ASP cc_start: 0.9011 (p0) cc_final: 0.8733 (p0) REVERT: B 519 MET cc_start: 0.9233 (mmm) cc_final: 0.8801 (mmm) REVERT: B 651 ASP cc_start: 0.8966 (m-30) cc_final: 0.8363 (t0) REVERT: C 6 GLN cc_start: 0.7432 (pm20) cc_final: 0.7220 (pm20) REVERT: C 7 ASP cc_start: 0.7269 (m-30) cc_final: 0.6463 (t70) REVERT: C 193 ILE cc_start: 0.8903 (mt) cc_final: 0.8493 (mm) REVERT: C 227 ASP cc_start: 0.8455 (m-30) cc_final: 0.8178 (m-30) REVERT: C 231 MET cc_start: 0.8804 (mmp) cc_final: 0.8307 (mmm) REVERT: D 208 LEU cc_start: 0.8984 (tp) cc_final: 0.8768 (tp) REVERT: E 21 MET cc_start: 0.2957 (mtt) cc_final: 0.2305 (ttp) REVERT: E 56 TYR cc_start: 0.7873 (t80) cc_final: 0.7668 (t80) REVERT: E 196 ASN cc_start: 0.9383 (t0) cc_final: 0.9048 (t0) REVERT: E 197 TYR cc_start: 0.8649 (m-10) cc_final: 0.8252 (m-10) REVERT: E 202 ASN cc_start: 0.9174 (m-40) cc_final: 0.8734 (p0) REVERT: E 205 LYS cc_start: 0.9315 (mttt) cc_final: 0.9013 (tptt) REVERT: F 44 PHE cc_start: 0.8202 (m-10) cc_final: 0.7580 (m-10) REVERT: F 89 GLN cc_start: 0.9452 (mm-40) cc_final: 0.9084 (mm-40) REVERT: F 169 LYS cc_start: 0.8271 (mttt) cc_final: 0.7105 (tttt) REVERT: F 202 ASN cc_start: 0.9730 (m110) cc_final: 0.9287 (t0) REVERT: F 290 MET cc_start: 0.8853 (tpt) cc_final: 0.8548 (tpp) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1720 time to fit residues: 73.9129 Evaluate side-chains 208 residues out of total 2555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 240 optimal weight: 0.7980 chunk 219 optimal weight: 0.7980 chunk 213 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 277 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 254 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** 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 = 0.3637 r_free = 0.3637 target = 0.068477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.050353 restraints weight = 133364.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.052000 restraints weight = 77427.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.053041 restraints weight = 53229.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.053828 restraints weight = 40899.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.054296 restraints weight = 33716.715| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23773 Z= 0.118 Angle : 0.617 10.431 32072 Z= 0.317 Chirality : 0.043 0.395 3422 Planarity : 0.004 0.053 4114 Dihedral : 4.604 25.907 3097 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.32 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.16), residues: 2801 helix: 0.92 (0.14), residues: 1531 sheet: 0.00 (0.35), residues: 215 loop : -1.23 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 38 TYR 0.014 0.001 TYR B 596 PHE 0.042 0.001 PHE D 13 TRP 0.026 0.002 TRP D 72 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00262 (23772) covalent geometry : angle 0.61680 (32072) hydrogen bonds : bond 0.03461 ( 1103) hydrogen bonds : angle 4.44444 ( 3153) Misc. bond : bond 0.00057 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4105.55 seconds wall clock time: 72 minutes 7.48 seconds (4327.48 seconds total)