Starting phenix.real_space_refine on Sat Mar 7 12:10:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vvy_32149/03_2026/7vvy_32149.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vvy_32149/03_2026/7vvy_32149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vvy_32149/03_2026/7vvy_32149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vvy_32149/03_2026/7vvy_32149.map" model { file = "/net/cci-nas-00/data/ceres_data/7vvy_32149/03_2026/7vvy_32149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vvy_32149/03_2026/7vvy_32149.cif" } resolution = 3.1 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= 0.001 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 174 5.16 5 C 27371 2.51 5 N 7131 2.21 5 O 7862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 291 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42546 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3448 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 24, 'TRANS': 390} Chain breaks: 4 Chain: "F" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "G" Number of atoms: 2788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2788 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 18, 'TRANS': 338} Chain breaks: 1 Chain: "K" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1989 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain breaks: 3 Chain: "H" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2250 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 12, 'TRANS': 256} Chain breaks: 2 Chain: "L" Number of atoms: 28729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3513, 28729 Classifications: {'peptide': 3513} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 148, 'TRANS': 3363} Chain breaks: 11 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.79, per 1000 atoms: 0.21 Number of scatterers: 42546 At special positions: 0 Unit cell: (229.49, 159.127, 210.005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 174 16.00 P 6 15.00 Mg 2 11.99 O 7862 8.00 N 7131 7.00 C 27371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.7 seconds 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10096 Finding SS restraints... Secondary structure from input PDB file: 268 helices and 23 sheets defined 62.5% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'E' and resid 241 through 248 Processing helix chain 'E' and resid 286 through 295 removed outlier: 3.885A pdb=" N LEU E 290 " --> pdb=" O PRO E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 297 No H-bonds generated for 'chain 'E' and resid 296 through 297' Processing helix chain 'E' and resid 298 through 302 Processing helix chain 'E' and resid 312 through 337 removed outlier: 3.541A pdb=" N ASN E 316 " --> pdb=" O THR E 312 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 337 " --> pdb=" O GLU E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 397 Processing helix chain 'E' and resid 550 through 552 No H-bonds generated for 'chain 'E' and resid 550 through 552' Processing helix chain 'E' and resid 553 through 563 Processing helix chain 'E' and resid 612 through 617 removed outlier: 4.088A pdb=" N SER E 616 " --> pdb=" O ILE E 612 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS E 617 " --> pdb=" O SER E 613 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 612 through 617' Processing helix chain 'E' and resid 627 through 631 Processing helix chain 'E' and resid 653 through 666 Processing helix chain 'E' and resid 670 through 677 Processing helix chain 'E' and resid 692 through 704 Processing helix chain 'E' and resid 716 through 735 Processing helix chain 'E' and resid 745 through 748 removed outlier: 3.896A pdb=" N ILE E 748 " --> pdb=" O THR E 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 745 through 748' Processing helix chain 'E' and resid 749 through 753 removed outlier: 3.526A pdb=" N HIS E 752 " --> pdb=" O GLN E 749 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG E 753 " --> pdb=" O ARG E 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 749 through 753' Processing helix chain 'E' and resid 756 through 772 Processing helix chain 'E' and resid 796 through 807 Processing helix chain 'F' and resid 82 through 98 Processing helix chain 'F' and resid 117 through 130 Processing helix chain 'F' and resid 142 through 151 Processing helix chain 'F' and resid 177 through 180 Processing helix chain 'F' and resid 186 through 198 Processing helix chain 'F' and resid 205 through 207 No H-bonds generated for 'chain 'F' and resid 205 through 207' Processing helix chain 'F' and resid 226 through 237 removed outlier: 3.742A pdb=" N TYR F 230 " --> pdb=" O ASP F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 247 removed outlier: 3.546A pdb=" N CYS F 247 " --> pdb=" O LYS F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 264 removed outlier: 4.121A pdb=" N GLU F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 4.824A pdb=" N ALA F 289 " --> pdb=" O ARG F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 395 Processing helix chain 'F' and resid 400 through 407 Processing helix chain 'F' and resid 413 through 417 removed outlier: 3.526A pdb=" N ILE F 417 " --> pdb=" O THR F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 432 Processing helix chain 'F' and resid 444 through 449 Processing helix chain 'F' and resid 450 through 461 Processing helix chain 'F' and resid 465 through 469 removed outlier: 3.612A pdb=" N TRP F 469 " --> pdb=" O HIS F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 479 Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 92 Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.608A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 127 Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 181 through 194 removed outlier: 3.783A pdb=" N SER G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 205 through 217 Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 255 through 260 Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 290 through 295 Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 348 Processing helix chain 'G' and resid 350 through 355 removed outlier: 3.797A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 368 through 374 removed outlier: 4.054A pdb=" N HIS G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 50 Processing helix chain 'K' and resid 109 through 115 Processing helix chain 'K' and resid 124 through 132 Processing helix chain 'K' and resid 165 through 179 Processing helix chain 'K' and resid 182 through 190 Processing helix chain 'K' and resid 198 through 216 Processing helix chain 'K' and resid 220 through 225 Processing helix chain 'K' and resid 229 through 245 Processing helix chain 'K' and resid 247 through 266 Processing helix chain 'K' and resid 267 through 283 Processing helix chain 'K' and resid 290 through 295 removed outlier: 4.365A pdb=" N GLN K 293 " --> pdb=" O THR K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 309 Processing helix chain 'K' and resid 324 through 329 removed outlier: 3.604A pdb=" N LYS K 328 " --> pdb=" O ASN K 324 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN K 329 " --> pdb=" O PRO K 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 324 through 329' Processing helix chain 'H' and resid 504 through 531 removed outlier: 3.566A pdb=" N ASP H 531 " --> pdb=" O ARG H 527 " (cutoff:3.500A) Processing helix chain 'H' and resid 559 through 562 Processing helix chain 'H' and resid 563 through 568 Processing helix chain 'H' and resid 580 through 587 Processing helix chain 'H' and resid 610 through 616 Processing helix chain 'H' and resid 666 through 671 removed outlier: 3.772A pdb=" N ASP H 669 " --> pdb=" O SER H 666 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE H 670 " --> pdb=" O LEU H 667 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL H 671 " --> pdb=" O MET H 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 666 through 671' Processing helix chain 'H' and resid 672 through 681 removed outlier: 3.513A pdb=" N ILE H 676 " --> pdb=" O ASP H 672 " (cutoff:3.500A) Processing helix chain 'H' and resid 697 through 711 removed outlier: 3.813A pdb=" N GLU H 701 " --> pdb=" O SER H 697 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TRP H 709 " --> pdb=" O LEU H 705 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TYR H 711 " --> pdb=" O ASP H 707 " (cutoff:3.500A) Processing helix chain 'H' and resid 713 through 717 removed outlier: 3.570A pdb=" N GLU H 717 " --> pdb=" O PRO H 714 " (cutoff:3.500A) Processing helix chain 'H' and resid 724 through 731 Processing helix chain 'H' and resid 734 through 766 removed outlier: 3.700A pdb=" N VAL H 738 " --> pdb=" O ASN H 734 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR H 766 " --> pdb=" O ARG H 762 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 removed outlier: 3.638A pdb=" N GLN L 6 " --> pdb=" O LEU L 3 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU L 8 " --> pdb=" O GLU L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 31 removed outlier: 3.744A pdb=" N GLU L 30 " --> pdb=" O THR L 27 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU L 31 " --> pdb=" O LEU L 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 27 through 31' Processing helix chain 'L' and resid 44 through 61 removed outlier: 4.165A pdb=" N GLN L 49 " --> pdb=" O HIS L 45 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ALA L 50 " --> pdb=" O PHE L 46 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE L 52 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Proline residue: L 53 - end of helix removed outlier: 4.043A pdb=" N GLU L 61 " --> pdb=" O ASN L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 86 Processing helix chain 'L' and resid 91 through 97 removed outlier: 3.952A pdb=" N TYR L 95 " --> pdb=" O THR L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 104 removed outlier: 4.116A pdb=" N LEU L 103 " --> pdb=" O VAL L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 132 removed outlier: 4.430A pdb=" N THR L 123 " --> pdb=" O MET L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 157 removed outlier: 4.524A pdb=" N ILE L 144 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE L 145 " --> pdb=" O ILE L 141 " (cutoff:3.500A) Proline residue: L 152 - end of helix Processing helix chain 'L' and resid 231 through 243 removed outlier: 4.662A pdb=" N LEU L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER L 243 " --> pdb=" O LYS L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 254 removed outlier: 3.577A pdb=" N ILE L 253 " --> pdb=" O THR L 250 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 309 removed outlier: 3.593A pdb=" N ALA L 297 " --> pdb=" O ASP L 293 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 314 Processing helix chain 'L' and resid 324 through 335 removed outlier: 3.508A pdb=" N LEU L 328 " --> pdb=" O PHE L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 341 through 356 removed outlier: 4.017A pdb=" N LYS L 345 " --> pdb=" O SER L 341 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU L 346 " --> pdb=" O SER L 342 " (cutoff:3.500A) Processing helix chain 'L' and resid 363 through 369 Processing helix chain 'L' and resid 374 through 378 Processing helix chain 'L' and resid 387 through 403 Processing helix chain 'L' and resid 407 through 424 removed outlier: 3.594A pdb=" N ILE L 417 " --> pdb=" O LYS L 413 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY L 420 " --> pdb=" O LYS L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 428 through 453 removed outlier: 3.722A pdb=" N GLN L 432 " --> pdb=" O ALA L 428 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU L 444 " --> pdb=" O LEU L 440 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG L 445 " --> pdb=" O ASN L 441 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN L 453 " --> pdb=" O LEU L 449 " (cutoff:3.500A) Processing helix chain 'L' and resid 456 through 480 removed outlier: 3.762A pdb=" N LEU L 463 " --> pdb=" O ARG L 459 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE L 468 " --> pdb=" O LEU L 464 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP L 469 " --> pdb=" O MET L 465 " (cutoff:3.500A) Processing helix chain 'L' and resid 481 through 501 removed outlier: 3.558A pdb=" N LYS L 496 " --> pdb=" O TYR L 492 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS L 499 " --> pdb=" O HIS L 495 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU L 501 " --> pdb=" O LYS L 497 " (cutoff:3.500A) Processing helix chain 'L' and resid 512 through 520 Processing helix chain 'L' and resid 561 through 567 removed outlier: 3.886A pdb=" N ALA L 567 " --> pdb=" O LYS L 564 " (cutoff:3.500A) Processing helix chain 'L' and resid 578 through 601 Processing helix chain 'L' and resid 602 through 605 removed outlier: 3.972A pdb=" N ASN L 605 " --> pdb=" O LYS L 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 602 through 605' Processing helix chain 'L' and resid 627 through 644 removed outlier: 3.732A pdb=" N VAL L 633 " --> pdb=" O GLU L 629 " (cutoff:3.500A) Processing helix chain 'L' and resid 645 through 647 No H-bonds generated for 'chain 'L' and resid 645 through 647' Processing helix chain 'L' and resid 676 through 690 Processing helix chain 'L' and resid 694 through 714 removed outlier: 3.976A pdb=" N GLU L 700 " --> pdb=" O ALA L 696 " (cutoff:3.500A) Proline residue: L 707 - end of helix Processing helix chain 'L' and resid 716 through 718 No H-bonds generated for 'chain 'L' and resid 716 through 718' Processing helix chain 'L' and resid 719 through 728 removed outlier: 3.860A pdb=" N ALA L 723 " --> pdb=" O LEU L 719 " (cutoff:3.500A) Processing helix chain 'L' and resid 732 through 748 removed outlier: 3.779A pdb=" N GLY L 746 " --> pdb=" O ARG L 742 " (cutoff:3.500A) Processing helix chain 'L' and resid 749 through 751 No H-bonds generated for 'chain 'L' and resid 749 through 751' Processing helix chain 'L' and resid 755 through 776 removed outlier: 3.823A pdb=" N VAL L 773 " --> pdb=" O SER L 769 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN L 774 " --> pdb=" O PHE L 770 " (cutoff:3.500A) Processing helix chain 'L' and resid 788 through 799 Processing helix chain 'L' and resid 806 through 819 removed outlier: 3.528A pdb=" N ILE L 819 " --> pdb=" O LEU L 815 " (cutoff:3.500A) Processing helix chain 'L' and resid 827 through 830 removed outlier: 4.079A pdb=" N SER L 830 " --> pdb=" O LEU L 827 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 827 through 830' Processing helix chain 'L' and resid 831 through 844 Processing helix chain 'L' and resid 853 through 863 Processing helix chain 'L' and resid 879 through 890 removed outlier: 4.115A pdb=" N TYR L 890 " --> pdb=" O ALA L 886 " (cutoff:3.500A) Processing helix chain 'L' and resid 893 through 907 removed outlier: 4.115A pdb=" N ASN L 907 " --> pdb=" O LEU L 903 " (cutoff:3.500A) Processing helix chain 'L' and resid 913 through 918 Processing helix chain 'L' and resid 920 through 931 removed outlier: 3.547A pdb=" N ASN L 930 " --> pdb=" O LYS L 926 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU L 931 " --> pdb=" O ALA L 927 " (cutoff:3.500A) Processing helix chain 'L' and resid 942 through 952 Processing helix chain 'L' and resid 996 through 1006 removed outlier: 3.542A pdb=" N SER L1006 " --> pdb=" O ASN L1002 " (cutoff:3.500A) Processing helix chain 'L' and resid 1011 through 1030 Processing helix chain 'L' and resid 1031 through 1033 No H-bonds generated for 'chain 'L' and resid 1031 through 1033' Processing helix chain 'L' and resid 1038 through 1049 Processing helix chain 'L' and resid 1068 through 1090 removed outlier: 3.780A pdb=" N THR L1090 " --> pdb=" O VAL L1086 " (cutoff:3.500A) Processing helix chain 'L' and resid 1095 through 1122 removed outlier: 3.820A pdb=" N LEU L1112 " --> pdb=" O ASP L1108 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL L1115 " --> pdb=" O CYS L1111 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASN L1116 " --> pdb=" O LEU L1112 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR L1117 " --> pdb=" O LEU L1113 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS L1122 " --> pdb=" O THR L1118 " (cutoff:3.500A) Processing helix chain 'L' and resid 1148 through 1154 removed outlier: 3.518A pdb=" N SER L1154 " --> pdb=" O PRO L1150 " (cutoff:3.500A) Processing helix chain 'L' and resid 1157 through 1180 removed outlier: 3.598A pdb=" N ARG L1161 " --> pdb=" O ILE L1157 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL L1163 " --> pdb=" O GLU L1159 " (cutoff:3.500A) Processing helix chain 'L' and resid 1180 through 1188 removed outlier: 4.090A pdb=" N LEU L1185 " --> pdb=" O GLU L1181 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER L1186 " --> pdb=" O GLU L1182 " (cutoff:3.500A) Processing helix chain 'L' and resid 1188 through 1201 removed outlier: 4.495A pdb=" N GLU L1192 " --> pdb=" O SER L1188 " (cutoff:3.500A) Processing helix chain 'L' and resid 1205 through 1223 Processing helix chain 'L' and resid 1228 through 1233 Processing helix chain 'L' and resid 1233 through 1247 removed outlier: 3.597A pdb=" N LEU L1245 " --> pdb=" O LEU L1241 " (cutoff:3.500A) Processing helix chain 'L' and resid 1254 through 1272 Processing helix chain 'L' and resid 1283 through 1294 removed outlier: 3.603A pdb=" N ASN L1287 " --> pdb=" O LYS L1283 " (cutoff:3.500A) Processing helix chain 'L' and resid 1300 through 1316 Processing helix chain 'L' and resid 1321 through 1326 Processing helix chain 'L' and resid 1329 through 1340 removed outlier: 3.663A pdb=" N LEU L1333 " --> pdb=" O SER L1329 " (cutoff:3.500A) Proline residue: L1336 - end of helix removed outlier: 3.709A pdb=" N LYS L1340 " --> pdb=" O PRO L1336 " (cutoff:3.500A) Processing helix chain 'L' and resid 1346 through 1363 Processing helix chain 'L' and resid 1371 through 1383 Processing helix chain 'L' and resid 1404 through 1424 Processing helix chain 'L' and resid 1436 through 1447 removed outlier: 3.742A pdb=" N VAL L1443 " --> pdb=" O ARG L1439 " (cutoff:3.500A) Processing helix chain 'L' and resid 1452 through 1467 removed outlier: 3.684A pdb=" N ILE L1456 " --> pdb=" O SER L1452 " (cutoff:3.500A) Processing helix chain 'L' and resid 1468 through 1470 No H-bonds generated for 'chain 'L' and resid 1468 through 1470' Processing helix chain 'L' and resid 1477 through 1482 removed outlier: 4.062A pdb=" N LEU L1482 " --> pdb=" O LEU L1478 " (cutoff:3.500A) Processing helix chain 'L' and resid 1482 through 1489 Processing helix chain 'L' and resid 1496 through 1508 Processing helix chain 'L' and resid 1517 through 1530 removed outlier: 3.532A pdb=" N LYS L1521 " --> pdb=" O GLU L1517 " (cutoff:3.500A) Processing helix chain 'L' and resid 1532 through 1538 Processing helix chain 'L' and resid 1546 through 1558 Processing helix chain 'L' and resid 1570 through 1584 Processing helix chain 'L' and resid 1593 through 1604 removed outlier: 3.952A pdb=" N ARG L1602 " --> pdb=" O ARG L1598 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE L1603 " --> pdb=" O TYR L1599 " (cutoff:3.500A) Processing helix chain 'L' and resid 1605 through 1613 removed outlier: 3.922A pdb=" N GLU L1609 " --> pdb=" O ASN L1605 " (cutoff:3.500A) Processing helix chain 'L' and resid 1617 through 1629 removed outlier: 3.994A pdb=" N GLN L1629 " --> pdb=" O CYS L1625 " (cutoff:3.500A) Processing helix chain 'L' and resid 1630 through 1632 No H-bonds generated for 'chain 'L' and resid 1630 through 1632' Processing helix chain 'L' and resid 1633 through 1641 removed outlier: 4.376A pdb=" N GLU L1638 " --> pdb=" O LYS L1634 " (cutoff:3.500A) Processing helix chain 'L' and resid 1643 through 1659 Proline residue: L1656 - end of helix Processing helix chain 'L' and resid 1661 through 1679 Processing helix chain 'L' and resid 1690 through 1709 Processing helix chain 'L' and resid 1715 through 1734 Processing helix chain 'L' and resid 1739 through 1750 removed outlier: 3.886A pdb=" N LEU L1743 " --> pdb=" O ASP L1739 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU L1744 " --> pdb=" O GLN L1740 " (cutoff:3.500A) Processing helix chain 'L' and resid 1762 through 1770 Processing helix chain 'L' and resid 1771 through 1775 removed outlier: 3.606A pdb=" N SER L1774 " --> pdb=" O ILE L1771 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN L1775 " --> pdb=" O ALA L1772 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1771 through 1775' Processing helix chain 'L' and resid 1777 through 1792 removed outlier: 3.600A pdb=" N ASN L1781 " --> pdb=" O GLU L1777 " (cutoff:3.500A) Processing helix chain 'L' and resid 1796 through 1817 Processing helix chain 'L' and resid 1833 through 1843 Processing helix chain 'L' and resid 1844 through 1845 No H-bonds generated for 'chain 'L' and resid 1844 through 1845' Processing helix chain 'L' and resid 1846 through 1850 removed outlier: 3.561A pdb=" N LEU L1849 " --> pdb=" O ASN L1846 " (cutoff:3.500A) Processing helix chain 'L' and resid 1858 through 1875 removed outlier: 3.540A pdb=" N PHE L1862 " --> pdb=" O ASP L1858 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP L1875 " --> pdb=" O PHE L1871 " (cutoff:3.500A) Processing helix chain 'L' and resid 1882 through 1893 removed outlier: 3.738A pdb=" N PHE L1893 " --> pdb=" O PHE L1889 " (cutoff:3.500A) Processing helix chain 'L' and resid 1899 through 1916 Processing helix chain 'L' and resid 1920 through 1931 removed outlier: 4.559A pdb=" N THR L1924 " --> pdb=" O ILE L1920 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN L1925 " --> pdb=" O LYS L1921 " (cutoff:3.500A) Processing helix chain 'L' and resid 1935 through 1937 No H-bonds generated for 'chain 'L' and resid 1935 through 1937' Processing helix chain 'L' and resid 1938 through 1958 removed outlier: 3.652A pdb=" N VAL L1942 " --> pdb=" O ALA L1938 " (cutoff:3.500A) Proline residue: L1951 - end of helix removed outlier: 4.003A pdb=" N GLU L1955 " --> pdb=" O PRO L1951 " (cutoff:3.500A) Processing helix chain 'L' and resid 1964 through 1975 removed outlier: 3.937A pdb=" N ASN L1968 " --> pdb=" O ASP L1964 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL L1970 " --> pdb=" O TRP L1966 " (cutoff:3.500A) Processing helix chain 'L' and resid 1982 through 1988 removed outlier: 4.266A pdb=" N TYR L1986 " --> pdb=" O ASN L1982 " (cutoff:3.500A) Processing helix chain 'L' and resid 2001 through 2015 Processing helix chain 'L' and resid 2024 through 2043 removed outlier: 3.686A pdb=" N ALA L2028 " --> pdb=" O SER L2024 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU L2043 " --> pdb=" O GLU L2039 " (cutoff:3.500A) Processing helix chain 'L' and resid 2090 through 2107 removed outlier: 3.789A pdb=" N GLU L2094 " --> pdb=" O LEU L2090 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER L2107 " --> pdb=" O TYR L2103 " (cutoff:3.500A) Processing helix chain 'L' and resid 2116 through 2129 removed outlier: 3.962A pdb=" N SER L2129 " --> pdb=" O SER L2125 " (cutoff:3.500A) Processing helix chain 'L' and resid 2155 through 2173 removed outlier: 4.088A pdb=" N TYR L2169 " --> pdb=" O LEU L2165 " (cutoff:3.500A) Processing helix chain 'L' and resid 2183 through 2196 removed outlier: 4.813A pdb=" N LYS L2193 " --> pdb=" O ASN L2189 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N CYS L2194 " --> pdb=" O LEU L2190 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS L2196 " --> pdb=" O GLU L2192 " (cutoff:3.500A) Processing helix chain 'L' and resid 2203 through 2217 removed outlier: 4.855A pdb=" N GLN L2211 " --> pdb=" O GLN L2207 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL L2212 " --> pdb=" O LYS L2208 " (cutoff:3.500A) Processing helix chain 'L' and resid 2228 through 2245 removed outlier: 3.807A pdb=" N GLY L2232 " --> pdb=" O GLU L2228 " (cutoff:3.500A) Processing helix chain 'L' and resid 2251 through 2267 removed outlier: 4.075A pdb=" N ALA L2255 " --> pdb=" O SER L2251 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY L2256 " --> pdb=" O SER L2252 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL L2257 " --> pdb=" O VAL L2253 " (cutoff:3.500A) Processing helix chain 'L' and resid 2275 through 2290 Processing helix chain 'L' and resid 2302 through 2321 removed outlier: 4.777A pdb=" N THR L2308 " --> pdb=" O ALA L2304 " (cutoff:3.500A) Processing helix chain 'L' and resid 2328 through 2342 Processing helix chain 'L' and resid 2345 through 2361 removed outlier: 4.217A pdb=" N LYS L2351 " --> pdb=" O ASN L2347 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE L2361 " --> pdb=" O ARG L2357 " (cutoff:3.500A) Processing helix chain 'L' and resid 2369 through 2378 Processing helix chain 'L' and resid 2381 through 2386 Processing helix chain 'L' and resid 2387 through 2404 Processing helix chain 'L' and resid 2412 through 2424 removed outlier: 3.541A pdb=" N GLU L2417 " --> pdb=" O THR L2413 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN L2418 " --> pdb=" O VAL L2414 " (cutoff:3.500A) Proline residue: L2419 - end of helix removed outlier: 3.693A pdb=" N VAL L2422 " --> pdb=" O GLN L2418 " (cutoff:3.500A) Processing helix chain 'L' and resid 2428 through 2443 removed outlier: 3.861A pdb=" N LEU L2443 " --> pdb=" O LEU L2439 " (cutoff:3.500A) Processing helix chain 'L' and resid 2446 through 2456 Processing helix chain 'L' and resid 2468 through 2477 Processing helix chain 'L' and resid 2478 through 2480 No H-bonds generated for 'chain 'L' and resid 2478 through 2480' Processing helix chain 'L' and resid 2499 through 2503 removed outlier: 3.660A pdb=" N TYR L2503 " --> pdb=" O LEU L2500 " (cutoff:3.500A) Processing helix chain 'L' and resid 2518 through 2534 removed outlier: 3.619A pdb=" N GLY L2532 " --> pdb=" O ALA L2528 " (cutoff:3.500A) Processing helix chain 'L' and resid 2537 through 2550 removed outlier: 4.242A pdb=" N PHE L2541 " --> pdb=" O ILE L2537 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU L2547 " --> pdb=" O ASP L2543 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE L2548 " --> pdb=" O SER L2544 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR L2550 " --> pdb=" O ILE L2546 " (cutoff:3.500A) Processing helix chain 'L' and resid 2552 through 2568 removed outlier: 4.173A pdb=" N ILE L2556 " --> pdb=" O ASP L2552 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS L2557 " --> pdb=" O PRO L2553 " (cutoff:3.500A) Proline residue: L2565 - end of helix Processing helix chain 'L' and resid 2569 through 2571 No H-bonds generated for 'chain 'L' and resid 2569 through 2571' Processing helix chain 'L' and resid 2575 through 2588 Processing helix chain 'L' and resid 2589 through 2596 removed outlier: 3.797A pdb=" N HIS L2592 " --> pdb=" O LYS L2589 " (cutoff:3.500A) Processing helix chain 'L' and resid 2601 through 2611 removed outlier: 3.671A pdb=" N SER L2609 " --> pdb=" O MET L2605 " (cutoff:3.500A) Processing helix chain 'L' and resid 2623 through 2627 Processing helix chain 'L' and resid 2632 through 2642 Processing helix chain 'L' and resid 2654 through 2669 Processing helix chain 'L' and resid 2671 through 2683 Processing helix chain 'L' and resid 2685 through 2698 removed outlier: 4.016A pdb=" N ASN L2689 " --> pdb=" O TYR L2685 " (cutoff:3.500A) Processing helix chain 'L' and resid 2699 through 2716 Processing helix chain 'L' and resid 2720 through 2723 removed outlier: 4.065A pdb=" N GLN L2723 " --> pdb=" O PRO L2720 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2720 through 2723' Processing helix chain 'L' and resid 2724 through 2740 Processing helix chain 'L' and resid 2742 through 2752 removed outlier: 3.855A pdb=" N GLU L2748 " --> pdb=" O ASP L2744 " (cutoff:3.500A) Processing helix chain 'L' and resid 2757 through 2761 Processing helix chain 'L' and resid 2772 through 2784 removed outlier: 3.773A pdb=" N SER L2779 " --> pdb=" O ALA L2775 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL L2783 " --> pdb=" O SER L2779 " (cutoff:3.500A) Processing helix chain 'L' and resid 2788 through 2806 Processing helix chain 'L' and resid 2812 through 2831 removed outlier: 3.773A pdb=" N ASP L2818 " --> pdb=" O ARG L2814 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU L2831 " --> pdb=" O LYS L2827 " (cutoff:3.500A) Processing helix chain 'L' and resid 2837 through 2864 removed outlier: 4.278A pdb=" N TRP L2841 " --> pdb=" O PRO L2837 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU L2842 " --> pdb=" O ALA L2838 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR L2864 " --> pdb=" O ALA L2860 " (cutoff:3.500A) Processing helix chain 'L' and resid 2865 through 2868 Processing helix chain 'L' and resid 2873 through 2886 removed outlier: 3.812A pdb=" N ILE L2877 " --> pdb=" O LYS L2873 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP L2886 " --> pdb=" O GLN L2882 " (cutoff:3.500A) Processing helix chain 'L' and resid 2894 through 2916 removed outlier: 3.719A pdb=" N ILE L2912 " --> pdb=" O ALA L2908 " (cutoff:3.500A) Processing helix chain 'L' and resid 2920 through 2924 removed outlier: 3.997A pdb=" N GLN L2924 " --> pdb=" O PRO L2921 " (cutoff:3.500A) Processing helix chain 'L' and resid 2942 through 2957 removed outlier: 3.915A pdb=" N VAL L2946 " --> pdb=" O GLU L2942 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE L2950 " --> pdb=" O VAL L2946 " (cutoff:3.500A) Processing helix chain 'L' and resid 2959 through 2967 removed outlier: 3.520A pdb=" N LEU L2967 " --> pdb=" O CYS L2963 " (cutoff:3.500A) Processing helix chain 'L' and resid 2979 through 2992 removed outlier: 3.523A pdb=" N LEU L2983 " --> pdb=" O GLN L2979 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS L2992 " --> pdb=" O GLN L2988 " (cutoff:3.500A) Processing helix chain 'L' and resid 2993 through 2994 No H-bonds generated for 'chain 'L' and resid 2993 through 2994' Processing helix chain 'L' and resid 2995 through 2997 No H-bonds generated for 'chain 'L' and resid 2995 through 2997' Processing helix chain 'L' and resid 2998 through 3007 removed outlier: 3.975A pdb=" N VAL L3005 " --> pdb=" O THR L3001 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE L3006 " --> pdb=" O GLY L3002 " (cutoff:3.500A) Processing helix chain 'L' and resid 3016 through 3033 removed outlier: 4.126A pdb=" N ALA L3020 " --> pdb=" O THR L3016 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU L3033 " --> pdb=" O PHE L3029 " (cutoff:3.500A) Processing helix chain 'L' and resid 3036 through 3048 removed outlier: 3.624A pdb=" N ASN L3040 " --> pdb=" O TYR L3036 " (cutoff:3.500A) Processing helix chain 'L' and resid 3053 through 3069 Processing helix chain 'L' and resid 3076 through 3091 removed outlier: 3.996A pdb=" N ASN L3080 " --> pdb=" O SER L3076 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA L3081 " --> pdb=" O PHE L3077 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU L3091 " --> pdb=" O GLN L3087 " (cutoff:3.500A) Processing helix chain 'L' and resid 3097 through 3109 removed outlier: 3.777A pdb=" N SER L3109 " --> pdb=" O LEU L3105 " (cutoff:3.500A) Processing helix chain 'L' and resid 3115 through 3123 Processing helix chain 'L' and resid 3129 through 3135 removed outlier: 4.015A pdb=" N THR L3135 " --> pdb=" O TYR L3132 " (cutoff:3.500A) Processing helix chain 'L' and resid 3136 through 3142 Processing helix chain 'L' and resid 3151 through 3163 removed outlier: 4.185A pdb=" N ILE L3155 " --> pdb=" O MET L3151 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER L3162 " --> pdb=" O ARG L3158 " (cutoff:3.500A) Processing helix chain 'L' and resid 3163 through 3180 removed outlier: 3.856A pdb=" N LEU L3167 " --> pdb=" O TYR L3163 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N PHE L3169 " --> pdb=" O GLN L3165 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLN L3170 " --> pdb=" O ALA L3166 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL L3180 " --> pdb=" O GLU L3176 " (cutoff:3.500A) Processing helix chain 'L' and resid 3203 through 3218 Processing helix chain 'L' and resid 3219 through 3237 Processing helix chain 'L' and resid 3240 through 3263 Processing helix chain 'L' and resid 3273 through 3287 removed outlier: 3.858A pdb=" N THR L3285 " --> pdb=" O VAL L3281 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR L3286 " --> pdb=" O LYS L3282 " (cutoff:3.500A) Processing helix chain 'L' and resid 3291 through 3302 removed outlier: 3.966A pdb=" N LYS L3295 " --> pdb=" O TYR L3291 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP L3299 " --> pdb=" O LYS L3295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE L3300 " --> pdb=" O PHE L3296 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP L3302 " --> pdb=" O ALA L3298 " (cutoff:3.500A) Processing helix chain 'L' and resid 3308 through 3327 Processing helix chain 'L' and resid 3333 through 3338 Processing helix chain 'L' and resid 3338 through 3343 Processing helix chain 'L' and resid 3343 through 3348 removed outlier: 3.640A pdb=" N GLN L3347 " --> pdb=" O ASN L3343 " (cutoff:3.500A) Processing helix chain 'L' and resid 3412 through 3426 removed outlier: 3.875A pdb=" N GLU L3416 " --> pdb=" O HIS L3412 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE L3426 " --> pdb=" O LEU L3422 " (cutoff:3.500A) Processing helix chain 'L' and resid 3428 through 3433 Processing helix chain 'L' and resid 3433 through 3439 removed outlier: 3.658A pdb=" N ARG L3439 " --> pdb=" O GLU L3435 " (cutoff:3.500A) Processing helix chain 'L' and resid 3467 through 3478 Processing helix chain 'L' and resid 3483 through 3496 removed outlier: 3.631A pdb=" N ALA L3496 " --> pdb=" O LYS L3492 " (cutoff:3.500A) Processing helix chain 'L' and resid 3505 through 3521 Processing helix chain 'L' and resid 3525 through 3535 removed outlier: 3.837A pdb=" N PHE L3535 " --> pdb=" O PHE L3531 " (cutoff:3.500A) Processing helix chain 'L' and resid 3537 through 3561 removed outlier: 3.524A pdb=" N PHE L3541 " --> pdb=" O GLN L3537 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER L3550 " --> pdb=" O LYS L3546 " (cutoff:3.500A) Processing helix chain 'L' and resid 3562 through 3564 No H-bonds generated for 'chain 'L' and resid 3562 through 3564' Processing helix chain 'L' and resid 3625 through 3633 Processing helix chain 'L' and resid 3634 through 3640 Processing helix chain 'L' and resid 3640 through 3654 removed outlier: 3.776A pdb=" N SER L3649 " --> pdb=" O LEU L3645 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE L3653 " --> pdb=" O SER L3649 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU L3654 " --> pdb=" O ARG L3650 " (cutoff:3.500A) Processing helix chain 'L' and resid 3658 through 3678 removed outlier: 4.081A pdb=" N LEU L3665 " --> pdb=" O THR L3661 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU L3670 " --> pdb=" O PHE L3666 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU L3678 " --> pdb=" O TRP L3674 " (cutoff:3.500A) Processing helix chain 'L' and resid 3685 through 3705 removed outlier: 3.939A pdb=" N ARG L3689 " --> pdb=" O ASN L3685 " (cutoff:3.500A) Processing helix chain 'L' and resid 3718 through 3727 Processing helix chain 'L' and resid 3729 through 3734 Processing sheet with id=AA1, first strand: chain 'H' and resid 593 through 595 removed outlier: 3.518A pdb=" N ARG H 593 " --> pdb=" O LEU E 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 280 through 282 Processing sheet with id=AA3, first strand: chain 'E' and resid 546 through 548 removed outlier: 4.783A pdb=" N LYS H 648 " --> pdb=" O ILE K 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 742 through 743 removed outlier: 6.329A pdb=" N GLY E 742 " --> pdb=" O VAL H 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 38 through 41 Processing sheet with id=AA6, first strand: chain 'F' and resid 55 through 56 Processing sheet with id=AA7, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AA8, first strand: chain 'F' and resid 174 through 175 Processing sheet with id=AA9, first strand: chain 'F' and resid 174 through 175 Processing sheet with id=AB1, first strand: chain 'F' and resid 209 through 211 Processing sheet with id=AB2, first strand: chain 'F' and resid 277 through 280 removed outlier: 4.079A pdb=" N ARG F 268 " --> pdb=" O PHE F 280 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.331A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 35 through 36 Processing sheet with id=AB5, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AB6, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AB7, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.226A pdb=" N ILE G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'K' and resid 78 through 84 Processing sheet with id=AC1, first strand: chain 'H' and resid 546 through 549 removed outlier: 5.975A pdb=" N VAL H 546 " --> pdb=" O SER H 575 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER H 575 " --> pdb=" O VAL H 546 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASP H 548 " --> pdb=" O ASP H 573 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 977 through 980 Processing sheet with id=AC3, first strand: chain 'L' and resid 3331 through 3332 Processing sheet with id=AC4, first strand: chain 'L' and resid 3331 through 3332 removed outlier: 4.285A pdb=" N ARG L3389 " --> pdb=" O VAL L3405 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 3464 through 3466 2161 hydrogen bonds defined for protein. 6237 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: 13.32 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 7037 1.31 - 1.43: 11471 1.43 - 1.56: 24669 1.56 - 1.69: 12 1.69 - 1.82: 295 Bond restraints: 43484 Sorted by residual: bond pdb=" CB GLN L3629 " pdb=" CG GLN L3629 " ideal model delta sigma weight residual 1.520 1.400 0.120 3.00e-02 1.11e+03 1.61e+01 bond pdb=" CB PHE L2755 " pdb=" CG PHE L2755 " ideal model delta sigma weight residual 1.502 1.412 0.090 2.30e-02 1.89e+03 1.52e+01 bond pdb=" CB GLU L3512 " pdb=" CG GLU L3512 " ideal model delta sigma weight residual 1.520 1.419 0.101 3.00e-02 1.11e+03 1.12e+01 bond pdb=" CB VAL L3728 " pdb=" CG2 VAL L3728 " ideal model delta sigma weight residual 1.521 1.413 0.108 3.30e-02 9.18e+02 1.07e+01 bond pdb=" CB ASN L2658 " pdb=" CG ASN L2658 " ideal model delta sigma weight residual 1.516 1.438 0.078 2.50e-02 1.60e+03 9.81e+00 ... (remaining 43479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 57175 2.54 - 5.08: 1558 5.08 - 7.62: 130 7.62 - 10.17: 21 10.17 - 12.71: 5 Bond angle restraints: 58889 Sorted by residual: angle pdb=" PB ATP G 502 " pdb=" O3B ATP G 502 " pdb=" PG ATP G 502 " ideal model delta sigma weight residual 139.87 130.72 9.15 1.00e+00 1.00e+00 8.37e+01 angle pdb=" PB ATP F1002 " pdb=" O3B ATP F1002 " pdb=" PG ATP F1002 " ideal model delta sigma weight residual 139.87 132.12 7.75 1.00e+00 1.00e+00 6.01e+01 angle pdb=" PA ATP G 502 " pdb=" O3A ATP G 502 " pdb=" PB ATP G 502 " ideal model delta sigma weight residual 136.83 130.96 5.87 1.00e+00 1.00e+00 3.45e+01 angle pdb=" N PRO L 852 " pdb=" CA PRO L 852 " pdb=" C PRO L 852 " ideal model delta sigma weight residual 112.47 100.72 11.75 2.06e+00 2.36e-01 3.25e+01 angle pdb=" N LEU E 310 " pdb=" CA LEU E 310 " pdb=" C LEU E 310 " ideal model delta sigma weight residual 112.45 119.74 -7.29 1.39e+00 5.18e-01 2.75e+01 ... (remaining 58884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 23793 17.89 - 35.78: 2162 35.78 - 53.66: 366 53.66 - 71.55: 112 71.55 - 89.44: 42 Dihedral angle restraints: 26475 sinusoidal: 10999 harmonic: 15476 Sorted by residual: dihedral pdb=" CA HIS L2621 " pdb=" C HIS L2621 " pdb=" N LEU L2622 " pdb=" CA LEU L2622 " ideal model delta harmonic sigma weight residual 180.00 149.53 30.47 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" CA THR L2756 " pdb=" C THR L2756 " pdb=" N ASP L2757 " pdb=" CA ASP L2757 " ideal model delta harmonic sigma weight residual 180.00 152.47 27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ARG L2425 " pdb=" C ARG L2425 " pdb=" N VAL L2426 " pdb=" CA VAL L2426 " ideal model delta harmonic sigma weight residual -180.00 -153.53 -26.47 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 26472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 6377 0.127 - 0.254: 245 0.254 - 0.381: 5 0.381 - 0.508: 0 0.508 - 0.635: 1 Chirality restraints: 6628 Sorted by residual: chirality pdb=" CB VAL L3728 " pdb=" CA VAL L3728 " pdb=" CG1 VAL L3728 " pdb=" CG2 VAL L3728 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CB VAL L2414 " pdb=" CA VAL L2414 " pdb=" CG1 VAL L2414 " pdb=" CG2 VAL L2414 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA ASN H 544 " pdb=" N ASN H 544 " pdb=" C ASN H 544 " pdb=" CB ASN H 544 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 6625 not shown) Planarity restraints: 7476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN L2418 " 0.091 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO L2419 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO L2419 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO L2419 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE L2755 " 0.048 2.00e-02 2.50e+03 3.26e-02 1.86e+01 pdb=" CG PHE L2755 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE L2755 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE L2755 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE L2755 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE L2755 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE L2755 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L2492 " -0.042 2.00e-02 2.50e+03 2.91e-02 1.69e+01 pdb=" CG TYR L2492 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR L2492 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR L2492 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR L2492 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR L2492 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR L2492 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR L2492 " -0.007 2.00e-02 2.50e+03 ... (remaining 7473 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 275 2.49 - 3.09: 32235 3.09 - 3.69: 65540 3.69 - 4.30: 94301 4.30 - 4.90: 156855 Nonbonded interactions: 349206 Sorted by model distance: nonbonded pdb=" OG1 THR E 312 " pdb=" O VAL L3728 " model vdw 1.885 3.040 nonbonded pdb=" NH2 ARG E 640 " pdb=" OE1 GLU E 726 " model vdw 1.981 3.120 nonbonded pdb=" OD1 ASN L 944 " pdb=" NH2 ARG L 947 " model vdw 2.010 3.120 nonbonded pdb=" OD2 ASP E 350 " pdb=" OH TYR K 206 " model vdw 2.105 3.040 nonbonded pdb=" O PRO F 433 " pdb=" OG SER F 434 " model vdw 2.108 3.040 ... (remaining 349201 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 43.120 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 : 0.013 0.120 43484 Z= 0.567 Angle : 0.975 12.707 58889 Z= 0.549 Chirality : 0.059 0.635 6628 Planarity : 0.007 0.136 7476 Dihedral : 14.647 89.441 16379 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.90 % Favored : 92.00 % Rotamer: Outliers : 0.48 % Allowed : 7.26 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: -2.65 (0.11), residues: 5149 helix: -1.25 (0.09), residues: 2969 sheet: -0.14 (0.38), residues: 210 loop : -2.65 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG L3313 TYR 0.068 0.004 TYR L2492 PHE 0.068 0.003 PHE L2755 TRP 0.030 0.003 TRP E 340 HIS 0.012 0.002 HIS L1012 Details of bonding type rmsd covalent geometry : bond 0.01274 (43484) covalent geometry : angle 0.97538 (58889) hydrogen bonds : bond 0.14272 ( 2151) hydrogen bonds : angle 5.92589 ( 6237) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 695 time to evaluate : 1.572 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: L 472 MET cc_start: 0.9346 (tmm) cc_final: 0.9018 (tmm) REVERT: L 588 ARG cc_start: 0.8764 (ttp-170) cc_final: 0.8460 (ttp80) REVERT: L 628 TYR cc_start: 0.8515 (t80) cc_final: 0.8067 (t80) REVERT: L 688 PHE cc_start: 0.8864 (t80) cc_final: 0.8618 (t80) REVERT: L 693 MET cc_start: 0.8631 (mtp) cc_final: 0.8370 (ttm) REVERT: L 711 GLU cc_start: 0.9112 (pt0) cc_final: 0.8905 (tm-30) REVERT: L 824 PHE cc_start: 0.8219 (p90) cc_final: 0.7935 (p90) REVERT: L 832 LYS cc_start: 0.8448 (mttt) cc_final: 0.7929 (mttt) REVERT: L 922 ASP cc_start: 0.7846 (p0) cc_final: 0.7602 (p0) REVERT: L 1294 CYS cc_start: 0.8851 (t) cc_final: 0.8468 (p) REVERT: L 1295 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7561 (mm-30) REVERT: L 1302 LYS cc_start: 0.8630 (mttm) cc_final: 0.8416 (mmtt) REVERT: L 1329 SER cc_start: 0.8577 (p) cc_final: 0.8367 (t) REVERT: L 1347 PHE cc_start: 0.8269 (m-10) cc_final: 0.7772 (m-10) REVERT: L 1407 GLN cc_start: 0.8618 (mt0) cc_final: 0.8212 (pt0) REVERT: L 1410 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7911 (tm-30) REVERT: L 1501 ASP cc_start: 0.8399 (t0) cc_final: 0.8165 (t0) REVERT: L 1556 ILE cc_start: 0.8921 (mt) cc_final: 0.8702 (tt) REVERT: L 1589 ASP cc_start: 0.7582 (m-30) cc_final: 0.7068 (m-30) REVERT: L 1594 THR cc_start: 0.8882 (m) cc_final: 0.8650 (m) REVERT: L 1624 MET cc_start: 0.9289 (mmm) cc_final: 0.8946 (mmp) REVERT: L 1631 PRO cc_start: 0.8715 (Cg_exo) cc_final: 0.8243 (Cg_endo) REVERT: L 1648 TYR cc_start: 0.6176 (m-80) cc_final: 0.5883 (m-80) REVERT: L 1699 LEU cc_start: 0.9282 (tp) cc_final: 0.9001 (tp) REVERT: L 1974 MET cc_start: 0.8150 (ttt) cc_final: 0.7793 (tpp) REVERT: L 2103 TYR cc_start: 0.7677 (t80) cc_final: 0.7435 (t80) REVERT: L 2387 GLU cc_start: 0.7464 (mp0) cc_final: 0.7256 (mp0) REVERT: L 2490 ASN cc_start: 0.7028 (t0) cc_final: 0.6778 (t0) REVERT: L 2621 HIS cc_start: 0.7881 (p-80) cc_final: 0.7648 (p-80) outliers start: 23 outliers final: 9 residues processed: 714 average time/residue: 0.2813 time to fit residues: 323.7111 Evaluate side-chains 409 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 400 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain H residue 560 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 1853 VAL Chi-restraints excluded: chain L residue 2415 ARG Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3493 LEU Chi-restraints excluded: chain L residue 3498 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 394 optimal weight: 4.9990 chunk 430 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 1.9990 chunk 497 optimal weight: 0.9990 chunk 414 optimal weight: 0.7980 chunk 310 optimal weight: 1.9990 chunk 488 optimal weight: 0.8980 chunk 366 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 516 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 222 ASN F 103 ASN F 282 ASN F 303 ASN G 78 ASN H 559 ASN L 6 GLN ** L 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 843 ASN L 889 GLN L 998 GLN L1105 ASN L1379 GLN L1629 GLN L1658 ASN L1700 ASN ** L1754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1958 ASN L1981 GLN L1992 HIS L1998 ASN L2207 GLN L2354 ASN L2474 GLN L2592 HIS L2811 GLN L2907 HIS L2948 ASN L2992 HIS ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.108405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.075875 restraints weight = 150460.045| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.72 r_work: 0.3215 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 43484 Z= 0.156 Angle : 0.708 15.820 58889 Z= 0.359 Chirality : 0.044 0.285 6628 Planarity : 0.005 0.115 7476 Dihedral : 6.784 86.709 5723 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.03 % Favored : 92.89 % Rotamer: Outliers : 1.62 % Allowed : 11.75 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % 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 are not related in a simple way. whole: -1.46 (0.11), residues: 5149 helix: -0.10 (0.09), residues: 2974 sheet: 0.11 (0.40), residues: 184 loop : -2.42 (0.13), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 632 TYR 0.025 0.002 TYR L2316 PHE 0.041 0.002 PHE L1747 TRP 0.020 0.002 TRP L2179 HIS 0.010 0.001 HIS L1328 Details of bonding type rmsd covalent geometry : bond 0.00314 (43484) covalent geometry : angle 0.70830 (58889) hydrogen bonds : bond 0.04502 ( 2151) hydrogen bonds : angle 4.61526 ( 6237) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 484 time to evaluate : 1.708 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: E 248 MET cc_start: 0.7590 (mpp) cc_final: 0.7310 (mmm) REVERT: E 293 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8767 (mmm) REVERT: E 545 LEU cc_start: 0.8883 (mm) cc_final: 0.8605 (mm) REVERT: E 580 LEU cc_start: 0.8983 (pp) cc_final: 0.8636 (tp) REVERT: E 651 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8868 (tp) REVERT: E 726 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8140 (tm-30) REVERT: F 59 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7639 (tt0) REVERT: F 206 LEU cc_start: 0.8670 (tp) cc_final: 0.7944 (tt) REVERT: G 355 MET cc_start: 0.9016 (mtt) cc_final: 0.8763 (mtt) REVERT: K 289 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.6618 (mt0) REVERT: L 79 MET cc_start: 0.5450 (ptp) cc_final: 0.5135 (ptp) REVERT: L 465 MET cc_start: 0.9113 (mmt) cc_final: 0.8800 (mmm) REVERT: L 472 MET cc_start: 0.9377 (tmm) cc_final: 0.9146 (tmm) REVERT: L 588 ARG cc_start: 0.8748 (ttp-170) cc_final: 0.8513 (ttp80) REVERT: L 591 MET cc_start: 0.9308 (mtp) cc_final: 0.8827 (mmm) REVERT: L 824 PHE cc_start: 0.8405 (p90) cc_final: 0.8154 (p90) REVERT: L 845 MET cc_start: 0.8236 (mtm) cc_final: 0.7947 (mtp) REVERT: L 922 ASP cc_start: 0.8725 (p0) cc_final: 0.8390 (p0) REVERT: L 1294 CYS cc_start: 0.9140 (t) cc_final: 0.8616 (m) REVERT: L 1298 ASN cc_start: 0.8248 (t0) cc_final: 0.7873 (t0) REVERT: L 1302 LYS cc_start: 0.8815 (mttm) cc_final: 0.8423 (mmtt) REVERT: L 1329 SER cc_start: 0.8386 (p) cc_final: 0.7987 (t) REVERT: L 1407 GLN cc_start: 0.8290 (mt0) cc_final: 0.7953 (pt0) REVERT: L 1410 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7745 (tm-30) REVERT: L 1501 ASP cc_start: 0.8381 (t0) cc_final: 0.8080 (t0) REVERT: L 1589 ASP cc_start: 0.7942 (m-30) cc_final: 0.7206 (m-30) REVERT: L 1624 MET cc_start: 0.9426 (mmm) cc_final: 0.9113 (mmp) REVERT: L 1657 LYS cc_start: 0.8108 (tttt) cc_final: 0.7857 (ptmt) REVERT: L 1691 MET cc_start: 0.6467 (mtt) cc_final: 0.6149 (mtt) REVERT: L 1974 MET cc_start: 0.8520 (ttt) cc_final: 0.7980 (tpt) REVERT: L 2103 TYR cc_start: 0.7915 (t80) cc_final: 0.7565 (t80) REVERT: L 2119 ARG cc_start: 0.8686 (mtm110) cc_final: 0.8433 (mtm110) REVERT: L 2387 GLU cc_start: 0.8118 (mp0) cc_final: 0.7906 (mp0) REVERT: L 2490 ASN cc_start: 0.8514 (t0) cc_final: 0.7889 (t0) REVERT: L 2656 GLU cc_start: 0.8506 (pt0) cc_final: 0.7981 (tt0) REVERT: L 2723 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8642 (tm-30) REVERT: L 3307 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7162 (t80) REVERT: L 3416 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8583 (tt0) outliers start: 77 outliers final: 30 residues processed: 539 average time/residue: 0.2594 time to fit residues: 233.9067 Evaluate side-chains 406 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 371 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 293 MET Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 718 HIS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain K residue 289 GLN Chi-restraints excluded: chain H residue 553 LYS Chi-restraints excluded: chain H residue 560 VAL Chi-restraints excluded: chain L residue 355 LEU Chi-restraints excluded: chain L residue 731 ILE Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 998 GLN Chi-restraints excluded: chain L residue 1549 THR Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1684 TRP Chi-restraints excluded: chain L residue 1992 HIS Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 3119 ASN Chi-restraints excluded: chain L residue 3171 LEU Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3416 GLU Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3728 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 45 optimal weight: 10.0000 chunk 1 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 353 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 381 optimal weight: 0.8980 chunk 151 optimal weight: 6.9990 chunk 471 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 744 ASN ** L 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 889 GLN L1234 GLN L1740 GLN ** L1992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2188 GLN L2592 HIS L2863 HIS L3073 ASN ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3494 ASN L3657 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.107769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.075159 restraints weight = 150659.090| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.56 r_work: 0.3209 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 43484 Z= 0.142 Angle : 0.656 16.111 58889 Z= 0.330 Chirality : 0.044 0.270 6628 Planarity : 0.004 0.061 7476 Dihedral : 6.364 76.647 5715 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.64 % Rotamer: Outliers : 1.89 % Allowed : 12.99 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % 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 are not related in a simple way. whole: -0.88 (0.12), residues: 5149 helix: 0.46 (0.10), residues: 2982 sheet: 0.14 (0.40), residues: 182 loop : -2.31 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L2879 TYR 0.027 0.001 TYR L2316 PHE 0.054 0.001 PHE L1747 TRP 0.040 0.001 TRP L1842 HIS 0.009 0.001 HIS L1838 Details of bonding type rmsd covalent geometry : bond 0.00310 (43484) covalent geometry : angle 0.65622 (58889) hydrogen bonds : bond 0.04031 ( 2151) hydrogen bonds : angle 4.34125 ( 6237) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 394 time to evaluate : 1.670 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: E 293 MET cc_start: 0.9087 (tpp) cc_final: 0.8811 (mmm) REVERT: E 545 LEU cc_start: 0.8869 (mm) cc_final: 0.8656 (mm) REVERT: E 580 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8668 (tp) REVERT: E 726 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8133 (tm-30) REVERT: E 799 MET cc_start: 0.8822 (mmt) cc_final: 0.8431 (mmm) REVERT: F 59 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7490 (tt0) REVERT: F 206 LEU cc_start: 0.8676 (tp) cc_final: 0.7956 (tt) REVERT: F 241 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8507 (mp0) REVERT: F 444 HIS cc_start: 0.8456 (t-170) cc_final: 0.8240 (t-170) REVERT: G 119 MET cc_start: 0.8440 (ttp) cc_final: 0.8213 (tmm) REVERT: G 355 MET cc_start: 0.9236 (mtt) cc_final: 0.8737 (mtm) REVERT: K 289 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.6704 (mt0) REVERT: L 304 PHE cc_start: 0.8691 (m-10) cc_final: 0.8217 (m-80) REVERT: L 472 MET cc_start: 0.9352 (tmm) cc_final: 0.9119 (tmm) REVERT: L 560 MET cc_start: 0.6914 (tpt) cc_final: 0.6685 (tpt) REVERT: L 588 ARG cc_start: 0.8763 (ttp-170) cc_final: 0.8545 (ttp80) REVERT: L 591 MET cc_start: 0.9314 (mtp) cc_final: 0.9036 (mmm) REVERT: L 700 GLU cc_start: 0.8814 (pt0) cc_final: 0.8437 (pt0) REVERT: L 844 GLN cc_start: 0.8887 (pp30) cc_final: 0.8572 (pp30) REVERT: L 845 MET cc_start: 0.8117 (mtm) cc_final: 0.7716 (mtp) REVERT: L 922 ASP cc_start: 0.8670 (p0) cc_final: 0.8291 (p0) REVERT: L 1294 CYS cc_start: 0.9150 (t) cc_final: 0.8598 (m) REVERT: L 1295 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7969 (mm-30) REVERT: L 1298 ASN cc_start: 0.8388 (t0) cc_final: 0.7932 (t0) REVERT: L 1302 LYS cc_start: 0.8825 (mttm) cc_final: 0.8421 (mmtt) REVERT: L 1329 SER cc_start: 0.8442 (p) cc_final: 0.8155 (t) REVERT: L 1410 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7780 (tm-30) REVERT: L 1501 ASP cc_start: 0.8411 (t0) cc_final: 0.8103 (t0) REVERT: L 1588 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7741 (mm) REVERT: L 1589 ASP cc_start: 0.7967 (m-30) cc_final: 0.7155 (m-30) REVERT: L 1624 MET cc_start: 0.9459 (mmm) cc_final: 0.9146 (mmp) REVERT: L 1657 LYS cc_start: 0.8082 (tttt) cc_final: 0.7834 (ptmt) REVERT: L 1691 MET cc_start: 0.6350 (mtt) cc_final: 0.6122 (mtt) REVERT: L 1695 LEU cc_start: 0.9228 (mt) cc_final: 0.8986 (mp) REVERT: L 1954 HIS cc_start: 0.7595 (t70) cc_final: 0.6618 (t70) REVERT: L 1974 MET cc_start: 0.8568 (ttt) cc_final: 0.8174 (tpt) REVERT: L 1996 PHE cc_start: 0.7654 (m-10) cc_final: 0.7325 (m-10) REVERT: L 2103 TYR cc_start: 0.7945 (t80) cc_final: 0.7656 (t80) REVERT: L 2214 MET cc_start: 0.8713 (ppp) cc_final: 0.8228 (ppp) REVERT: L 2387 GLU cc_start: 0.8115 (mp0) cc_final: 0.7896 (mp0) REVERT: L 2490 ASN cc_start: 0.8558 (t0) cc_final: 0.7803 (t0) REVERT: L 2621 HIS cc_start: 0.8488 (p-80) cc_final: 0.8285 (p-80) REVERT: L 2656 GLU cc_start: 0.8434 (pt0) cc_final: 0.7995 (tt0) REVERT: L 2723 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8616 (tm-30) REVERT: L 3092 TYR cc_start: 0.7589 (t80) cc_final: 0.6446 (t80) REVERT: L 3307 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7346 (t80) REVERT: L 3416 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8499 (tt0) outliers start: 90 outliers final: 41 residues processed: 460 average time/residue: 0.2351 time to fit residues: 182.4968 Evaluate side-chains 403 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 356 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 681 THR Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain K residue 289 GLN Chi-restraints excluded: chain H residue 539 THR Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain L residue 612 THR Chi-restraints excluded: chain L residue 702 ILE Chi-restraints excluded: chain L residue 731 ILE Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 851 LEU Chi-restraints excluded: chain L residue 1549 THR Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1684 TRP Chi-restraints excluded: chain L residue 1824 TYR Chi-restraints excluded: chain L residue 1992 HIS Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2033 SER Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2356 SER Chi-restraints excluded: chain L residue 2491 ILE Chi-restraints excluded: chain L residue 2537 ILE Chi-restraints excluded: chain L residue 2574 ASN Chi-restraints excluded: chain L residue 2679 TRP Chi-restraints excluded: chain L residue 2758 LEU Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 2888 LEU Chi-restraints excluded: chain L residue 3049 ILE Chi-restraints excluded: chain L residue 3119 ASN Chi-restraints excluded: chain L residue 3152 VAL Chi-restraints excluded: chain L residue 3211 LEU Chi-restraints excluded: chain L residue 3286 THR Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3416 GLU Chi-restraints excluded: chain L residue 3449 ILE Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3657 ASN Chi-restraints excluded: chain L residue 3709 LEU Chi-restraints excluded: chain L residue 3728 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 285 optimal weight: 0.1980 chunk 212 optimal weight: 6.9990 chunk 423 optimal weight: 0.9990 chunk 512 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 367 optimal weight: 6.9990 chunk 277 optimal weight: 3.9990 chunk 388 optimal weight: 4.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 96 ASN K 302 GLN H 559 ASN H 630 HIS L 889 GLN L 896 GLN L 998 GLN L1234 GLN L1305 ASN L1629 GLN ** L1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2592 HIS ** L3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L3234 ASN ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.105731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.072763 restraints weight = 150144.090| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.67 r_work: 0.3145 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 43484 Z= 0.222 Angle : 0.693 16.571 58889 Z= 0.351 Chirality : 0.046 0.409 6628 Planarity : 0.005 0.072 7476 Dihedral : 6.213 75.852 5713 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.55 % Favored : 92.39 % Rotamer: Outliers : 2.16 % Allowed : 14.33 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % 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 are not related in a simple way. whole: -0.60 (0.12), residues: 5149 helix: 0.72 (0.10), residues: 2970 sheet: -0.08 (0.38), residues: 195 loop : -2.22 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 76 TYR 0.030 0.002 TYR L2316 PHE 0.045 0.002 PHE L1747 TRP 0.048 0.002 TRP L1842 HIS 0.007 0.001 HIS L1604 Details of bonding type rmsd covalent geometry : bond 0.00498 (43484) covalent geometry : angle 0.69314 (58889) hydrogen bonds : bond 0.04221 ( 2151) hydrogen bonds : angle 4.33638 ( 6237) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 368 time to evaluate : 1.596 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: E 248 MET cc_start: 0.7572 (mpp) cc_final: 0.7144 (mmm) REVERT: E 293 MET cc_start: 0.9184 (tpp) cc_final: 0.8913 (mmm) REVERT: E 580 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8567 (tp) REVERT: E 651 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.8878 (tp) REVERT: E 726 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8341 (tm-30) REVERT: F 59 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7523 (tt0) REVERT: F 241 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: F 444 HIS cc_start: 0.8566 (t-170) cc_final: 0.8125 (t-170) REVERT: K 289 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7543 (mp10) REVERT: L 359 TYR cc_start: 0.8101 (p90) cc_final: 0.7663 (p90) REVERT: L 472 MET cc_start: 0.9373 (tmm) cc_final: 0.9096 (tmm) REVERT: L 588 ARG cc_start: 0.8819 (ttp-170) cc_final: 0.8597 (ttp80) REVERT: L 591 MET cc_start: 0.9316 (mtp) cc_final: 0.9050 (mmm) REVERT: L 700 GLU cc_start: 0.8942 (pt0) cc_final: 0.8637 (pt0) REVERT: L 845 MET cc_start: 0.8177 (mtm) cc_final: 0.7845 (mtp) REVERT: L 922 ASP cc_start: 0.8713 (p0) cc_final: 0.8326 (p0) REVERT: L 1295 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8230 (mm-30) REVERT: L 1298 ASN cc_start: 0.8420 (t0) cc_final: 0.7919 (t0) REVERT: L 1302 LYS cc_start: 0.8871 (mttm) cc_final: 0.8464 (mmtt) REVERT: L 1362 SER cc_start: 0.8318 (t) cc_final: 0.7965 (p) REVERT: L 1410 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7738 (tm-30) REVERT: L 1588 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8149 (mm) REVERT: L 1624 MET cc_start: 0.9451 (mmm) cc_final: 0.9215 (mmp) REVERT: L 1648 TYR cc_start: 0.6706 (m-80) cc_final: 0.5751 (m-80) REVERT: L 1657 LYS cc_start: 0.8114 (tttt) cc_final: 0.7776 (ptmt) REVERT: L 1691 MET cc_start: 0.6492 (mtt) cc_final: 0.6103 (tpp) REVERT: L 1974 MET cc_start: 0.8586 (ttt) cc_final: 0.8148 (tpp) REVERT: L 2103 TYR cc_start: 0.7938 (t80) cc_final: 0.7722 (t80) REVERT: L 2119 ARG cc_start: 0.9099 (mtp-110) cc_final: 0.8779 (mtm110) REVERT: L 2214 MET cc_start: 0.8504 (ppp) cc_final: 0.8065 (ppp) REVERT: L 2387 GLU cc_start: 0.8121 (mp0) cc_final: 0.7897 (mp0) REVERT: L 2490 ASN cc_start: 0.8665 (t0) cc_final: 0.7840 (t0) REVERT: L 2574 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.7114 (m-40) REVERT: L 2621 HIS cc_start: 0.8636 (p-80) cc_final: 0.8399 (p-80) REVERT: L 2656 GLU cc_start: 0.8600 (pt0) cc_final: 0.8267 (tt0) REVERT: L 2723 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8665 (tm-30) REVERT: L 2791 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.7995 (mtm180) REVERT: L 3075 ILE cc_start: 0.4417 (OUTLIER) cc_final: 0.4175 (mp) REVERT: L 3307 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7270 (t80) REVERT: L 3486 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.8755 (tm-30) outliers start: 103 outliers final: 60 residues processed: 444 average time/residue: 0.2316 time to fit residues: 175.6511 Evaluate side-chains 406 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 336 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 589 VAL Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 662 ILE Chi-restraints excluded: chain E residue 681 THR Chi-restraints excluded: chain E residue 708 ASN Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 718 HIS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain K residue 217 ASP Chi-restraints excluded: chain K residue 289 GLN Chi-restraints excluded: chain H residue 539 THR Chi-restraints excluded: chain H residue 553 LYS Chi-restraints excluded: chain H residue 559 ASN Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain L residue 354 ILE Chi-restraints excluded: chain L residue 612 THR Chi-restraints excluded: chain L residue 731 ILE Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 851 LEU Chi-restraints excluded: chain L residue 1251 GLU Chi-restraints excluded: chain L residue 1534 VAL Chi-restraints excluded: chain L residue 1549 THR Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1824 TYR Chi-restraints excluded: chain L residue 1899 THR Chi-restraints excluded: chain L residue 1950 THR Chi-restraints excluded: chain L residue 1992 HIS Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2027 LEU Chi-restraints excluded: chain L residue 2033 SER Chi-restraints excluded: chain L residue 2127 LEU Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2320 LEU Chi-restraints excluded: chain L residue 2356 SER Chi-restraints excluded: chain L residue 2465 ASP Chi-restraints excluded: chain L residue 2491 ILE Chi-restraints excluded: chain L residue 2537 ILE Chi-restraints excluded: chain L residue 2574 ASN Chi-restraints excluded: chain L residue 2601 ASN Chi-restraints excluded: chain L residue 2618 LEU Chi-restraints excluded: chain L residue 2679 TRP Chi-restraints excluded: chain L residue 2791 ARG Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 2888 LEU Chi-restraints excluded: chain L residue 3029 PHE Chi-restraints excluded: chain L residue 3049 ILE Chi-restraints excluded: chain L residue 3075 ILE Chi-restraints excluded: chain L residue 3119 ASN Chi-restraints excluded: chain L residue 3152 VAL Chi-restraints excluded: chain L residue 3171 LEU Chi-restraints excluded: chain L residue 3211 LEU Chi-restraints excluded: chain L residue 3286 THR Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3449 ILE Chi-restraints excluded: chain L residue 3486 GLN Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3657 ASN Chi-restraints excluded: chain L residue 3709 LEU Chi-restraints excluded: chain L residue 3728 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 468 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 147 optimal weight: 0.0010 chunk 60 optimal weight: 0.0970 chunk 107 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 399 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 559 ASN L 889 GLN L 998 GLN L2592 HIS ** L3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L3657 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.106681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.073561 restraints weight = 149842.811| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.34 r_work: 0.3198 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 43484 Z= 0.139 Angle : 0.639 17.072 58889 Z= 0.319 Chirality : 0.043 0.273 6628 Planarity : 0.004 0.049 7476 Dihedral : 6.018 71.796 5713 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.38 % Favored : 92.58 % Rotamer: Outliers : 1.97 % Allowed : 15.15 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % 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 are not related in a simple way. whole: -0.37 (0.12), residues: 5149 helix: 0.93 (0.10), residues: 2964 sheet: 0.06 (0.39), residues: 185 loop : -2.14 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 517 TYR 0.034 0.001 TYR L2316 PHE 0.039 0.001 PHE L1747 TRP 0.066 0.002 TRP L1842 HIS 0.007 0.001 HIS L1954 Details of bonding type rmsd covalent geometry : bond 0.00311 (43484) covalent geometry : angle 0.63932 (58889) hydrogen bonds : bond 0.03733 ( 2151) hydrogen bonds : angle 4.19249 ( 6237) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 373 time to evaluate : 1.681 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: E 248 MET cc_start: 0.7378 (mpp) cc_final: 0.7087 (mmm) REVERT: E 293 MET cc_start: 0.9105 (tpp) cc_final: 0.8791 (mmm) REVERT: E 580 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8660 (tp) REVERT: E 651 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8818 (tp) REVERT: E 726 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8275 (tm-30) REVERT: F 59 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7557 (tt0) REVERT: F 241 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8398 (mp0) REVERT: F 444 HIS cc_start: 0.8502 (t-170) cc_final: 0.8257 (t-170) REVERT: G 119 MET cc_start: 0.8402 (tmm) cc_final: 0.8011 (tmm) REVERT: K 274 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8080 (mt-10) REVERT: K 289 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7499 (mp10) REVERT: L 359 TYR cc_start: 0.8007 (p90) cc_final: 0.7602 (p90) REVERT: L 472 MET cc_start: 0.9371 (tmm) cc_final: 0.9112 (tmm) REVERT: L 560 MET cc_start: 0.6870 (tpt) cc_final: 0.6585 (tpt) REVERT: L 588 ARG cc_start: 0.8791 (ttp-170) cc_final: 0.8583 (ttp80) REVERT: L 591 MET cc_start: 0.9268 (mtp) cc_final: 0.9022 (mmm) REVERT: L 700 GLU cc_start: 0.8835 (pt0) cc_final: 0.8579 (pt0) REVERT: L 845 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7712 (mtp) REVERT: L 922 ASP cc_start: 0.8626 (p0) cc_final: 0.8257 (p0) REVERT: L 1295 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8157 (mm-30) REVERT: L 1298 ASN cc_start: 0.8489 (t0) cc_final: 0.7993 (t0) REVERT: L 1302 LYS cc_start: 0.8852 (mttm) cc_final: 0.8438 (mmtt) REVERT: L 1362 SER cc_start: 0.8286 (t) cc_final: 0.7962 (p) REVERT: L 1410 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7702 (tm-30) REVERT: L 1588 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7887 (mm) REVERT: L 1624 MET cc_start: 0.9433 (mmm) cc_final: 0.9176 (mmp) REVERT: L 1657 LYS cc_start: 0.8091 (tttt) cc_final: 0.7747 (ptmt) REVERT: L 1846 ASN cc_start: 0.8221 (m-40) cc_final: 0.8020 (t0) REVERT: L 1974 MET cc_start: 0.8659 (ttt) cc_final: 0.8299 (tpt) REVERT: L 1986 TYR cc_start: 0.8169 (m-80) cc_final: 0.7945 (m-80) REVERT: L 2103 TYR cc_start: 0.7919 (t80) cc_final: 0.7718 (t80) REVERT: L 2119 ARG cc_start: 0.9109 (mtp-110) cc_final: 0.8752 (mtm110) REVERT: L 2214 MET cc_start: 0.8517 (ppp) cc_final: 0.8149 (ppp) REVERT: L 2574 ASN cc_start: 0.7316 (m-40) cc_final: 0.7043 (m-40) REVERT: L 2621 HIS cc_start: 0.8521 (p-80) cc_final: 0.8305 (p-80) REVERT: L 2656 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: L 2723 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8698 (tm-30) REVERT: L 2735 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8311 (mp10) REVERT: L 2791 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.7884 (mtm180) REVERT: L 3075 ILE cc_start: 0.4337 (OUTLIER) cc_final: 0.4068 (mp) REVERT: L 3307 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7282 (t80) REVERT: L 3486 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.9089 (tm-30) outliers start: 94 outliers final: 57 residues processed: 441 average time/residue: 0.2415 time to fit residues: 180.2985 Evaluate side-chains 409 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 340 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 662 ILE Chi-restraints excluded: chain E residue 681 THR Chi-restraints excluded: chain E residue 708 ASN Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 718 HIS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 217 CYS Chi-restraints excluded: chain K residue 217 ASP Chi-restraints excluded: chain K residue 289 GLN Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain H residue 539 THR Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 612 THR Chi-restraints excluded: chain L residue 731 ILE Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 845 MET Chi-restraints excluded: chain L residue 1251 GLU Chi-restraints excluded: chain L residue 1534 VAL Chi-restraints excluded: chain L residue 1549 THR Chi-restraints excluded: chain L residue 1558 ILE Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1824 TYR Chi-restraints excluded: chain L residue 1936 VAL Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2027 LEU Chi-restraints excluded: chain L residue 2033 SER Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2272 VAL Chi-restraints excluded: chain L residue 2410 THR Chi-restraints excluded: chain L residue 2465 ASP Chi-restraints excluded: chain L residue 2491 ILE Chi-restraints excluded: chain L residue 2537 ILE Chi-restraints excluded: chain L residue 2616 LEU Chi-restraints excluded: chain L residue 2618 LEU Chi-restraints excluded: chain L residue 2656 GLU Chi-restraints excluded: chain L residue 2679 TRP Chi-restraints excluded: chain L residue 2735 GLN Chi-restraints excluded: chain L residue 2752 HIS Chi-restraints excluded: chain L residue 2758 LEU Chi-restraints excluded: chain L residue 2791 ARG Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 2888 LEU Chi-restraints excluded: chain L residue 3049 ILE Chi-restraints excluded: chain L residue 3075 ILE Chi-restraints excluded: chain L residue 3119 ASN Chi-restraints excluded: chain L residue 3152 VAL Chi-restraints excluded: chain L residue 3171 LEU Chi-restraints excluded: chain L residue 3211 LEU Chi-restraints excluded: chain L residue 3286 THR Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3360 LEU Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3449 ILE Chi-restraints excluded: chain L residue 3486 GLN Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3657 ASN Chi-restraints excluded: chain L residue 3709 LEU Chi-restraints excluded: chain L residue 3728 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 210 optimal weight: 7.9990 chunk 189 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 322 optimal weight: 7.9990 chunk 441 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 chunk 297 optimal weight: 8.9990 chunk 176 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 257 HIS ** E 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 HIS K 302 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 753 ASN L1012 HIS ** L1954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2354 ASN L2601 ASN L2670 GLN L2861 ASN L2906 GLN ** L3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.102976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.070272 restraints weight = 151270.277| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.53 r_work: 0.3079 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.099 43484 Z= 0.383 Angle : 0.827 17.077 58889 Z= 0.421 Chirality : 0.051 0.382 6628 Planarity : 0.005 0.081 7476 Dihedral : 6.456 72.176 5713 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.80 % Favored : 91.16 % Rotamer: Outliers : 2.62 % Allowed : 15.99 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % 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 are not related in a simple way. whole: -0.72 (0.12), residues: 5149 helix: 0.63 (0.10), residues: 2962 sheet: -0.33 (0.36), residues: 209 loop : -2.26 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 517 TYR 0.046 0.002 TYR L2625 PHE 0.058 0.002 PHE L1747 TRP 0.082 0.003 TRP L1842 HIS 0.016 0.002 HIS L1838 Details of bonding type rmsd covalent geometry : bond 0.00868 (43484) covalent geometry : angle 0.82716 (58889) hydrogen bonds : bond 0.05002 ( 2151) hydrogen bonds : angle 4.63636 ( 6237) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 343 time to evaluate : 1.715 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: E 248 MET cc_start: 0.7545 (mpp) cc_final: 0.7269 (mmm) REVERT: E 580 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8711 (tp) REVERT: E 651 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.8774 (tp) REVERT: E 726 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8329 (tm-30) REVERT: F 241 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8535 (mp0) REVERT: F 444 HIS cc_start: 0.8655 (t-170) cc_final: 0.8308 (t-170) REVERT: G 299 MET cc_start: 0.7556 (mtt) cc_final: 0.6973 (mpp) REVERT: G 313 MET cc_start: 0.7933 (tpp) cc_final: 0.7326 (ptp) REVERT: K 274 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8269 (mt-10) REVERT: K 289 GLN cc_start: 0.8151 (mp10) cc_final: 0.7772 (mp10) REVERT: L 359 TYR cc_start: 0.8247 (p90) cc_final: 0.7925 (p90) REVERT: L 472 MET cc_start: 0.9394 (tmm) cc_final: 0.9085 (tmm) REVERT: L 588 ARG cc_start: 0.8859 (ttp-170) cc_final: 0.8594 (ttp80) REVERT: L 591 MET cc_start: 0.9356 (mtp) cc_final: 0.9092 (mmm) REVERT: L 700 GLU cc_start: 0.8926 (pt0) cc_final: 0.8696 (pt0) REVERT: L 844 GLN cc_start: 0.9134 (pp30) cc_final: 0.8911 (pp30) REVERT: L 845 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7857 (mtp) REVERT: L 856 GLU cc_start: 0.8708 (mp0) cc_final: 0.8480 (mp0) REVERT: L 922 ASP cc_start: 0.8811 (p0) cc_final: 0.8508 (p0) REVERT: L 1295 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8282 (mm-30) REVERT: L 1298 ASN cc_start: 0.8493 (t0) cc_final: 0.7955 (t0) REVERT: L 1302 LYS cc_start: 0.8893 (mttm) cc_final: 0.8526 (mmtt) REVERT: L 1362 SER cc_start: 0.8307 (t) cc_final: 0.7945 (p) REVERT: L 1410 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7580 (tm-30) REVERT: L 1551 ILE cc_start: 0.8744 (tt) cc_final: 0.8529 (pt) REVERT: L 1588 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8246 (mm) REVERT: L 1624 MET cc_start: 0.9478 (mmm) cc_final: 0.9204 (mmp) REVERT: L 1974 MET cc_start: 0.8727 (ttt) cc_final: 0.8225 (tpp) REVERT: L 2103 TYR cc_start: 0.8046 (t80) cc_final: 0.7804 (t80) REVERT: L 2127 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7956 (mt) REVERT: L 2214 MET cc_start: 0.8600 (ppp) cc_final: 0.8194 (ppp) REVERT: L 2614 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8489 (tm-30) REVERT: L 2656 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: L 2723 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8635 (tm-30) REVERT: L 2735 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8429 (mp10) REVERT: L 3092 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7412 (t80) REVERT: L 3307 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.7168 (t80) REVERT: L 3486 GLN cc_start: 0.9402 (OUTLIER) cc_final: 0.8914 (tm-30) outliers start: 125 outliers final: 77 residues processed: 438 average time/residue: 0.2496 time to fit residues: 184.8611 Evaluate side-chains 405 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 317 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 589 VAL Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 681 THR Chi-restraints excluded: chain E residue 708 ASN Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 753 ARG Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 217 CYS Chi-restraints excluded: chain G residue 255 PHE Chi-restraints excluded: chain K residue 217 ASP Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain H residue 490 VAL Chi-restraints excluded: chain H residue 539 THR Chi-restraints excluded: chain H residue 553 LYS Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 354 ILE Chi-restraints excluded: chain L residue 612 THR Chi-restraints excluded: chain L residue 633 VAL Chi-restraints excluded: chain L residue 689 MET Chi-restraints excluded: chain L residue 731 ILE Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 845 MET Chi-restraints excluded: chain L residue 1098 ASP Chi-restraints excluded: chain L residue 1225 SER Chi-restraints excluded: chain L residue 1251 GLU Chi-restraints excluded: chain L residue 1337 ILE Chi-restraints excluded: chain L residue 1357 ILE Chi-restraints excluded: chain L residue 1463 LEU Chi-restraints excluded: chain L residue 1534 VAL Chi-restraints excluded: chain L residue 1549 THR Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1824 TYR Chi-restraints excluded: chain L residue 1899 THR Chi-restraints excluded: chain L residue 1936 VAL Chi-restraints excluded: chain L residue 1950 THR Chi-restraints excluded: chain L residue 1954 HIS Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2027 LEU Chi-restraints excluded: chain L residue 2033 SER Chi-restraints excluded: chain L residue 2127 LEU Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2272 VAL Chi-restraints excluded: chain L residue 2320 LEU Chi-restraints excluded: chain L residue 2356 SER Chi-restraints excluded: chain L residue 2410 THR Chi-restraints excluded: chain L residue 2465 ASP Chi-restraints excluded: chain L residue 2491 ILE Chi-restraints excluded: chain L residue 2574 ASN Chi-restraints excluded: chain L residue 2601 ASN Chi-restraints excluded: chain L residue 2616 LEU Chi-restraints excluded: chain L residue 2618 LEU Chi-restraints excluded: chain L residue 2656 GLU Chi-restraints excluded: chain L residue 2679 TRP Chi-restraints excluded: chain L residue 2735 GLN Chi-restraints excluded: chain L residue 2758 LEU Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 2888 LEU Chi-restraints excluded: chain L residue 3029 PHE Chi-restraints excluded: chain L residue 3049 ILE Chi-restraints excluded: chain L residue 3092 TYR Chi-restraints excluded: chain L residue 3119 ASN Chi-restraints excluded: chain L residue 3152 VAL Chi-restraints excluded: chain L residue 3167 LEU Chi-restraints excluded: chain L residue 3171 LEU Chi-restraints excluded: chain L residue 3211 LEU Chi-restraints excluded: chain L residue 3286 THR Chi-restraints excluded: chain L residue 3288 LEU Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3449 ILE Chi-restraints excluded: chain L residue 3486 GLN Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3657 ASN Chi-restraints excluded: chain L residue 3709 LEU Chi-restraints excluded: chain L residue 3728 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 426 optimal weight: 1.9990 chunk 320 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 396 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 chunk 464 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 380 optimal weight: 0.2980 chunk 123 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 317 ASN K 302 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1012 HIS L2592 HIS ** L2601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3657 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.105633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.072999 restraints weight = 149312.751| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.75 r_work: 0.3150 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 43484 Z= 0.138 Angle : 0.676 19.980 58889 Z= 0.336 Chirality : 0.044 0.288 6628 Planarity : 0.004 0.061 7476 Dihedral : 6.105 68.127 5713 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.42 % Favored : 92.54 % Rotamer: Outliers : 2.12 % Allowed : 16.83 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: -0.35 (0.12), residues: 5149 helix: 0.95 (0.10), residues: 2966 sheet: -0.14 (0.37), residues: 195 loop : -2.13 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG L2415 TYR 0.036 0.001 TYR L2316 PHE 0.049 0.001 PHE L3029 TRP 0.069 0.002 TRP L1842 HIS 0.008 0.001 HIS L1954 Details of bonding type rmsd covalent geometry : bond 0.00303 (43484) covalent geometry : angle 0.67584 (58889) hydrogen bonds : bond 0.03849 ( 2151) hydrogen bonds : angle 4.24437 ( 6237) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 350 time to evaluate : 1.624 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: E 295 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8733 (pp30) REVERT: E 580 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8674 (tp) REVERT: E 651 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8788 (tp) REVERT: E 726 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8314 (tm-30) REVERT: F 170 ILE cc_start: 0.9383 (mm) cc_final: 0.9113 (mm) REVERT: F 241 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: F 444 HIS cc_start: 0.8558 (t-170) cc_final: 0.8260 (t-170) REVERT: G 119 MET cc_start: 0.8425 (tmm) cc_final: 0.8061 (tmm) REVERT: G 299 MET cc_start: 0.7562 (mtt) cc_final: 0.6919 (mpp) REVERT: G 313 MET cc_start: 0.7901 (tpp) cc_final: 0.7296 (ptp) REVERT: K 274 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8145 (mt-10) REVERT: L 359 TYR cc_start: 0.7996 (p90) cc_final: 0.7657 (p90) REVERT: L 363 PHE cc_start: 0.7866 (p90) cc_final: 0.7595 (p90) REVERT: L 472 MET cc_start: 0.9398 (tmm) cc_final: 0.9147 (tmm) REVERT: L 588 ARG cc_start: 0.8839 (ttp-170) cc_final: 0.8540 (ttp80) REVERT: L 591 MET cc_start: 0.9305 (mtp) cc_final: 0.9103 (mmm) REVERT: L 691 MET cc_start: 0.8820 (mtp) cc_final: 0.8371 (mpp) REVERT: L 700 GLU cc_start: 0.8926 (pt0) cc_final: 0.8675 (pt0) REVERT: L 789 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8307 (m-40) REVERT: L 845 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7935 (mtp) REVERT: L 856 GLU cc_start: 0.8752 (mp0) cc_final: 0.8520 (mp0) REVERT: L 922 ASP cc_start: 0.8687 (p0) cc_final: 0.8313 (p0) REVERT: L 1295 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8183 (mm-30) REVERT: L 1298 ASN cc_start: 0.8350 (t0) cc_final: 0.7932 (t0) REVERT: L 1302 LYS cc_start: 0.8858 (mttm) cc_final: 0.8488 (mmtt) REVERT: L 1362 SER cc_start: 0.8325 (t) cc_final: 0.7989 (p) REVERT: L 1410 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7592 (tm-30) REVERT: L 1588 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8069 (mm) REVERT: L 1624 MET cc_start: 0.9493 (mmm) cc_final: 0.9208 (mmm) REVERT: L 1974 MET cc_start: 0.8788 (ttt) cc_final: 0.8377 (tpt) REVERT: L 2103 TYR cc_start: 0.8042 (t80) cc_final: 0.7820 (t80) REVERT: L 2119 ARG cc_start: 0.9102 (mtp-110) cc_final: 0.8571 (ptm-80) REVERT: L 2127 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7801 (mt) REVERT: L 2214 MET cc_start: 0.8559 (ppp) cc_final: 0.8174 (ppp) REVERT: L 2614 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8457 (tm-30) REVERT: L 2656 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: L 2723 GLN cc_start: 0.9025 (tm-30) cc_final: 0.8687 (tm-30) REVERT: L 2735 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8364 (mp10) REVERT: L 3028 MET cc_start: 0.8937 (mmm) cc_final: 0.8493 (tpt) REVERT: L 3092 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7213 (t80) REVERT: L 3307 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.7080 (t80) REVERT: L 3486 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.8710 (tm-30) REVERT: L 3595 ARG cc_start: 0.7416 (mpp-170) cc_final: 0.6475 (tpm170) outliers start: 101 outliers final: 67 residues processed: 427 average time/residue: 0.2416 time to fit residues: 175.4646 Evaluate side-chains 410 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 330 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 662 ILE Chi-restraints excluded: chain E residue 681 THR Chi-restraints excluded: chain E residue 708 ASN Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 718 HIS Chi-restraints excluded: chain E residue 753 ARG Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 217 CYS Chi-restraints excluded: chain G residue 255 PHE Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain H residue 539 THR Chi-restraints excluded: chain H residue 553 LYS Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 612 THR Chi-restraints excluded: chain L residue 731 ILE Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 789 ASN Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 845 MET Chi-restraints excluded: chain L residue 939 HIS Chi-restraints excluded: chain L residue 1251 GLU Chi-restraints excluded: chain L residue 1326 MET Chi-restraints excluded: chain L residue 1463 LEU Chi-restraints excluded: chain L residue 1534 VAL Chi-restraints excluded: chain L residue 1549 THR Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2027 LEU Chi-restraints excluded: chain L residue 2033 SER Chi-restraints excluded: chain L residue 2094 GLU Chi-restraints excluded: chain L residue 2127 LEU Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2272 VAL Chi-restraints excluded: chain L residue 2410 THR Chi-restraints excluded: chain L residue 2465 ASP Chi-restraints excluded: chain L residue 2491 ILE Chi-restraints excluded: chain L residue 2537 ILE Chi-restraints excluded: chain L residue 2601 ASN Chi-restraints excluded: chain L residue 2616 LEU Chi-restraints excluded: chain L residue 2618 LEU Chi-restraints excluded: chain L residue 2656 GLU Chi-restraints excluded: chain L residue 2679 TRP Chi-restraints excluded: chain L residue 2719 LEU Chi-restraints excluded: chain L residue 2735 GLN Chi-restraints excluded: chain L residue 2758 LEU Chi-restraints excluded: chain L residue 2856 THR Chi-restraints excluded: chain L residue 2858 ILE Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 2888 LEU Chi-restraints excluded: chain L residue 3049 ILE Chi-restraints excluded: chain L residue 3092 TYR Chi-restraints excluded: chain L residue 3152 VAL Chi-restraints excluded: chain L residue 3171 LEU Chi-restraints excluded: chain L residue 3211 LEU Chi-restraints excluded: chain L residue 3288 LEU Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3360 LEU Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3449 ILE Chi-restraints excluded: chain L residue 3486 GLN Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3657 ASN Chi-restraints excluded: chain L residue 3709 LEU Chi-restraints excluded: chain L residue 3711 SER Chi-restraints excluded: chain L residue 3728 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 447 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 176 optimal weight: 8.9990 chunk 278 optimal weight: 0.4980 chunk 229 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 355 optimal weight: 5.9990 chunk 352 optimal weight: 0.7980 chunk 497 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 302 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1629 GLN L2644 GLN ** L3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.106248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.073520 restraints weight = 150123.549| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.27 r_work: 0.3195 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 43484 Z= 0.125 Angle : 0.657 17.730 58889 Z= 0.324 Chirality : 0.044 0.309 6628 Planarity : 0.004 0.056 7476 Dihedral : 5.826 68.114 5710 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.71 % Favored : 92.27 % Rotamer: Outliers : 1.87 % Allowed : 17.27 % Favored : 80.86 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.43 % 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 are not related in a simple way. whole: -0.17 (0.12), residues: 5149 helix: 1.08 (0.10), residues: 2966 sheet: 0.03 (0.38), residues: 195 loop : -2.05 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 517 TYR 0.043 0.001 TYR L2316 PHE 0.046 0.001 PHE L1747 TRP 0.080 0.002 TRP L2179 HIS 0.006 0.001 HIS L2621 Details of bonding type rmsd covalent geometry : bond 0.00272 (43484) covalent geometry : angle 0.65747 (58889) hydrogen bonds : bond 0.03538 ( 2151) hydrogen bonds : angle 4.13784 ( 6237) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 364 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 580 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8641 (tp) REVERT: E 651 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8747 (tp) REVERT: E 689 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8372 (mt-10) REVERT: E 726 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8260 (tm-30) REVERT: F 170 ILE cc_start: 0.9384 (mm) cc_final: 0.9115 (mm) REVERT: F 241 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8482 (mp0) REVERT: F 444 HIS cc_start: 0.8483 (t-170) cc_final: 0.8264 (t-170) REVERT: G 119 MET cc_start: 0.8425 (tmm) cc_final: 0.8017 (tmm) REVERT: G 299 MET cc_start: 0.7581 (mtt) cc_final: 0.6968 (mpp) REVERT: G 313 MET cc_start: 0.7849 (tpp) cc_final: 0.7249 (ptp) REVERT: K 274 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8181 (mt-10) REVERT: L 359 TYR cc_start: 0.7872 (p90) cc_final: 0.7654 (p90) REVERT: L 363 PHE cc_start: 0.7732 (p90) cc_final: 0.7394 (p90) REVERT: L 383 MET cc_start: 0.5839 (pmm) cc_final: 0.5601 (pmm) REVERT: L 465 MET cc_start: 0.9052 (mmt) cc_final: 0.8758 (mmt) REVERT: L 472 MET cc_start: 0.9403 (tmm) cc_final: 0.9151 (tmm) REVERT: L 560 MET cc_start: 0.6887 (tpt) cc_final: 0.6551 (tpt) REVERT: L 588 ARG cc_start: 0.8781 (ttp-170) cc_final: 0.8534 (ttp80) REVERT: L 700 GLU cc_start: 0.8826 (pt0) cc_final: 0.8576 (pt0) REVERT: L 789 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8295 (m-40) REVERT: L 845 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7787 (mtp) REVERT: L 856 GLU cc_start: 0.8647 (mp0) cc_final: 0.8407 (mp0) REVERT: L 922 ASP cc_start: 0.8570 (p0) cc_final: 0.8204 (p0) REVERT: L 1295 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8148 (mm-30) REVERT: L 1298 ASN cc_start: 0.8380 (t0) cc_final: 0.7957 (t0) REVERT: L 1302 LYS cc_start: 0.8835 (mttm) cc_final: 0.8444 (mmtt) REVERT: L 1362 SER cc_start: 0.8280 (t) cc_final: 0.7944 (p) REVERT: L 1410 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7604 (tm-30) REVERT: L 1568 MET cc_start: 0.8334 (pmm) cc_final: 0.7308 (pmm) REVERT: L 1588 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7913 (mm) REVERT: L 1624 MET cc_start: 0.9492 (mmm) cc_final: 0.9171 (mmp) REVERT: L 1935 HIS cc_start: 0.5400 (OUTLIER) cc_final: 0.4679 (p-80) REVERT: L 1974 MET cc_start: 0.8741 (ttt) cc_final: 0.8357 (tpp) REVERT: L 2214 MET cc_start: 0.8539 (ppp) cc_final: 0.8158 (ppp) REVERT: L 2614 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8335 (tm-30) REVERT: L 2656 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: L 2723 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8701 (tm-30) REVERT: L 2735 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8368 (mp10) REVERT: L 3028 MET cc_start: 0.8948 (mmm) cc_final: 0.8664 (mmm) REVERT: L 3092 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.6991 (t80) REVERT: L 3307 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.7373 (t80) REVERT: L 3411 ARG cc_start: 0.7394 (ttp80) cc_final: 0.7058 (tmm-80) REVERT: L 3486 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.9085 (tm-30) REVERT: L 3563 MET cc_start: 0.9265 (mpp) cc_final: 0.9040 (mpp) REVERT: L 3595 ARG cc_start: 0.7275 (mpp-170) cc_final: 0.6401 (tpm170) outliers start: 89 outliers final: 63 residues processed: 428 average time/residue: 0.2478 time to fit residues: 180.1999 Evaluate side-chains 410 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 335 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 589 VAL Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 681 THR Chi-restraints excluded: chain E residue 708 ASN Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 718 HIS Chi-restraints excluded: chain E residue 753 ARG Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 217 CYS Chi-restraints excluded: chain G residue 255 PHE Chi-restraints excluded: chain K residue 289 GLN Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain H residue 539 THR Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 633 VAL Chi-restraints excluded: chain L residue 731 ILE Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 789 ASN Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 845 MET Chi-restraints excluded: chain L residue 851 LEU Chi-restraints excluded: chain L residue 1251 GLU Chi-restraints excluded: chain L residue 1463 LEU Chi-restraints excluded: chain L residue 1534 VAL Chi-restraints excluded: chain L residue 1549 THR Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1935 HIS Chi-restraints excluded: chain L residue 1936 VAL Chi-restraints excluded: chain L residue 1950 THR Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2027 LEU Chi-restraints excluded: chain L residue 2127 LEU Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2272 VAL Chi-restraints excluded: chain L residue 2276 THR Chi-restraints excluded: chain L residue 2356 SER Chi-restraints excluded: chain L residue 2465 ASP Chi-restraints excluded: chain L residue 2491 ILE Chi-restraints excluded: chain L residue 2504 LEU Chi-restraints excluded: chain L residue 2616 LEU Chi-restraints excluded: chain L residue 2618 LEU Chi-restraints excluded: chain L residue 2656 GLU Chi-restraints excluded: chain L residue 2679 TRP Chi-restraints excluded: chain L residue 2735 GLN Chi-restraints excluded: chain L residue 2752 HIS Chi-restraints excluded: chain L residue 2758 LEU Chi-restraints excluded: chain L residue 2858 ILE Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 2888 LEU Chi-restraints excluded: chain L residue 3049 ILE Chi-restraints excluded: chain L residue 3092 TYR Chi-restraints excluded: chain L residue 3152 VAL Chi-restraints excluded: chain L residue 3288 LEU Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3360 LEU Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3449 ILE Chi-restraints excluded: chain L residue 3486 GLN Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3657 ASN Chi-restraints excluded: chain L residue 3709 LEU Chi-restraints excluded: chain L residue 3728 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 408 optimal weight: 0.6980 chunk 304 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 243 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 483 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 276 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 317 ASN ** E 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 302 GLN L 6 GLN L 836 GLN L1546 GLN L2644 GLN ** L3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L3657 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.105849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.073120 restraints weight = 149899.610| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.23 r_work: 0.3186 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 43484 Z= 0.144 Angle : 0.671 17.546 58889 Z= 0.330 Chirality : 0.044 0.300 6628 Planarity : 0.004 0.059 7476 Dihedral : 5.741 68.142 5710 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.90 % Favored : 92.08 % Rotamer: Outliers : 1.87 % Allowed : 17.83 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % 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 are not related in a simple way. whole: -0.13 (0.12), residues: 5149 helix: 1.12 (0.10), residues: 2980 sheet: -0.08 (0.37), residues: 200 loop : -2.04 (0.14), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 517 TYR 0.048 0.001 TYR L2625 PHE 0.046 0.001 PHE L1747 TRP 0.081 0.002 TRP L2179 HIS 0.007 0.001 HIS L1954 Details of bonding type rmsd covalent geometry : bond 0.00324 (43484) covalent geometry : angle 0.67091 (58889) hydrogen bonds : bond 0.03611 ( 2151) hydrogen bonds : angle 4.11870 ( 6237) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 348 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 689 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8329 (mt-10) REVERT: E 726 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8277 (tm-30) REVERT: F 170 ILE cc_start: 0.9384 (mm) cc_final: 0.9120 (mm) REVERT: F 241 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8499 (mp0) REVERT: F 444 HIS cc_start: 0.8516 (t-170) cc_final: 0.8283 (t-170) REVERT: G 119 MET cc_start: 0.8402 (tmm) cc_final: 0.7872 (tmm) REVERT: G 123 MET cc_start: 0.8149 (ttm) cc_final: 0.7701 (mtp) REVERT: G 299 MET cc_start: 0.7573 (mtt) cc_final: 0.7023 (mpp) REVERT: G 313 MET cc_start: 0.7875 (tpp) cc_final: 0.7254 (ptp) REVERT: K 274 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8102 (mt-10) REVERT: H 721 LYS cc_start: 0.8003 (pttt) cc_final: 0.7742 (ptmt) REVERT: L 359 TYR cc_start: 0.7952 (p90) cc_final: 0.7730 (p90) REVERT: L 465 MET cc_start: 0.9050 (mmt) cc_final: 0.8729 (mmt) REVERT: L 472 MET cc_start: 0.9388 (tmm) cc_final: 0.9127 (tmm) REVERT: L 560 MET cc_start: 0.6867 (tpt) cc_final: 0.6579 (tpt) REVERT: L 588 ARG cc_start: 0.8839 (ttp-170) cc_final: 0.8561 (ttp80) REVERT: L 691 MET cc_start: 0.8753 (mtp) cc_final: 0.8298 (mpp) REVERT: L 700 GLU cc_start: 0.8838 (pt0) cc_final: 0.8586 (pt0) REVERT: L 789 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8330 (m-40) REVERT: L 845 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7620 (mtp) REVERT: L 856 GLU cc_start: 0.8616 (mp0) cc_final: 0.8379 (mp0) REVERT: L 922 ASP cc_start: 0.8577 (p0) cc_final: 0.8223 (p0) REVERT: L 1233 TYR cc_start: 0.8457 (m-80) cc_final: 0.8064 (m-80) REVERT: L 1295 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8210 (mm-30) REVERT: L 1298 ASN cc_start: 0.8488 (t0) cc_final: 0.8020 (t0) REVERT: L 1302 LYS cc_start: 0.8858 (mttm) cc_final: 0.8484 (mmtt) REVERT: L 1362 SER cc_start: 0.8174 (t) cc_final: 0.7902 (p) REVERT: L 1410 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7605 (tm-30) REVERT: L 1448 MET cc_start: 0.6458 (mmm) cc_final: 0.6243 (mmm) REVERT: L 1588 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7895 (mm) REVERT: L 1624 MET cc_start: 0.9481 (mmm) cc_final: 0.9200 (mmm) REVERT: L 1935 HIS cc_start: 0.5409 (OUTLIER) cc_final: 0.4681 (p-80) REVERT: L 1974 MET cc_start: 0.8768 (ttt) cc_final: 0.8404 (tpp) REVERT: L 1996 PHE cc_start: 0.7684 (m-80) cc_final: 0.7382 (t80) REVERT: L 2214 MET cc_start: 0.8544 (ppp) cc_final: 0.8166 (ppp) REVERT: L 2614 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8332 (tm-30) REVERT: L 2656 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: L 2723 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8726 (tm-30) REVERT: L 2735 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8400 (mp10) REVERT: L 3028 MET cc_start: 0.8966 (mmm) cc_final: 0.8683 (mmm) REVERT: L 3092 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7025 (t80) REVERT: L 3307 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.7122 (t80) REVERT: L 3486 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.9105 (tm-30) REVERT: L 3563 MET cc_start: 0.9276 (mpp) cc_final: 0.9050 (mpp) REVERT: L 3595 ARG cc_start: 0.7070 (mpp-170) cc_final: 0.6505 (tpm170) outliers start: 89 outliers final: 71 residues processed: 414 average time/residue: 0.2424 time to fit residues: 170.3876 Evaluate side-chains 413 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 332 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 589 VAL Chi-restraints excluded: chain E residue 708 ASN Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 718 HIS Chi-restraints excluded: chain E residue 753 ARG Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 217 CYS Chi-restraints excluded: chain G residue 255 PHE Chi-restraints excluded: chain K residue 217 ASP Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain H residue 539 THR Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 336 CYS Chi-restraints excluded: chain L residue 633 VAL Chi-restraints excluded: chain L residue 689 MET Chi-restraints excluded: chain L residue 731 ILE Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 789 ASN Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 845 MET Chi-restraints excluded: chain L residue 851 LEU Chi-restraints excluded: chain L residue 939 HIS Chi-restraints excluded: chain L residue 1251 GLU Chi-restraints excluded: chain L residue 1378 LEU Chi-restraints excluded: chain L residue 1463 LEU Chi-restraints excluded: chain L residue 1534 VAL Chi-restraints excluded: chain L residue 1549 THR Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1899 THR Chi-restraints excluded: chain L residue 1935 HIS Chi-restraints excluded: chain L residue 1936 VAL Chi-restraints excluded: chain L residue 1950 THR Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2027 LEU Chi-restraints excluded: chain L residue 2127 LEU Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2272 VAL Chi-restraints excluded: chain L residue 2276 THR Chi-restraints excluded: chain L residue 2356 SER Chi-restraints excluded: chain L residue 2465 ASP Chi-restraints excluded: chain L residue 2491 ILE Chi-restraints excluded: chain L residue 2504 LEU Chi-restraints excluded: chain L residue 2616 LEU Chi-restraints excluded: chain L residue 2618 LEU Chi-restraints excluded: chain L residue 2656 GLU Chi-restraints excluded: chain L residue 2679 TRP Chi-restraints excluded: chain L residue 2719 LEU Chi-restraints excluded: chain L residue 2735 GLN Chi-restraints excluded: chain L residue 2752 HIS Chi-restraints excluded: chain L residue 2758 LEU Chi-restraints excluded: chain L residue 2856 THR Chi-restraints excluded: chain L residue 2858 ILE Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 2888 LEU Chi-restraints excluded: chain L residue 3049 ILE Chi-restraints excluded: chain L residue 3092 TYR Chi-restraints excluded: chain L residue 3152 VAL Chi-restraints excluded: chain L residue 3171 LEU Chi-restraints excluded: chain L residue 3211 LEU Chi-restraints excluded: chain L residue 3288 LEU Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3360 LEU Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3449 ILE Chi-restraints excluded: chain L residue 3486 GLN Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3657 ASN Chi-restraints excluded: chain L residue 3709 LEU Chi-restraints excluded: chain L residue 3728 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 342 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 136 optimal weight: 0.0870 chunk 295 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 260 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 336 optimal weight: 0.9980 chunk 446 optimal weight: 10.0000 chunk 359 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 257 HIS E 317 ASN ** E 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 302 GLN L 998 GLN L1560 HIS ** L1866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2507 ASN L2644 GLN L2668 ASN ** L3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L3657 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.106632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.074053 restraints weight = 149904.894| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.30 r_work: 0.3212 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 43484 Z= 0.121 Angle : 0.664 17.760 58889 Z= 0.324 Chirality : 0.044 0.293 6628 Planarity : 0.004 0.061 7476 Dihedral : 5.617 67.170 5710 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.61 % Favored : 92.37 % Rotamer: Outliers : 1.64 % Allowed : 18.30 % Favored : 80.07 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.43 % 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 are not related in a simple way. whole: -0.05 (0.12), residues: 5149 helix: 1.18 (0.10), residues: 2980 sheet: 0.02 (0.37), residues: 200 loop : -2.00 (0.14), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 850 TYR 0.065 0.001 TYR L2625 PHE 0.048 0.001 PHE L1747 TRP 0.053 0.001 TRP L1842 HIS 0.007 0.001 HIS L1954 Details of bonding type rmsd covalent geometry : bond 0.00264 (43484) covalent geometry : angle 0.66368 (58889) hydrogen bonds : bond 0.03390 ( 2151) hydrogen bonds : angle 4.05084 ( 6237) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 352 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 726 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8280 (tm-30) REVERT: F 170 ILE cc_start: 0.9381 (mm) cc_final: 0.9117 (mm) REVERT: F 241 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: G 123 MET cc_start: 0.8271 (ttm) cc_final: 0.7919 (mtp) REVERT: G 299 MET cc_start: 0.7510 (mtt) cc_final: 0.6985 (mpp) REVERT: G 313 MET cc_start: 0.7888 (tpp) cc_final: 0.7226 (ptp) REVERT: K 274 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8078 (mt-10) REVERT: L 383 MET cc_start: 0.5897 (pmm) cc_final: 0.5558 (pmm) REVERT: L 465 MET cc_start: 0.9021 (mmt) cc_final: 0.8709 (mmt) REVERT: L 472 MET cc_start: 0.9378 (tmm) cc_final: 0.9123 (tmm) REVERT: L 560 MET cc_start: 0.6843 (tpt) cc_final: 0.6586 (tpt) REVERT: L 588 ARG cc_start: 0.8828 (ttp-170) cc_final: 0.8576 (ttp80) REVERT: L 700 GLU cc_start: 0.8812 (pt0) cc_final: 0.8581 (pt0) REVERT: L 789 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8315 (m-40) REVERT: L 856 GLU cc_start: 0.8576 (mp0) cc_final: 0.8364 (mp0) REVERT: L 922 ASP cc_start: 0.8515 (p0) cc_final: 0.8133 (p0) REVERT: L 1295 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8191 (mm-30) REVERT: L 1298 ASN cc_start: 0.8513 (t0) cc_final: 0.8069 (t0) REVERT: L 1302 LYS cc_start: 0.8849 (mttm) cc_final: 0.8472 (mmtt) REVERT: L 1362 SER cc_start: 0.8202 (t) cc_final: 0.7914 (p) REVERT: L 1415 CYS cc_start: 0.8585 (m) cc_final: 0.8150 (t) REVERT: L 1448 MET cc_start: 0.6499 (mmm) cc_final: 0.6291 (mmm) REVERT: L 1588 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7926 (mm) REVERT: L 1624 MET cc_start: 0.9462 (mmm) cc_final: 0.9156 (mmp) REVERT: L 1935 HIS cc_start: 0.5418 (OUTLIER) cc_final: 0.4707 (p-80) REVERT: L 1974 MET cc_start: 0.8816 (ttt) cc_final: 0.8484 (tpp) REVERT: L 1996 PHE cc_start: 0.7748 (m-80) cc_final: 0.7453 (t80) REVERT: L 2214 MET cc_start: 0.8521 (ppp) cc_final: 0.8147 (ppp) REVERT: L 2614 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8276 (tm-30) REVERT: L 2656 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: L 2723 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8788 (tm-30) REVERT: L 2735 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8410 (mp10) REVERT: L 3028 MET cc_start: 0.8952 (mmm) cc_final: 0.8676 (mmm) REVERT: L 3092 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.6853 (t80) REVERT: L 3307 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7338 (t80) REVERT: L 3411 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7127 (tmm-80) REVERT: L 3563 MET cc_start: 0.9248 (mpp) cc_final: 0.9019 (mpp) REVERT: L 3595 ARG cc_start: 0.6970 (mpp-170) cc_final: 0.6485 (tpm170) outliers start: 78 outliers final: 62 residues processed: 406 average time/residue: 0.2504 time to fit residues: 171.8942 Evaluate side-chains 401 residues out of total 4766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 331 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 589 VAL Chi-restraints excluded: chain E residue 644 ASN Chi-restraints excluded: chain E residue 708 ASN Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 753 ARG Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 217 CYS Chi-restraints excluded: chain G residue 255 PHE Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain H residue 539 THR Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 336 CYS Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 633 VAL Chi-restraints excluded: chain L residue 689 MET Chi-restraints excluded: chain L residue 731 ILE Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 789 ASN Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 939 HIS Chi-restraints excluded: chain L residue 998 GLN Chi-restraints excluded: chain L residue 1251 GLU Chi-restraints excluded: chain L residue 1463 LEU Chi-restraints excluded: chain L residue 1534 VAL Chi-restraints excluded: chain L residue 1549 THR Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1899 THR Chi-restraints excluded: chain L residue 1935 HIS Chi-restraints excluded: chain L residue 1936 VAL Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2027 LEU Chi-restraints excluded: chain L residue 2094 GLU Chi-restraints excluded: chain L residue 2127 LEU Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2276 THR Chi-restraints excluded: chain L residue 2356 SER Chi-restraints excluded: chain L residue 2465 ASP Chi-restraints excluded: chain L residue 2491 ILE Chi-restraints excluded: chain L residue 2504 LEU Chi-restraints excluded: chain L residue 2618 LEU Chi-restraints excluded: chain L residue 2656 GLU Chi-restraints excluded: chain L residue 2679 TRP Chi-restraints excluded: chain L residue 2719 LEU Chi-restraints excluded: chain L residue 2735 GLN Chi-restraints excluded: chain L residue 2752 HIS Chi-restraints excluded: chain L residue 2758 LEU Chi-restraints excluded: chain L residue 2858 ILE Chi-restraints excluded: chain L residue 2888 LEU Chi-restraints excluded: chain L residue 3049 ILE Chi-restraints excluded: chain L residue 3092 TYR Chi-restraints excluded: chain L residue 3211 LEU Chi-restraints excluded: chain L residue 3288 LEU Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3360 LEU Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3449 ILE Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3657 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 224 optimal weight: 0.0020 chunk 127 optimal weight: 6.9990 chunk 422 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 379 optimal weight: 0.5980 chunk 281 optimal weight: 5.9990 chunk 256 optimal weight: 0.9980 chunk 480 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 437 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 257 HIS E 317 ASN ** E 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 302 GLN ** L1866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2507 ASN L2644 GLN ** L2948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.106586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.073978 restraints weight = 150994.110| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.30 r_work: 0.3209 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.277 43484 Z= 0.164 Angle : 0.737 59.046 58889 Z= 0.382 Chirality : 0.045 0.611 6628 Planarity : 0.004 0.058 7476 Dihedral : 5.619 67.167 5710 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.57 % Favored : 92.41 % Rotamer: Outliers : 1.66 % Allowed : 18.40 % Favored : 79.94 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.43 % 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 are not related in a simple way. whole: -0.05 (0.12), residues: 5149 helix: 1.18 (0.10), residues: 2980 sheet: 0.02 (0.37), residues: 200 loop : -2.00 (0.14), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 850 TYR 0.057 0.001 TYR L2625 PHE 0.049 0.001 PHE L1747 TRP 0.048 0.002 TRP L1842 HIS 0.025 0.001 HIS F 444 Details of bonding type rmsd covalent geometry : bond 0.00369 (43484) covalent geometry : angle 0.73705 (58889) hydrogen bonds : bond 0.03402 ( 2151) hydrogen bonds : angle 4.05643 ( 6237) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15697.97 seconds wall clock time: 268 minutes 22.70 seconds (16102.70 seconds total)