Starting phenix.real_space_refine on Sun Feb 8 11:00:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mhp_48280/02_2026/9mhp_48280.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mhp_48280/02_2026/9mhp_48280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mhp_48280/02_2026/9mhp_48280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mhp_48280/02_2026/9mhp_48280.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mhp_48280/02_2026/9mhp_48280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mhp_48280/02_2026/9mhp_48280.map" } resolution = 3.97 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= 0.001 sd= 0.047 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: 5 Type Number sf(0) Gaussians S 96 5.16 5 C 13941 2.51 5 N 3575 2.21 5 O 4040 1.98 5 H 21634 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43286 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 43286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2703, 43286 Classifications: {'peptide': 2703} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 105, 'TRANS': 2597} Chain breaks: 6 Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 11, 'GLN:plan1': 4, 'ARG:plan': 7, 'HIS:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 8, 'PHE:plan': 4, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 175 Time building chain proxies: 7.84, per 1000 atoms: 0.18 Number of scatterers: 43286 At special positions: 0 Unit cell: (145.2, 154.275, 186.038, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 O 4040 8.00 N 3575 7.00 C 13941 6.00 H 21634 1.00 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: 4.08 Conformation dependent library (CDL) restraints added in 1.2 seconds 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5228 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 2 sheets defined 62.2% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 removed outlier: 3.850A pdb=" N ALA A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 11 " --> pdb=" O CYS A 7 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 28 Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 50 through 72 removed outlier: 4.216A pdb=" N TRP A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Proline residue: A 56 - end of helix removed outlier: 3.592A pdb=" N LYS A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 111 removed outlier: 4.326A pdb=" N TYR A 96 " --> pdb=" O HIS A 92 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 100 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 101 " --> pdb=" O CYS A 97 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 removed outlier: 4.099A pdb=" N VAL A 116 " --> pdb=" O ASN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 119 No H-bonds generated for 'chain 'A' and resid 118 through 119' Processing helix chain 'A' and resid 120 through 127 removed outlier: 4.319A pdb=" N MET A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 151 removed outlier: 3.523A pdb=" N LYS A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.970A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A 169 " --> pdb=" O HIS A 165 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 203 through 206 Processing helix chain 'A' and resid 250 through 260 removed outlier: 3.975A pdb=" N ALA A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 281 removed outlier: 3.887A pdb=" N SER A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 309 removed outlier: 3.636A pdb=" N ILE A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 318 removed outlier: 4.538A pdb=" N SER A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 356 Processing helix chain 'A' and resid 361 through 370 Processing helix chain 'A' and resid 377 through 392 removed outlier: 3.688A pdb=" N LEU A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ARG A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 413 removed outlier: 3.760A pdb=" N ARG A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE A 404 " --> pdb=" O TYR A 400 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 441 through 456 removed outlier: 4.603A pdb=" N LEU A 445 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 468 removed outlier: 3.959A pdb=" N THR A 462 " --> pdb=" O ASN A 458 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 486 removed outlier: 4.796A pdb=" N ALA A 479 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 523 removed outlier: 3.541A pdb=" N LEU A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 539 through 549 removed outlier: 3.631A pdb=" N LYS A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 553 Processing helix chain 'A' and resid 555 through 572 removed outlier: 3.880A pdb=" N THR A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 560 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 569 " --> pdb=" O VAL A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 581 removed outlier: 3.525A pdb=" N LEU A 579 " --> pdb=" O ILE A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 590 Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.610A pdb=" N LEU A 595 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 Processing helix chain 'A' and resid 605 through 614 removed outlier: 3.700A pdb=" N VAL A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A 614 " --> pdb=" O VAL A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 625 Processing helix chain 'A' and resid 627 through 633 removed outlier: 3.982A pdb=" N ASN A 631 " --> pdb=" O GLY A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 646 removed outlier: 3.764A pdb=" N ILE A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A 645 " --> pdb=" O HIS A 641 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 664 removed outlier: 3.891A pdb=" N GLU A 653 " --> pdb=" O ASP A 649 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 654 " --> pdb=" O ARG A 650 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 660 " --> pdb=" O THR A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 668 through 683 removed outlier: 3.572A pdb=" N ILE A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 686 No H-bonds generated for 'chain 'A' and resid 684 through 686' Processing helix chain 'A' and resid 729 through 745 removed outlier: 3.545A pdb=" N LEU A 745 " --> pdb=" O PHE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 751 removed outlier: 3.542A pdb=" N SER A 751 " --> pdb=" O GLY A 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 748 through 751' Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 758 through 766 removed outlier: 3.620A pdb=" N PHE A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE A 766 " --> pdb=" O PHE A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 removed outlier: 4.025A pdb=" N PHE A 776 " --> pdb=" O TYR A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 795 removed outlier: 3.917A pdb=" N GLN A 789 " --> pdb=" O THR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 799 removed outlier: 4.267A pdb=" N ALA A 799 " --> pdb=" O GLU A 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 796 through 799' Processing helix chain 'A' and resid 800 through 814 removed outlier: 3.562A pdb=" N LEU A 814 " --> pdb=" O GLN A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 830 removed outlier: 3.541A pdb=" N ARG A 830 " --> pdb=" O PHE A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 857 removed outlier: 3.892A pdb=" N SER A 838 " --> pdb=" O ASN A 834 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 843 " --> pdb=" O CYS A 839 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 855 " --> pdb=" O ASN A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 879 removed outlier: 3.699A pdb=" N ILE A 871 " --> pdb=" O ARG A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 900 removed outlier: 3.939A pdb=" N ASN A 885 " --> pdb=" O SER A 881 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET A 898 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR A 899 " --> pdb=" O LEU A 895 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE A 900 " --> pdb=" O GLU A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 905 removed outlier: 3.880A pdb=" N MET A 904 " --> pdb=" O ARG A 901 " (cutoff:3.500A) Proline residue: A 905 - end of helix No H-bonds generated for 'chain 'A' and resid 901 through 905' Processing helix chain 'A' and resid 906 through 912 removed outlier: 3.894A pdb=" N THR A 910 " --> pdb=" O ASP A 906 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A 911 " --> pdb=" O SER A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 937 removed outlier: 4.585A pdb=" N GLY A 937 " --> pdb=" O PRO A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 972 removed outlier: 3.564A pdb=" N THR A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 958 " --> pdb=" O MET A 954 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 960 " --> pdb=" O THR A 956 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE A 972 " --> pdb=" O LEU A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 980 removed outlier: 4.013A pdb=" N ARG A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1008 removed outlier: 3.567A pdb=" N GLU A 991 " --> pdb=" O ASP A 987 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 992 " --> pdb=" O LEU A 988 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS A 993 " --> pdb=" O THR A 989 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASN A1001 " --> pdb=" O ASN A 997 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A1002 " --> pdb=" O VAL A 998 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A1003 " --> pdb=" O VAL A 999 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A1004 " --> pdb=" O GLU A1000 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET A1005 " --> pdb=" O ASN A1001 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A1006 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1029 Processing helix chain 'A' and resid 1044 through 1053 Processing helix chain 'A' and resid 1056 through 1072 removed outlier: 3.887A pdb=" N HIS A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A1062 " --> pdb=" O LEU A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1109 removed outlier: 3.629A pdb=" N LEU A1092 " --> pdb=" O SER A1088 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS A1096 " --> pdb=" O LEU A1092 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU A1097 " --> pdb=" O THR A1093 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A1098 " --> pdb=" O LEU A1094 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN A1099 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET A1108 " --> pdb=" O TYR A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1143 removed outlier: 3.870A pdb=" N VAL A1138 " --> pdb=" O LYS A1134 " (cutoff:3.500A) Proline residue: A1139 - end of helix Processing helix chain 'A' and resid 1144 through 1154 Processing helix chain 'A' and resid 1166 through 1181 removed outlier: 3.921A pdb=" N PHE A1170 " --> pdb=" O PRO A1166 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS A1171 " --> pdb=" O TYR A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1208 removed outlier: 4.298A pdb=" N ILE A1206 " --> pdb=" O PRO A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1226 Processing helix chain 'A' and resid 1278 through 1285 removed outlier: 4.360A pdb=" N THR A1282 " --> pdb=" O GLU A1278 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A1283 " --> pdb=" O LEU A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1290 Processing helix chain 'A' and resid 1291 through 1296 removed outlier: 3.755A pdb=" N VAL A1295 " --> pdb=" O ARG A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1299 No H-bonds generated for 'chain 'A' and resid 1297 through 1299' Processing helix chain 'A' and resid 1300 through 1301 No H-bonds generated for 'chain 'A' and resid 1300 through 1301' Processing helix chain 'A' and resid 1302 through 1317 removed outlier: 3.825A pdb=" N ALA A1307 " --> pdb=" O VAL A1303 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS A1308 " --> pdb=" O ASN A1304 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A1309 " --> pdb=" O ALA A1305 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS A1316 " --> pdb=" O GLN A1312 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR A1317 " --> pdb=" O ILE A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1334 removed outlier: 3.814A pdb=" N ALA A1325 " --> pdb=" O THR A1321 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU A1334 " --> pdb=" O ASP A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1356 removed outlier: 4.153A pdb=" N SER A1345 " --> pdb=" O ALA A1341 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS A1348 " --> pdb=" O SER A1344 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A1356 " --> pdb=" O ILE A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1362 No H-bonds generated for 'chain 'A' and resid 1360 through 1362' Processing helix chain 'A' and resid 1363 through 1376 removed outlier: 3.563A pdb=" N LYS A1376 " --> pdb=" O GLU A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1403 Processing helix chain 'A' and resid 1430 through 1442 removed outlier: 3.740A pdb=" N LYS A1434 " --> pdb=" O PRO A1430 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A1435 " --> pdb=" O ASP A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1464 removed outlier: 4.018A pdb=" N PHE A1462 " --> pdb=" O ARG A1458 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR A1463 " --> pdb=" O ILE A1459 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A1464 " --> pdb=" O LEU A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1475 Processing helix chain 'A' and resid 1477 through 1489 removed outlier: 3.799A pdb=" N ARG A1481 " --> pdb=" O GLY A1477 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS A1484 " --> pdb=" O SER A1480 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A1486 " --> pdb=" O LEU A1482 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A1487 " --> pdb=" O LEU A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1511 removed outlier: 3.967A pdb=" N PHE A1510 " --> pdb=" O THR A1506 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A1511 " --> pdb=" O ARG A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1528 removed outlier: 3.578A pdb=" N ALA A1518 " --> pdb=" O GLU A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1542 through 1550 removed outlier: 4.544A pdb=" N GLU A1548 " --> pdb=" O THR A1544 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1567 removed outlier: 3.968A pdb=" N GLU A1567 " --> pdb=" O ASP A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1625 removed outlier: 4.105A pdb=" N GLU A1625 " --> pdb=" O MET A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1637 through 1641 Processing helix chain 'A' and resid 1651 through 1671 removed outlier: 4.051A pdb=" N ALA A1655 " --> pdb=" O ASN A1651 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER A1669 " --> pdb=" O VAL A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1680 removed outlier: 3.961A pdb=" N GLU A1677 " --> pdb=" O GLN A1673 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1703 Processing helix chain 'A' and resid 1715 through 1738 removed outlier: 3.938A pdb=" N LEU A1737 " --> pdb=" O ILE A1733 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1738 " --> pdb=" O ILE A1734 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1774 removed outlier: 3.811A pdb=" N PHE A1759 " --> pdb=" O PRO A1755 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A1763 " --> pdb=" O PHE A1759 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A1770 " --> pdb=" O GLU A1766 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A1771 " --> pdb=" O ALA A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1778 through 1783 Processing helix chain 'A' and resid 1785 through 1801 removed outlier: 4.013A pdb=" N ARG A1794 " --> pdb=" O ASP A1790 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A1796 " --> pdb=" O TRP A1792 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A1797 " --> pdb=" O PHE A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1814 No H-bonds generated for 'chain 'A' and resid 1812 through 1814' Processing helix chain 'A' and resid 1815 through 1830 removed outlier: 4.162A pdb=" N ASP A1819 " --> pdb=" O LYS A1815 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A1820 " --> pdb=" O VAL A1816 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL A1827 " --> pdb=" O LEU A1823 " (cutoff:3.500A) Processing helix chain 'A' and resid 1831 through 1841 removed outlier: 3.736A pdb=" N GLU A1838 " --> pdb=" O SER A1834 " (cutoff:3.500A) Processing helix chain 'A' and resid 1849 through 1869 removed outlier: 3.791A pdb=" N ALA A1857 " --> pdb=" O ILE A1853 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A1858 " --> pdb=" O PHE A1854 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU A1859 " --> pdb=" O ASN A1855 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A1860 " --> pdb=" O VAL A1856 " (cutoff:3.500A) Processing helix chain 'A' and resid 2226 through 2238 removed outlier: 3.570A pdb=" N TRP A2231 " --> pdb=" O THR A2227 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS A2232 " --> pdb=" O VAL A2228 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP A2233 " --> pdb=" O SER A2229 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A2234 " --> pdb=" O ARG A2230 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A2238 " --> pdb=" O ILE A2234 " (cutoff:3.500A) Processing helix chain 'A' and resid 2243 through 2247 Processing helix chain 'A' and resid 2248 through 2257 removed outlier: 3.767A pdb=" N ILE A2253 " --> pdb=" O ILE A2249 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A2254 " --> pdb=" O PRO A2250 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG A2255 " --> pdb=" O THR A2251 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR A2257 " --> pdb=" O ILE A2253 " (cutoff:3.500A) Processing helix chain 'A' and resid 2262 through 2276 removed outlier: 3.966A pdb=" N ARG A2271 " --> pdb=" O LEU A2267 " (cutoff:3.500A) Processing helix chain 'A' and resid 2459 through 2464 Processing helix chain 'A' and resid 2474 through 2487 removed outlier: 4.288A pdb=" N ILE A2478 " --> pdb=" O ILE A2474 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR A2479 " --> pdb=" O GLN A2475 " (cutoff:3.500A) Processing helix chain 'A' and resid 2489 through 2506 removed outlier: 3.511A pdb=" N ASN A2494 " --> pdb=" O LYS A2490 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP A2495 " --> pdb=" O GLN A2491 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET A2497 " --> pdb=" O ARG A2493 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A2498 " --> pdb=" O ASN A2494 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE A2500 " --> pdb=" O LEU A2496 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE A2502 " --> pdb=" O ASN A2498 " (cutoff:3.500A) Processing helix chain 'A' and resid 2510 through 2524 removed outlier: 3.929A pdb=" N LEU A2514 " --> pdb=" O ASP A2510 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU A2515 " --> pdb=" O GLN A2511 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LYS A2516 " --> pdb=" O HIS A2512 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A2517 " --> pdb=" O SER A2513 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE A2520 " --> pdb=" O LYS A2516 " (cutoff:3.500A) Processing helix chain 'A' and resid 2542 through 2559 Processing helix chain 'A' and resid 2563 through 2569 removed outlier: 3.961A pdb=" N PHE A2567 " --> pdb=" O ARG A2563 " (cutoff:3.500A) Processing helix chain 'A' and resid 2596 through 2606 removed outlier: 4.228A pdb=" N HIS A2600 " --> pdb=" O TRP A2596 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU A2601 " --> pdb=" O PRO A2597 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A2605 " --> pdb=" O LEU A2601 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP A2606 " --> pdb=" O PHE A2602 " (cutoff:3.500A) Processing helix chain 'A' and resid 2613 through 2638 removed outlier: 3.691A pdb=" N MET A2617 " --> pdb=" O GLU A2613 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A2626 " --> pdb=" O ARG A2622 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS A2627 " --> pdb=" O ILE A2623 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A2635 " --> pdb=" O LEU A2631 " (cutoff:3.500A) Processing helix chain 'A' and resid 2644 through 2649 Processing helix chain 'A' and resid 2654 through 2663 removed outlier: 3.779A pdb=" N LYS A2660 " --> pdb=" O ASP A2656 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE A2661 " --> pdb=" O ASP A2657 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A2662 " --> pdb=" O LEU A2658 " (cutoff:3.500A) Processing helix chain 'A' and resid 2673 through 2687 removed outlier: 3.620A pdb=" N GLN A2677 " --> pdb=" O ARG A2673 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN A2680 " --> pdb=" O GLN A2676 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS A2687 " --> pdb=" O TYR A2683 " (cutoff:3.500A) Processing helix chain 'A' and resid 2691 through 2707 Processing helix chain 'A' and resid 2708 through 2719 removed outlier: 3.732A pdb=" N SER A2712 " --> pdb=" O SER A2708 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY A2716 " --> pdb=" O SER A2712 " (cutoff:3.500A) Processing helix chain 'A' and resid 2731 through 2740 removed outlier: 3.706A pdb=" N LEU A2735 " --> pdb=" O ASN A2731 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A2737 " --> pdb=" O GLU A2733 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE A2738 " --> pdb=" O LEU A2734 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A2740 " --> pdb=" O GLN A2736 " (cutoff:3.500A) Processing helix chain 'A' and resid 2744 through 2761 removed outlier: 4.087A pdb=" N LEU A2752 " --> pdb=" O LEU A2748 " (cutoff:3.500A) Processing helix chain 'A' and resid 2769 through 2780 removed outlier: 3.800A pdb=" N LEU A2773 " --> pdb=" O ASN A2769 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A2775 " --> pdb=" O LYS A2771 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR A2777 " --> pdb=" O LEU A2773 " (cutoff:3.500A) Processing helix chain 'A' and resid 2783 through 2794 removed outlier: 3.846A pdb=" N GLU A2791 " --> pdb=" O SER A2787 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N CYS A2792 " --> pdb=" O SER A2788 " (cutoff:3.500A) Processing helix chain 'A' and resid 2809 through 2820 removed outlier: 4.123A pdb=" N ILE A2813 " --> pdb=" O LEU A2809 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS A2820 " --> pdb=" O LEU A2816 " (cutoff:3.500A) Processing helix chain 'A' and resid 2860 through 2868 removed outlier: 3.616A pdb=" N MET A2866 " --> pdb=" O LEU A2862 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE A2867 " --> pdb=" O LEU A2863 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A2868 " --> pdb=" O ASN A2864 " (cutoff:3.500A) Processing helix chain 'A' and resid 2878 through 2888 removed outlier: 3.783A pdb=" N VAL A2882 " --> pdb=" O ALA A2879 " (cutoff:3.500A) Proline residue: A2885 - end of helix Processing helix chain 'A' and resid 2889 through 2903 removed outlier: 3.544A pdb=" N LYS A2893 " --> pdb=" O ASP A2889 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A2900 " --> pdb=" O PHE A2896 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS A2902 " --> pdb=" O ASN A2898 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER A2903 " --> pdb=" O ALA A2899 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2928 Processing helix chain 'A' and resid 2956 through 2970 removed outlier: 3.992A pdb=" N TRP A2960 " --> pdb=" O VAL A2956 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A2962 " --> pdb=" O ARG A2958 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A2969 " --> pdb=" O SER A2965 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN A2970 " --> pdb=" O ARG A2966 " (cutoff:3.500A) Processing helix chain 'A' and resid 2989 through 2995 removed outlier: 4.156A pdb=" N GLY A2993 " --> pdb=" O ARG A2990 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A2994 " --> pdb=" O THR A2991 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A2995 " --> pdb=" O SER A2992 " (cutoff:3.500A) Processing helix chain 'A' and resid 2997 through 3015 removed outlier: 3.772A pdb=" N PHE A3001 " --> pdb=" O GLU A2997 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A3003 " --> pdb=" O LEU A2999 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A3010 " --> pdb=" O GLY A3006 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3032 removed outlier: 3.932A pdb=" N VAL A3027 " --> pdb=" O PHE A3023 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE A3031 " --> pdb=" O VAL A3027 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A3032 " --> pdb=" O TYR A3028 " (cutoff:3.500A) Processing helix chain 'A' and resid 3039 through 3045 removed outlier: 3.903A pdb=" N SER A3043 " --> pdb=" O LYS A3039 " (cutoff:3.500A) Processing helix chain 'A' and resid 3045 through 3054 removed outlier: 4.198A pdb=" N TRP A3054 " --> pdb=" O LYS A3050 " (cutoff:3.500A) Processing helix chain 'A' and resid 3097 through 3111 Processing helix chain 'A' and resid 3113 through 3128 removed outlier: 3.652A pdb=" N ASN A3119 " --> pdb=" O GLU A3115 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A3120 " --> pdb=" O GLN A3116 " (cutoff:3.500A) Processing helix chain 'A' and resid 3129 through 3134 removed outlier: 3.638A pdb=" N ILE A3133 " --> pdb=" O SER A3129 " (cutoff:3.500A) Processing helix chain 'A' and resid 3139 through 3146 removed outlier: 4.312A pdb=" N LEU A3143 " --> pdb=" O GLN A3139 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3159 Processing helix chain 'A' and resid 3170 through 3182 removed outlier: 3.962A pdb=" N TYR A3174 " --> pdb=" O LYS A3170 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ARG A3180 " --> pdb=" O TRP A3176 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER A3181 " --> pdb=" O ARG A3177 " (cutoff:3.500A) Processing helix chain 'A' and resid 3183 through 3195 removed outlier: 3.586A pdb=" N LEU A3190 " --> pdb=" O GLU A3186 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A3194 " --> pdb=" O LEU A3190 " (cutoff:3.500A) Processing helix chain 'A' and resid 3248 through 3261 removed outlier: 3.729A pdb=" N GLY A3261 " --> pdb=" O ALA A3257 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 212 Processing sheet with id=AA2, first strand: chain 'A' and resid 3161 through 3162 removed outlier: 7.229A pdb=" N THR A3161 " --> pdb=" O ILE A3219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 882 hydrogen bonds defined for protein. 2571 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: 12.64 Time building geometry restraints manager: 5.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 21598 1.03 - 1.23: 39 1.23 - 1.42: 9060 1.42 - 1.62: 12868 1.62 - 1.82: 156 Bond restraints: 43721 Sorted by residual: bond pdb=" C LYS A1494 " pdb=" O LYS A1494 " ideal model delta sigma weight residual 1.236 1.258 -0.022 1.47e-02 4.63e+03 2.30e+00 bond pdb=" CA ARG A1690 " pdb=" C ARG A1690 " ideal model delta sigma weight residual 1.534 1.522 0.012 9.50e-03 1.11e+04 1.61e+00 bond pdb=" CA ARG A1417 " pdb=" C ARG A1417 " ideal model delta sigma weight residual 1.532 1.522 0.011 9.60e-03 1.09e+04 1.25e+00 bond pdb=" CA GLN A 928 " pdb=" CB GLN A 928 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.27e-02 6.20e+03 1.23e+00 bond pdb=" CA SER A 604 " pdb=" C SER A 604 " ideal model delta sigma weight residual 1.522 1.503 0.019 1.72e-02 3.38e+03 1.23e+00 ... (remaining 43716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 78391 1.83 - 3.67: 698 3.67 - 5.50: 55 5.50 - 7.33: 2 7.33 - 9.17: 2 Bond angle restraints: 79148 Sorted by residual: angle pdb=" N ILE A 333 " pdb=" CA ILE A 333 " pdb=" C ILE A 333 " ideal model delta sigma weight residual 106.21 111.87 -5.66 1.07e+00 8.73e-01 2.79e+01 angle pdb=" N VAL A1383 " pdb=" CA VAL A1383 " pdb=" C VAL A1383 " ideal model delta sigma weight residual 113.71 110.48 3.23 9.50e-01 1.11e+00 1.15e+01 angle pdb=" N ILE A2509 " pdb=" CA ILE A2509 " pdb=" C ILE A2509 " ideal model delta sigma weight residual 113.71 110.53 3.18 9.50e-01 1.11e+00 1.12e+01 angle pdb=" CB MET A3117 " pdb=" CG MET A3117 " pdb=" SD MET A3117 " ideal model delta sigma weight residual 112.70 121.87 -9.17 3.00e+00 1.11e-01 9.34e+00 angle pdb=" N VAL A3172 " pdb=" CA VAL A3172 " pdb=" C VAL A3172 " ideal model delta sigma weight residual 111.89 107.87 4.02 1.44e+00 4.82e-01 7.81e+00 ... (remaining 79143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 18168 17.84 - 35.69: 1824 35.69 - 53.53: 454 53.53 - 71.38: 108 71.38 - 89.22: 29 Dihedral angle restraints: 20583 sinusoidal: 11148 harmonic: 9435 Sorted by residual: dihedral pdb=" CA PRO A 925 " pdb=" C PRO A 925 " pdb=" N PRO A 926 " pdb=" CA PRO A 926 " ideal model delta harmonic sigma weight residual -180.00 -146.33 -33.67 0 5.00e+00 4.00e-02 4.53e+01 dihedral pdb=" CA GLU A1275 " pdb=" C GLU A1275 " pdb=" N LEU A1276 " pdb=" CA LEU A1276 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA PRO A 926 " pdb=" C PRO A 926 " pdb=" N LEU A 927 " pdb=" CA LEU A 927 " ideal model delta harmonic sigma weight residual 180.00 157.82 22.18 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 20580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2553 0.034 - 0.068: 660 0.068 - 0.103: 199 0.103 - 0.137: 49 0.137 - 0.171: 3 Chirality restraints: 3464 Sorted by residual: chirality pdb=" CA PRO A 926 " pdb=" N PRO A 926 " pdb=" C PRO A 926 " pdb=" CB PRO A 926 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" CA VAL A1165 " pdb=" N VAL A1165 " pdb=" C VAL A1165 " pdb=" CB VAL A1165 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA ILE A 917 " pdb=" N ILE A 917 " pdb=" C ILE A 917 " pdb=" CB ILE A 917 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 3461 not shown) Planarity restraints: 6357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 970 " 0.306 9.50e-02 1.11e+02 1.02e-01 1.20e+01 pdb=" NE ARG A 970 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 970 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 970 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 970 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 970 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 970 " -0.003 2.00e-02 2.50e+03 pdb="HH21 ARG A 970 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG A 970 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A1200 " -0.042 5.00e-02 4.00e+02 6.22e-02 6.18e+00 pdb=" N PRO A1201 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A1201 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A1201 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 415 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO A 416 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 416 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 416 " 0.034 5.00e-02 4.00e+02 ... (remaining 6354 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 2050 2.15 - 2.76: 84566 2.76 - 3.38: 121522 3.38 - 3.99: 142382 3.99 - 4.60: 224322 Nonbonded interactions: 574842 Sorted by model distance: nonbonded pdb=" O VAL A2979 " pdb=" H ASP A2982 " model vdw 1.541 2.450 nonbonded pdb=" OE1 GLU A3026 " pdb=" H GLU A3026 " model vdw 1.554 2.450 nonbonded pdb=" OD1 ASN A3082 " pdb=" H LYS A3088 " model vdw 1.567 2.450 nonbonded pdb=" O LYS A1379 " pdb=" H HIS A1382 " model vdw 1.568 2.450 nonbonded pdb=" O LEU A2624 " pdb=" HG1 THR A2628 " model vdw 1.570 2.450 ... (remaining 574837 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.210 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 42.890 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 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 : 0.003 0.052 22087 Z= 0.133 Angle : 0.577 9.169 29905 Z= 0.318 Chirality : 0.036 0.171 3464 Planarity : 0.005 0.136 3777 Dihedral : 16.332 89.221 8238 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 16.18 % Favored : 83.60 % Rotamer: Outliers : 1.98 % Allowed : 18.40 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -2.47 (0.16), residues: 2689 helix: -0.27 (0.14), residues: 1348 sheet: -5.52 (0.43), residues: 11 loop : -3.21 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 970 TYR 0.013 0.001 TYR A2895 PHE 0.017 0.001 PHE A2897 TRP 0.008 0.001 TRP A1196 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00278 (22087) covalent geometry : angle 0.57694 (29905) hydrogen bonds : bond 0.22564 ( 882) hydrogen bonds : angle 7.94922 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 2 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 339 is missing expected H atoms. Skipping. Residue LYS 935 is missing expected H atoms. Skipping. Residue LYS 1033 is missing expected H atoms. Skipping. Residue SER 1035 is missing expected H atoms. Skipping. Residue SER 1038 is missing expected H atoms. Skipping. Residue LYS 1357 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue LEU 1415 is missing expected H atoms. Skipping. Residue LEU 1416 is missing expected H atoms. Skipping. Residue LYS 1586 is missing expected H atoms. Skipping. Residue LEU 1589 is missing expected H atoms. Skipping. Residue LYS 1594 is missing expected H atoms. Skipping. Residue LYS 1603 is missing expected H atoms. Skipping. Residue LYS 1642 is missing expected H atoms. Skipping. Residue THR 1712 is missing expected H atoms. Skipping. Residue LYS 2764 is missing expected H atoms. Skipping. Residue THR 2804 is missing expected H atoms. Skipping. Residue LYS 2910 is missing expected H atoms. Skipping. Residue LEU 2911 is missing expected H atoms. Skipping. Residue THR 2944 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue TYR 3075 is missing expected H atoms. Skipping. Evaluate side-chains 303 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 255 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLU cc_start: 0.8395 (tp30) cc_final: 0.7991 (mm-30) REVERT: A 148 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7171 (tmt170) REVERT: A 169 LYS cc_start: 0.6673 (ptmt) cc_final: 0.6094 (tptt) REVERT: A 241 MET cc_start: 0.7403 (mpp) cc_final: 0.7195 (mpp) REVERT: A 453 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8472 (tm-30) REVERT: A 555 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7854 (tt) REVERT: A 954 MET cc_start: 0.7844 (tpp) cc_final: 0.7519 (tpt) REVERT: A 1147 MET cc_start: 0.7257 (ptt) cc_final: 0.6885 (ptt) REVERT: A 1404 LEU cc_start: 0.9378 (mm) cc_final: 0.9158 (mp) REVERT: A 1435 GLN cc_start: 0.9071 (tp40) cc_final: 0.8760 (tp-100) REVERT: A 1703 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: A 2481 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: A 2659 MET cc_start: 0.7974 (tmm) cc_final: 0.7383 (tmm) REVERT: A 2961 TYR cc_start: 0.9145 (m-80) cc_final: 0.8926 (m-80) REVERT: A 3207 GLU cc_start: 0.7809 (tt0) cc_final: 0.7544 (tt0) outliers start: 48 outliers final: 35 residues processed: 292 average time/residue: 0.3381 time to fit residues: 156.8609 Evaluate side-chains 262 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 443 ARG Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 1001 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1315 THR Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1627 ASP Chi-restraints excluded: chain A residue 1703 TYR Chi-restraints excluded: chain A residue 1757 MET Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1792 TRP Chi-restraints excluded: chain A residue 2237 MET Chi-restraints excluded: chain A residue 2248 ILE Chi-restraints excluded: chain A residue 2257 TYR Chi-restraints excluded: chain A residue 2462 SER Chi-restraints excluded: chain A residue 2481 GLU Chi-restraints excluded: chain A residue 2522 SER Chi-restraints excluded: chain A residue 2531 THR Chi-restraints excluded: chain A residue 2559 ASP Chi-restraints excluded: chain A residue 2613 GLU Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2668 ASP Chi-restraints excluded: chain A residue 2753 THR Chi-restraints excluded: chain A residue 2793 LEU Chi-restraints excluded: chain A residue 2820 CYS Chi-restraints excluded: chain A residue 2925 TYR Chi-restraints excluded: chain A residue 3048 TYR Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3165 TYR Chi-restraints excluded: chain A residue 3235 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN A 631 ASN A 770 ASN A 783 ASN A 810 GLN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1785 ASN A1862 ASN ** A3159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.128560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095265 restraints weight = 175523.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.099155 restraints weight = 84250.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.101641 restraints weight = 54091.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.103158 restraints weight = 41349.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.103982 restraints weight = 35133.940| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22087 Z= 0.190 Angle : 0.635 6.813 29905 Z= 0.349 Chirality : 0.039 0.166 3464 Planarity : 0.005 0.061 3777 Dihedral : 6.750 57.961 2995 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.55 % Favored : 83.27 % Rotamer: Outliers : 2.52 % Allowed : 18.89 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -2.49 (0.16), residues: 2689 helix: -0.34 (0.13), residues: 1453 sheet: -5.59 (0.61), residues: 9 loop : -3.38 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 11 TYR 0.026 0.002 TYR A 25 PHE 0.018 0.001 PHE A3120 TRP 0.008 0.001 TRP A1196 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00403 (22087) covalent geometry : angle 0.63545 (29905) hydrogen bonds : bond 0.07041 ( 882) hydrogen bonds : angle 6.34681 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 2 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 339 is missing expected H atoms. Skipping. Residue LYS 935 is missing expected H atoms. Skipping. Residue LYS 1033 is missing expected H atoms. Skipping. Residue SER 1035 is missing expected H atoms. Skipping. Residue SER 1038 is missing expected H atoms. Skipping. Residue LYS 1357 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue LEU 1415 is missing expected H atoms. Skipping. Residue LEU 1416 is missing expected H atoms. Skipping. Residue LYS 1586 is missing expected H atoms. Skipping. Residue LEU 1589 is missing expected H atoms. Skipping. Residue LYS 1594 is missing expected H atoms. Skipping. Residue LYS 1603 is missing expected H atoms. Skipping. Residue LYS 1642 is missing expected H atoms. Skipping. Residue THR 1712 is missing expected H atoms. Skipping. Residue LYS 2764 is missing expected H atoms. Skipping. Residue THR 2804 is missing expected H atoms. Skipping. Residue LYS 2910 is missing expected H atoms. Skipping. Residue LEU 2911 is missing expected H atoms. Skipping. Residue THR 2944 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue TYR 3075 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 234 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.6803 (m-80) REVERT: A 147 GLU cc_start: 0.7996 (tp30) cc_final: 0.7769 (tp30) REVERT: A 148 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7497 (tmt170) REVERT: A 169 LYS cc_start: 0.7073 (ptmt) cc_final: 0.6416 (tptt) REVERT: A 241 MET cc_start: 0.6873 (mpp) cc_final: 0.6376 (mpp) REVERT: A 555 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7782 (tt) REVERT: A 867 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7461 (tpt-90) REVERT: A 954 MET cc_start: 0.7554 (tpp) cc_final: 0.7235 (tpt) REVERT: A 970 ARG cc_start: 0.6886 (mtt180) cc_final: 0.6460 (mtt180) REVERT: A 1167 TYR cc_start: 0.8053 (p90) cc_final: 0.7850 (p90) REVERT: A 1319 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7896 (pp20) REVERT: A 1423 MET cc_start: 0.8406 (mmm) cc_final: 0.8056 (mmm) REVERT: A 1441 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7279 (tt) REVERT: A 1493 ASP cc_start: 0.7157 (p0) cc_final: 0.6774 (p0) REVERT: A 1703 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7628 (t80) REVERT: A 1806 TYR cc_start: 0.7160 (m-80) cc_final: 0.6799 (m-10) REVERT: A 2659 MET cc_start: 0.8492 (tmm) cc_final: 0.8263 (tmm) REVERT: A 3041 MET cc_start: 0.8317 (mmp) cc_final: 0.8111 (mmp) REVERT: A 3106 GLU cc_start: 0.8445 (tp30) cc_final: 0.7901 (tp30) REVERT: A 3207 GLU cc_start: 0.7666 (tt0) cc_final: 0.7392 (tt0) REVERT: A 3256 LEU cc_start: 0.9676 (tt) cc_final: 0.9407 (mt) outliers start: 61 outliers final: 37 residues processed: 280 average time/residue: 0.3255 time to fit residues: 147.3223 Evaluate side-chains 261 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 631 ASN Chi-restraints excluded: chain A residue 635 PHE Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 985 HIS Chi-restraints excluded: chain A residue 1001 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1147 MET Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1319 GLU Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1528 PHE Chi-restraints excluded: chain A residue 1627 ASP Chi-restraints excluded: chain A residue 1703 TYR Chi-restraints excluded: chain A residue 1792 TRP Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 2248 ILE Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2257 TYR Chi-restraints excluded: chain A residue 2568 LEU Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2663 SER Chi-restraints excluded: chain A residue 2718 SER Chi-restraints excluded: chain A residue 2793 LEU Chi-restraints excluded: chain A residue 2815 SER Chi-restraints excluded: chain A residue 2925 TYR Chi-restraints excluded: chain A residue 3165 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 233 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 268 optimal weight: 5.9990 chunk 243 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 631 ASN A 770 ASN ** A 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1846 ASN ** A3159 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 = 0.4005 r_free = 0.4005 target = 0.129714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096325 restraints weight = 174418.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.100259 restraints weight = 83354.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.102775 restraints weight = 53232.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.104321 restraints weight = 40396.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.105253 restraints weight = 34166.309| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22087 Z= 0.157 Angle : 0.596 7.688 29905 Z= 0.324 Chirality : 0.037 0.162 3464 Planarity : 0.005 0.061 3777 Dihedral : 6.241 58.301 2960 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.10 % Favored : 83.71 % Rotamer: Outliers : 2.48 % Allowed : 19.59 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -2.33 (0.16), residues: 2689 helix: -0.22 (0.14), residues: 1449 sheet: -5.49 (0.63), residues: 9 loop : -3.29 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 37 TYR 0.036 0.001 TYR A 25 PHE 0.016 0.001 PHE A 635 TRP 0.009 0.001 TRP A1196 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00335 (22087) covalent geometry : angle 0.59638 (29905) hydrogen bonds : bond 0.06185 ( 882) hydrogen bonds : angle 5.95020 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 2 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 339 is missing expected H atoms. Skipping. Residue LYS 935 is missing expected H atoms. Skipping. Residue LYS 1033 is missing expected H atoms. Skipping. Residue SER 1035 is missing expected H atoms. Skipping. Residue SER 1038 is missing expected H atoms. Skipping. Residue LYS 1357 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue LEU 1415 is missing expected H atoms. Skipping. Residue LEU 1416 is missing expected H atoms. Skipping. Residue LYS 1586 is missing expected H atoms. Skipping. Residue LEU 1589 is missing expected H atoms. Skipping. Residue LYS 1594 is missing expected H atoms. Skipping. Residue LYS 1603 is missing expected H atoms. Skipping. Residue LYS 1642 is missing expected H atoms. Skipping. Residue THR 1712 is missing expected H atoms. Skipping. Residue LYS 2764 is missing expected H atoms. Skipping. Residue THR 2804 is missing expected H atoms. Skipping. Residue LYS 2910 is missing expected H atoms. Skipping. Residue LEU 2911 is missing expected H atoms. Skipping. Residue THR 2944 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue TYR 3075 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 232 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.6778 (m-80) REVERT: A 147 GLU cc_start: 0.8027 (tp30) cc_final: 0.7739 (tp30) REVERT: A 148 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7334 (tmt170) REVERT: A 169 LYS cc_start: 0.7054 (ptmt) cc_final: 0.6405 (tptt) REVERT: A 241 MET cc_start: 0.6802 (mpp) cc_final: 0.6512 (mpp) REVERT: A 555 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7742 (tt) REVERT: A 867 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7389 (tpt-90) REVERT: A 930 TYR cc_start: 0.7702 (m-80) cc_final: 0.7235 (m-80) REVERT: A 954 MET cc_start: 0.7638 (tpp) cc_final: 0.7296 (tpt) REVERT: A 970 ARG cc_start: 0.6795 (mtt180) cc_final: 0.6473 (mtt180) REVERT: A 1319 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7836 (pp20) REVERT: A 1423 MET cc_start: 0.8399 (mmm) cc_final: 0.8042 (mmm) REVERT: A 1441 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7253 (tt) REVERT: A 1703 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.7125 (m-80) REVERT: A 1806 TYR cc_start: 0.7230 (m-80) cc_final: 0.6856 (m-10) REVERT: A 2541 CYS cc_start: 0.6177 (OUTLIER) cc_final: 0.5903 (m) REVERT: A 2659 MET cc_start: 0.8466 (tmm) cc_final: 0.7866 (tmm) REVERT: A 3106 GLU cc_start: 0.8417 (tp30) cc_final: 0.7817 (tp30) REVERT: A 3207 GLU cc_start: 0.7655 (tt0) cc_final: 0.7379 (tt0) outliers start: 60 outliers final: 42 residues processed: 279 average time/residue: 0.3197 time to fit residues: 143.9926 Evaluate side-chains 271 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 400 TYR Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 635 PHE Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 985 HIS Chi-restraints excluded: chain A residue 1001 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1147 MET Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1292 ILE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1319 GLU Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1528 PHE Chi-restraints excluded: chain A residue 1627 ASP Chi-restraints excluded: chain A residue 1703 TYR Chi-restraints excluded: chain A residue 1792 TRP Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1824 CYS Chi-restraints excluded: chain A residue 1846 ASN Chi-restraints excluded: chain A residue 2237 MET Chi-restraints excluded: chain A residue 2248 ILE Chi-restraints excluded: chain A residue 2257 TYR Chi-restraints excluded: chain A residue 2462 SER Chi-restraints excluded: chain A residue 2541 CYS Chi-restraints excluded: chain A residue 2568 LEU Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2718 SER Chi-restraints excluded: chain A residue 2793 LEU Chi-restraints excluded: chain A residue 2815 SER Chi-restraints excluded: chain A residue 2925 TYR Chi-restraints excluded: chain A residue 3165 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 74 optimal weight: 0.0570 chunk 179 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 198 optimal weight: 0.8980 chunk 235 optimal weight: 9.9990 chunk 174 optimal weight: 0.8980 chunk 221 optimal weight: 0.1980 chunk 101 optimal weight: 0.0070 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 770 ASN A 808 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1435 GLN A2511 GLN ** A3159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.130673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.097681 restraints weight = 172717.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.101725 restraints weight = 80605.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.104258 restraints weight = 50893.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.105859 restraints weight = 38448.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.106821 restraints weight = 32557.838| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 22087 Z= 0.120 Angle : 0.569 6.875 29905 Z= 0.303 Chirality : 0.037 0.149 3464 Planarity : 0.004 0.061 3777 Dihedral : 6.137 58.232 2960 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.80 % Favored : 85.01 % Rotamer: Outliers : 2.36 % Allowed : 19.80 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -2.01 (0.16), residues: 2689 helix: 0.07 (0.14), residues: 1453 sheet: -5.64 (0.64), residues: 9 loop : -3.18 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.036 0.001 TYR A 25 PHE 0.021 0.001 PHE A 635 TRP 0.010 0.001 TRP A1196 HIS 0.006 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00253 (22087) covalent geometry : angle 0.56867 (29905) hydrogen bonds : bond 0.05201 ( 882) hydrogen bonds : angle 5.38320 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 2 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 339 is missing expected H atoms. Skipping. Residue LYS 935 is missing expected H atoms. Skipping. Residue LYS 1033 is missing expected H atoms. Skipping. Residue SER 1035 is missing expected H atoms. Skipping. Residue SER 1038 is missing expected H atoms. Skipping. Residue LYS 1357 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue LEU 1415 is missing expected H atoms. Skipping. Residue LEU 1416 is missing expected H atoms. Skipping. Residue LYS 1586 is missing expected H atoms. Skipping. Residue LEU 1589 is missing expected H atoms. Skipping. Residue LYS 1594 is missing expected H atoms. Skipping. Residue LYS 1603 is missing expected H atoms. Skipping. Residue LYS 1642 is missing expected H atoms. Skipping. Residue THR 1712 is missing expected H atoms. Skipping. Residue LYS 2764 is missing expected H atoms. Skipping. Residue THR 2804 is missing expected H atoms. Skipping. Residue LYS 2910 is missing expected H atoms. Skipping. Residue LEU 2911 is missing expected H atoms. Skipping. Residue THR 2944 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue TYR 3075 is missing expected H atoms. Skipping. Evaluate side-chains 307 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 250 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.6789 (m-80) REVERT: A 147 GLU cc_start: 0.7900 (tp30) cc_final: 0.7562 (tp30) REVERT: A 148 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.7110 (tmt170) REVERT: A 169 LYS cc_start: 0.7020 (ptmt) cc_final: 0.6382 (tptt) REVERT: A 241 MET cc_start: 0.6685 (mpp) cc_final: 0.6460 (mpp) REVERT: A 555 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7634 (tt) REVERT: A 608 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7926 (t0) REVERT: A 860 LEU cc_start: 0.6576 (tt) cc_final: 0.5584 (mt) REVERT: A 867 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7220 (tpt-90) REVERT: A 930 TYR cc_start: 0.7983 (m-80) cc_final: 0.7529 (m-10) REVERT: A 954 MET cc_start: 0.7667 (tpp) cc_final: 0.7319 (tpt) REVERT: A 1086 ASP cc_start: 0.8325 (p0) cc_final: 0.8098 (p0) REVERT: A 1319 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7808 (pp20) REVERT: A 1423 MET cc_start: 0.8341 (mmm) cc_final: 0.8001 (mmm) REVERT: A 1441 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7280 (tt) REVERT: A 1493 ASP cc_start: 0.6361 (p0) cc_final: 0.6058 (p0) REVERT: A 1703 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.7155 (m-80) REVERT: A 1806 TYR cc_start: 0.7140 (m-80) cc_final: 0.6744 (m-10) REVERT: A 2479 TYR cc_start: 0.6586 (m-80) cc_final: 0.6190 (m-80) REVERT: A 2659 MET cc_start: 0.8408 (tmm) cc_final: 0.7808 (tmm) REVERT: A 2728 MET cc_start: 0.7002 (mmp) cc_final: 0.6429 (mtt) REVERT: A 3041 MET cc_start: 0.8468 (mmp) cc_final: 0.8079 (mmp) REVERT: A 3106 GLU cc_start: 0.8362 (tp30) cc_final: 0.7790 (tp30) REVERT: A 3146 SER cc_start: 0.7958 (OUTLIER) cc_final: 0.7731 (p) REVERT: A 3207 GLU cc_start: 0.7644 (tt0) cc_final: 0.7429 (tt0) outliers start: 57 outliers final: 36 residues processed: 296 average time/residue: 0.3159 time to fit residues: 150.7992 Evaluate side-chains 277 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 361 TRP Chi-restraints excluded: chain A residue 400 TYR Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1001 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1147 MET Chi-restraints excluded: chain A residue 1172 GLN Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1319 GLU Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1528 PHE Chi-restraints excluded: chain A residue 1703 TYR Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 2248 ILE Chi-restraints excluded: chain A residue 2257 TYR Chi-restraints excluded: chain A residue 2462 SER Chi-restraints excluded: chain A residue 2568 LEU Chi-restraints excluded: chain A residue 2663 SER Chi-restraints excluded: chain A residue 2718 SER Chi-restraints excluded: chain A residue 2790 SER Chi-restraints excluded: chain A residue 2793 LEU Chi-restraints excluded: chain A residue 2925 TYR Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3165 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 116 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 250 optimal weight: 20.0000 chunk 217 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 247 optimal weight: 10.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 770 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.130146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.096687 restraints weight = 174094.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.100600 restraints weight = 83278.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.103129 restraints weight = 53424.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.104676 restraints weight = 40565.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.105513 restraints weight = 34339.425| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22087 Z= 0.156 Angle : 0.584 6.798 29905 Z= 0.315 Chirality : 0.037 0.158 3464 Planarity : 0.004 0.060 3777 Dihedral : 6.030 58.404 2954 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.07 % Favored : 83.75 % Rotamer: Outliers : 2.85 % Allowed : 20.13 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -2.04 (0.16), residues: 2689 helix: 0.05 (0.14), residues: 1458 sheet: -5.56 (0.67), residues: 9 loop : -3.22 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 878 TYR 0.032 0.001 TYR A 25 PHE 0.025 0.001 PHE A 635 TRP 0.009 0.001 TRP A1196 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00337 (22087) covalent geometry : angle 0.58350 (29905) hydrogen bonds : bond 0.05039 ( 882) hydrogen bonds : angle 5.50100 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 2 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 339 is missing expected H atoms. Skipping. Residue LYS 935 is missing expected H atoms. Skipping. Residue LYS 1033 is missing expected H atoms. Skipping. Residue SER 1035 is missing expected H atoms. Skipping. Residue SER 1038 is missing expected H atoms. Skipping. Residue LYS 1357 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue LEU 1415 is missing expected H atoms. Skipping. Residue LEU 1416 is missing expected H atoms. Skipping. Residue LYS 1586 is missing expected H atoms. Skipping. Residue LEU 1589 is missing expected H atoms. Skipping. Residue LYS 1594 is missing expected H atoms. Skipping. Residue LYS 1603 is missing expected H atoms. Skipping. Residue LYS 1642 is missing expected H atoms. Skipping. Residue THR 1712 is missing expected H atoms. Skipping. Residue LYS 2764 is missing expected H atoms. Skipping. Residue THR 2804 is missing expected H atoms. Skipping. Residue LYS 2910 is missing expected H atoms. Skipping. Residue LEU 2911 is missing expected H atoms. Skipping. Residue THR 2944 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue TYR 3075 is missing expected H atoms. Skipping. Evaluate side-chains 301 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 232 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.6858 (m-80) REVERT: A 147 GLU cc_start: 0.7878 (tp30) cc_final: 0.7509 (mm-30) REVERT: A 148 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6922 (tmt170) REVERT: A 169 LYS cc_start: 0.7034 (ptmt) cc_final: 0.6408 (tptt) REVERT: A 508 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: A 555 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7710 (tt) REVERT: A 608 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7979 (t0) REVERT: A 867 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7408 (tpt-90) REVERT: A 930 TYR cc_start: 0.8000 (m-80) cc_final: 0.7627 (m-10) REVERT: A 954 MET cc_start: 0.7885 (tpp) cc_final: 0.7438 (tpt) REVERT: A 1319 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7817 (pp20) REVERT: A 1441 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7250 (tt) REVERT: A 2541 CYS cc_start: 0.6147 (OUTLIER) cc_final: 0.5825 (m) REVERT: A 2659 MET cc_start: 0.8447 (tmm) cc_final: 0.7835 (tmm) REVERT: A 3041 MET cc_start: 0.8477 (mmp) cc_final: 0.8052 (mmp) REVERT: A 3106 GLU cc_start: 0.8254 (tp30) cc_final: 0.7922 (mm-30) REVERT: A 3207 GLU cc_start: 0.7694 (tt0) cc_final: 0.7471 (tt0) outliers start: 69 outliers final: 46 residues processed: 290 average time/residue: 0.3037 time to fit residues: 142.1814 Evaluate side-chains 281 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 226 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 400 TYR Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 635 PHE Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1001 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1104 TYR Chi-restraints excluded: chain A residue 1147 MET Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1319 GLU Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1528 PHE Chi-restraints excluded: chain A residue 1627 ASP Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1824 CYS Chi-restraints excluded: chain A residue 2237 MET Chi-restraints excluded: chain A residue 2248 ILE Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2257 TYR Chi-restraints excluded: chain A residue 2462 SER Chi-restraints excluded: chain A residue 2541 CYS Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2663 SER Chi-restraints excluded: chain A residue 2718 SER Chi-restraints excluded: chain A residue 2790 SER Chi-restraints excluded: chain A residue 2793 LEU Chi-restraints excluded: chain A residue 2815 SER Chi-restraints excluded: chain A residue 2925 TYR Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3165 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 182 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 165 optimal weight: 0.0670 chunk 4 optimal weight: 0.0060 chunk 187 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 overall best weight: 1.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 770 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.128806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.095693 restraints weight = 174081.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.099676 restraints weight = 81698.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.102261 restraints weight = 51680.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.103766 restraints weight = 38958.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.104729 restraints weight = 33010.446| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22087 Z= 0.134 Angle : 0.572 7.804 29905 Z= 0.307 Chirality : 0.037 0.155 3464 Planarity : 0.004 0.060 3777 Dihedral : 5.916 58.370 2951 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.69 % Favored : 84.12 % Rotamer: Outliers : 2.85 % Allowed : 20.26 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -1.96 (0.16), residues: 2689 helix: 0.14 (0.14), residues: 1464 sheet: -5.55 (0.66), residues: 9 loop : -3.24 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 878 TYR 0.030 0.001 TYR A 25 PHE 0.023 0.001 PHE A 635 TRP 0.009 0.001 TRP A1196 HIS 0.006 0.001 HIS A1786 Details of bonding type rmsd covalent geometry : bond 0.00292 (22087) covalent geometry : angle 0.57154 (29905) hydrogen bonds : bond 0.04720 ( 882) hydrogen bonds : angle 5.30560 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 2 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 339 is missing expected H atoms. Skipping. Residue LYS 935 is missing expected H atoms. Skipping. Residue LYS 1033 is missing expected H atoms. Skipping. Residue SER 1035 is missing expected H atoms. Skipping. Residue SER 1038 is missing expected H atoms. Skipping. Residue LYS 1357 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue LEU 1415 is missing expected H atoms. Skipping. Residue LEU 1416 is missing expected H atoms. Skipping. Residue LYS 1586 is missing expected H atoms. Skipping. Residue LEU 1589 is missing expected H atoms. Skipping. Residue LYS 1594 is missing expected H atoms. Skipping. Residue LYS 1603 is missing expected H atoms. Skipping. Residue LYS 1642 is missing expected H atoms. Skipping. Residue THR 1712 is missing expected H atoms. Skipping. Residue LYS 2764 is missing expected H atoms. Skipping. Residue THR 2804 is missing expected H atoms. Skipping. Residue LYS 2910 is missing expected H atoms. Skipping. Residue LEU 2911 is missing expected H atoms. Skipping. Residue THR 2944 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue TYR 3075 is missing expected H atoms. Skipping. Evaluate side-chains 304 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 235 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.6863 (m-80) REVERT: A 147 GLU cc_start: 0.7886 (tp30) cc_final: 0.7385 (mm-30) REVERT: A 148 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6899 (tmt170) REVERT: A 169 LYS cc_start: 0.7005 (ptmt) cc_final: 0.6382 (tptt) REVERT: A 508 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7918 (mt-10) REVERT: A 555 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7701 (tt) REVERT: A 608 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7976 (t0) REVERT: A 867 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7378 (tpt-90) REVERT: A 930 TYR cc_start: 0.8002 (m-80) cc_final: 0.7584 (m-10) REVERT: A 954 MET cc_start: 0.8055 (tpp) cc_final: 0.7581 (tpt) REVERT: A 1319 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7806 (pp20) REVERT: A 1441 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7330 (tt) REVERT: A 1687 TYR cc_start: 0.8127 (m-80) cc_final: 0.7484 (m-80) REVERT: A 2479 TYR cc_start: 0.6700 (m-80) cc_final: 0.6333 (m-80) REVERT: A 2541 CYS cc_start: 0.6080 (OUTLIER) cc_final: 0.5756 (m) REVERT: A 2659 MET cc_start: 0.8394 (tmm) cc_final: 0.7782 (tmm) REVERT: A 3041 MET cc_start: 0.8484 (mmp) cc_final: 0.8032 (mmp) REVERT: A 3106 GLU cc_start: 0.8258 (tp30) cc_final: 0.7880 (mm-30) REVERT: A 3207 GLU cc_start: 0.7703 (tt0) cc_final: 0.7480 (tt0) outliers start: 69 outliers final: 52 residues processed: 291 average time/residue: 0.3052 time to fit residues: 143.6395 Evaluate side-chains 293 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 232 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 361 TRP Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 400 TYR Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1001 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1104 TYR Chi-restraints excluded: chain A residue 1147 MET Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1319 GLU Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1528 PHE Chi-restraints excluded: chain A residue 1627 ASP Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 2237 MET Chi-restraints excluded: chain A residue 2248 ILE Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2257 TYR Chi-restraints excluded: chain A residue 2462 SER Chi-restraints excluded: chain A residue 2541 CYS Chi-restraints excluded: chain A residue 2638 SER Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2663 SER Chi-restraints excluded: chain A residue 2718 SER Chi-restraints excluded: chain A residue 2724 ILE Chi-restraints excluded: chain A residue 2790 SER Chi-restraints excluded: chain A residue 2793 LEU Chi-restraints excluded: chain A residue 2815 SER Chi-restraints excluded: chain A residue 2925 TYR Chi-restraints excluded: chain A residue 3007 MET Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3165 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 128 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 262 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 770 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN ** A3159 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 = 0.3983 r_free = 0.3983 target = 0.128006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094855 restraints weight = 173324.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.098806 restraints weight = 82250.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.101317 restraints weight = 52288.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.102853 restraints weight = 39610.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.103619 restraints weight = 33522.363| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 22087 Z= 0.167 Angle : 0.588 7.589 29905 Z= 0.317 Chirality : 0.037 0.164 3464 Planarity : 0.004 0.059 3777 Dihedral : 5.959 58.410 2951 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.25 % Favored : 83.56 % Rotamer: Outliers : 3.02 % Allowed : 20.79 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -2.04 (0.16), residues: 2689 helix: 0.08 (0.14), residues: 1466 sheet: -5.57 (0.66), residues: 9 loop : -3.28 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 37 TYR 0.022 0.001 TYR A 25 PHE 0.029 0.001 PHE A 635 TRP 0.009 0.001 TRP A1196 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00368 (22087) covalent geometry : angle 0.58753 (29905) hydrogen bonds : bond 0.04710 ( 882) hydrogen bonds : angle 5.40391 ( 2571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 2 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 339 is missing expected H atoms. Skipping. Residue LYS 935 is missing expected H atoms. Skipping. Residue LYS 1033 is missing expected H atoms. Skipping. Residue SER 1035 is missing expected H atoms. Skipping. Residue SER 1038 is missing expected H atoms. Skipping. Residue LYS 1357 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue LEU 1415 is missing expected H atoms. Skipping. Residue LEU 1416 is missing expected H atoms. Skipping. Residue LYS 1586 is missing expected H atoms. Skipping. Residue LEU 1589 is missing expected H atoms. Skipping. Residue LYS 1594 is missing expected H atoms. Skipping. Residue LYS 1603 is missing expected H atoms. Skipping. Residue LYS 1642 is missing expected H atoms. Skipping. Residue THR 1712 is missing expected H atoms. Skipping. Residue LYS 2764 is missing expected H atoms. Skipping. Residue THR 2804 is missing expected H atoms. Skipping. Residue LYS 2910 is missing expected H atoms. Skipping. Residue LEU 2911 is missing expected H atoms. Skipping. Residue THR 2944 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue TYR 3075 is missing expected H atoms. Skipping. Evaluate side-chains 300 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 227 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.6898 (m-80) REVERT: A 147 GLU cc_start: 0.7952 (tp30) cc_final: 0.7219 (mm-30) REVERT: A 148 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6926 (tmt170) REVERT: A 169 LYS cc_start: 0.7009 (ptmt) cc_final: 0.6386 (tptt) REVERT: A 508 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: A 555 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7761 (tt) REVERT: A 608 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7994 (t0) REVERT: A 867 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7465 (tpt-90) REVERT: A 930 TYR cc_start: 0.8055 (m-80) cc_final: 0.7654 (m-10) REVERT: A 954 MET cc_start: 0.7966 (tpp) cc_final: 0.7466 (tpt) REVERT: A 1319 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7820 (pp20) REVERT: A 1441 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7355 (tt) REVERT: A 1666 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: A 1687 TYR cc_start: 0.8170 (m-80) cc_final: 0.7538 (m-80) REVERT: A 2541 CYS cc_start: 0.6127 (OUTLIER) cc_final: 0.5801 (m) REVERT: A 2659 MET cc_start: 0.8448 (tmm) cc_final: 0.7840 (tmm) REVERT: A 3041 MET cc_start: 0.8507 (mmp) cc_final: 0.8052 (mmp) REVERT: A 3106 GLU cc_start: 0.8119 (tp30) cc_final: 0.7664 (mm-30) REVERT: A 3207 GLU cc_start: 0.7711 (tt0) cc_final: 0.7492 (tt0) outliers start: 73 outliers final: 57 residues processed: 287 average time/residue: 0.2967 time to fit residues: 138.0480 Evaluate side-chains 292 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 225 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 TRP Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 400 TYR Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1001 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1104 TYR Chi-restraints excluded: chain A residue 1147 MET Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1172 GLN Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1271 CYS Chi-restraints excluded: chain A residue 1292 ILE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1319 GLU Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1528 PHE Chi-restraints excluded: chain A residue 1627 ASP Chi-restraints excluded: chain A residue 1666 GLU Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1824 CYS Chi-restraints excluded: chain A residue 2237 MET Chi-restraints excluded: chain A residue 2248 ILE Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2257 TYR Chi-restraints excluded: chain A residue 2462 SER Chi-restraints excluded: chain A residue 2541 CYS Chi-restraints excluded: chain A residue 2638 SER Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2663 SER Chi-restraints excluded: chain A residue 2718 SER Chi-restraints excluded: chain A residue 2790 SER Chi-restraints excluded: chain A residue 2793 LEU Chi-restraints excluded: chain A residue 2815 SER Chi-restraints excluded: chain A residue 2925 TYR Chi-restraints excluded: chain A residue 3007 MET Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3165 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 242 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 770 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN ** A3030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.128784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.095202 restraints weight = 174158.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.099141 restraints weight = 84082.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.101631 restraints weight = 54063.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.103008 restraints weight = 41339.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.104077 restraints weight = 35430.645| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22087 Z= 0.136 Angle : 0.570 8.245 29905 Z= 0.306 Chirality : 0.037 0.156 3464 Planarity : 0.004 0.060 3777 Dihedral : 5.922 58.321 2951 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.73 % Favored : 84.12 % Rotamer: Outliers : 2.94 % Allowed : 21.04 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -1.95 (0.16), residues: 2689 helix: 0.16 (0.14), residues: 1469 sheet: -5.52 (0.68), residues: 9 loop : -3.26 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 37 TYR 0.027 0.001 TYR A 25 PHE 0.024 0.001 PHE A 635 TRP 0.009 0.001 TRP A1196 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00299 (22087) covalent geometry : angle 0.57037 (29905) hydrogen bonds : bond 0.04472 ( 882) hydrogen bonds : angle 5.21398 ( 2571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 2 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 339 is missing expected H atoms. Skipping. Residue LYS 935 is missing expected H atoms. Skipping. Residue LYS 1033 is missing expected H atoms. Skipping. Residue SER 1035 is missing expected H atoms. Skipping. Residue SER 1038 is missing expected H atoms. Skipping. Residue LYS 1357 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue LEU 1415 is missing expected H atoms. Skipping. Residue LEU 1416 is missing expected H atoms. Skipping. Residue LYS 1586 is missing expected H atoms. Skipping. Residue LEU 1589 is missing expected H atoms. Skipping. Residue LYS 1594 is missing expected H atoms. Skipping. Residue LYS 1603 is missing expected H atoms. Skipping. Residue LYS 1642 is missing expected H atoms. Skipping. Residue THR 1712 is missing expected H atoms. Skipping. Residue LYS 2764 is missing expected H atoms. Skipping. Residue THR 2804 is missing expected H atoms. Skipping. Residue LYS 2910 is missing expected H atoms. Skipping. Residue LEU 2911 is missing expected H atoms. Skipping. Residue THR 2944 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue TYR 3075 is missing expected H atoms. Skipping. Evaluate side-chains 307 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 236 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: A 147 GLU cc_start: 0.7835 (tp30) cc_final: 0.7094 (mm-30) REVERT: A 148 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6892 (tmt170) REVERT: A 169 LYS cc_start: 0.7109 (ptmt) cc_final: 0.6470 (tptt) REVERT: A 508 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: A 555 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7698 (tt) REVERT: A 608 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7935 (t0) REVERT: A 867 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7347 (tpt-90) REVERT: A 930 TYR cc_start: 0.7991 (m-80) cc_final: 0.7656 (m-10) REVERT: A 954 MET cc_start: 0.7816 (tpp) cc_final: 0.7339 (tpt) REVERT: A 970 ARG cc_start: 0.6185 (mtt180) cc_final: 0.5934 (mtt180) REVERT: A 1319 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7906 (pp20) REVERT: A 1441 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7295 (tt) REVERT: A 1687 TYR cc_start: 0.8016 (m-80) cc_final: 0.7393 (m-80) REVERT: A 2541 CYS cc_start: 0.6062 (OUTLIER) cc_final: 0.5760 (m) REVERT: A 2659 MET cc_start: 0.8548 (tmm) cc_final: 0.7945 (tmm) REVERT: A 3041 MET cc_start: 0.8397 (mmp) cc_final: 0.7895 (mmp) REVERT: A 3106 GLU cc_start: 0.8114 (tp30) cc_final: 0.7658 (mm-30) outliers start: 71 outliers final: 55 residues processed: 295 average time/residue: 0.2635 time to fit residues: 127.0035 Evaluate side-chains 294 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 230 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 400 TYR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1001 ASN Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1104 TYR Chi-restraints excluded: chain A residue 1147 MET Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1172 GLN Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1271 CYS Chi-restraints excluded: chain A residue 1292 ILE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1319 GLU Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1528 PHE Chi-restraints excluded: chain A residue 1627 ASP Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1824 CYS Chi-restraints excluded: chain A residue 2237 MET Chi-restraints excluded: chain A residue 2248 ILE Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2257 TYR Chi-restraints excluded: chain A residue 2462 SER Chi-restraints excluded: chain A residue 2541 CYS Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2663 SER Chi-restraints excluded: chain A residue 2718 SER Chi-restraints excluded: chain A residue 2724 ILE Chi-restraints excluded: chain A residue 2790 SER Chi-restraints excluded: chain A residue 2793 LEU Chi-restraints excluded: chain A residue 2815 SER Chi-restraints excluded: chain A residue 2925 TYR Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3165 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 245 optimal weight: 0.9990 chunk 117 optimal weight: 0.0970 chunk 99 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 770 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.129707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096210 restraints weight = 173045.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.100199 restraints weight = 82952.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.102724 restraints weight = 53076.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.104273 restraints weight = 40443.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.105146 restraints weight = 34274.724| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22087 Z= 0.112 Angle : 0.561 8.701 29905 Z= 0.297 Chirality : 0.036 0.150 3464 Planarity : 0.004 0.060 3777 Dihedral : 5.850 58.075 2951 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.58 % Favored : 85.27 % Rotamer: Outliers : 2.69 % Allowed : 21.66 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -1.73 (0.17), residues: 2689 helix: 0.39 (0.14), residues: 1462 sheet: -5.52 (0.66), residues: 9 loop : -3.20 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 37 TYR 0.025 0.001 TYR A 25 PHE 0.035 0.001 PHE A 635 TRP 0.009 0.001 TRP A1196 HIS 0.008 0.001 HIS A1786 Details of bonding type rmsd covalent geometry : bond 0.00248 (22087) covalent geometry : angle 0.56137 (29905) hydrogen bonds : bond 0.04171 ( 882) hydrogen bonds : angle 4.95335 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 2 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 339 is missing expected H atoms. Skipping. Residue LYS 935 is missing expected H atoms. Skipping. Residue LYS 1033 is missing expected H atoms. Skipping. Residue SER 1035 is missing expected H atoms. Skipping. Residue SER 1038 is missing expected H atoms. Skipping. Residue LYS 1357 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue LEU 1415 is missing expected H atoms. Skipping. Residue LEU 1416 is missing expected H atoms. Skipping. Residue LYS 1586 is missing expected H atoms. Skipping. Residue LEU 1589 is missing expected H atoms. Skipping. Residue LYS 1594 is missing expected H atoms. Skipping. Residue LYS 1603 is missing expected H atoms. Skipping. Residue LYS 1642 is missing expected H atoms. Skipping. Residue THR 1712 is missing expected H atoms. Skipping. Residue LYS 2764 is missing expected H atoms. Skipping. Residue THR 2804 is missing expected H atoms. Skipping. Residue LYS 2910 is missing expected H atoms. Skipping. Residue LEU 2911 is missing expected H atoms. Skipping. Residue THR 2944 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue TYR 3075 is missing expected H atoms. Skipping. Evaluate side-chains 307 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 242 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.6686 (m-80) REVERT: A 147 GLU cc_start: 0.7792 (tp30) cc_final: 0.7150 (mm-30) REVERT: A 148 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6711 (tmt170) REVERT: A 169 LYS cc_start: 0.7063 (ptmt) cc_final: 0.6436 (tptt) REVERT: A 508 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: A 555 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7654 (tt) REVERT: A 608 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7844 (t0) REVERT: A 867 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7390 (tpt-90) REVERT: A 930 TYR cc_start: 0.8025 (m-80) cc_final: 0.7623 (m-10) REVERT: A 954 MET cc_start: 0.7835 (tpp) cc_final: 0.7352 (tpt) REVERT: A 970 ARG cc_start: 0.6019 (mtt180) cc_final: 0.5699 (mtp180) REVERT: A 1319 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7805 (pp20) REVERT: A 1441 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7433 (tt) REVERT: A 1687 TYR cc_start: 0.7899 (m-80) cc_final: 0.7414 (m-80) REVERT: A 2541 CYS cc_start: 0.5992 (OUTLIER) cc_final: 0.5676 (m) REVERT: A 2659 MET cc_start: 0.8519 (tmm) cc_final: 0.7874 (tmm) REVERT: A 3041 MET cc_start: 0.8407 (mmp) cc_final: 0.7900 (mmp) REVERT: A 3106 GLU cc_start: 0.8408 (tp30) cc_final: 0.8094 (mm-30) REVERT: A 3146 SER cc_start: 0.7944 (OUTLIER) cc_final: 0.7730 (p) outliers start: 65 outliers final: 49 residues processed: 294 average time/residue: 0.2693 time to fit residues: 128.6595 Evaluate side-chains 290 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 231 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 361 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1001 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1104 TYR Chi-restraints excluded: chain A residue 1147 MET Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1172 GLN Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1271 CYS Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1319 GLU Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1528 PHE Chi-restraints excluded: chain A residue 1627 ASP Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1824 CYS Chi-restraints excluded: chain A residue 2248 ILE Chi-restraints excluded: chain A residue 2257 TYR Chi-restraints excluded: chain A residue 2462 SER Chi-restraints excluded: chain A residue 2541 CYS Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2663 SER Chi-restraints excluded: chain A residue 2718 SER Chi-restraints excluded: chain A residue 2790 SER Chi-restraints excluded: chain A residue 2793 LEU Chi-restraints excluded: chain A residue 2925 TYR Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3165 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 8 optimal weight: 9.9990 chunk 133 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 264 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 770 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.129858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.096684 restraints weight = 172652.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.100704 restraints weight = 80718.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.103272 restraints weight = 51040.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.104818 restraints weight = 38532.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105803 restraints weight = 32551.908| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22087 Z= 0.111 Angle : 0.561 8.399 29905 Z= 0.296 Chirality : 0.036 0.159 3464 Planarity : 0.004 0.064 3777 Dihedral : 5.809 58.086 2951 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.69 % Favored : 85.12 % Rotamer: Outliers : 2.40 % Allowed : 21.99 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -1.66 (0.17), residues: 2689 helix: 0.45 (0.14), residues: 1463 sheet: -5.44 (0.68), residues: 9 loop : -3.19 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 37 TYR 0.021 0.001 TYR A 25 PHE 0.029 0.001 PHE A 635 TRP 0.009 0.001 TRP A1196 HIS 0.007 0.001 HIS A1786 Details of bonding type rmsd covalent geometry : bond 0.00247 (22087) covalent geometry : angle 0.56076 (29905) hydrogen bonds : bond 0.04044 ( 882) hydrogen bonds : angle 4.86480 ( 2571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5378 Ramachandran restraints generated. 2689 Oldfield, 0 Emsley, 2689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 2 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 339 is missing expected H atoms. Skipping. Residue LYS 935 is missing expected H atoms. Skipping. Residue LYS 1033 is missing expected H atoms. Skipping. Residue SER 1035 is missing expected H atoms. Skipping. Residue SER 1038 is missing expected H atoms. Skipping. Residue LYS 1357 is missing expected H atoms. Skipping. Residue LYS 1412 is missing expected H atoms. Skipping. Residue VAL 1414 is missing expected H atoms. Skipping. Residue LEU 1415 is missing expected H atoms. Skipping. Residue LEU 1416 is missing expected H atoms. Skipping. Residue LYS 1586 is missing expected H atoms. Skipping. Residue LEU 1589 is missing expected H atoms. Skipping. Residue LYS 1594 is missing expected H atoms. Skipping. Residue LYS 1603 is missing expected H atoms. Skipping. Residue LYS 1642 is missing expected H atoms. Skipping. Residue THR 1712 is missing expected H atoms. Skipping. Residue LYS 2764 is missing expected H atoms. Skipping. Residue THR 2804 is missing expected H atoms. Skipping. Residue LYS 2910 is missing expected H atoms. Skipping. Residue LEU 2911 is missing expected H atoms. Skipping. Residue THR 2944 is missing expected H atoms. Skipping. Residue VAL 3053 is missing expected H atoms. Skipping. Residue TYR 3075 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 239 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.6760 (m-80) REVERT: A 147 GLU cc_start: 0.7675 (tp30) cc_final: 0.6999 (mm-30) REVERT: A 169 LYS cc_start: 0.7033 (ptmt) cc_final: 0.6382 (tptt) REVERT: A 555 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7666 (tt) REVERT: A 608 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7839 (t0) REVERT: A 867 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7452 (tpt-90) REVERT: A 930 TYR cc_start: 0.8068 (m-80) cc_final: 0.7678 (m-10) REVERT: A 954 MET cc_start: 0.7895 (tpp) cc_final: 0.7404 (tpt) REVERT: A 970 ARG cc_start: 0.6355 (mtt180) cc_final: 0.5993 (mtp180) REVERT: A 1319 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7866 (pp20) REVERT: A 1441 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7438 (tt) REVERT: A 1687 TYR cc_start: 0.7954 (m-80) cc_final: 0.7468 (m-80) REVERT: A 2479 TYR cc_start: 0.6639 (m-80) cc_final: 0.6304 (m-80) REVERT: A 2541 CYS cc_start: 0.5785 (OUTLIER) cc_final: 0.5478 (m) REVERT: A 2659 MET cc_start: 0.8466 (tmm) cc_final: 0.7816 (tmm) REVERT: A 3041 MET cc_start: 0.8412 (mmp) cc_final: 0.7900 (mmp) REVERT: A 3106 GLU cc_start: 0.8407 (tp30) cc_final: 0.8090 (mm-30) REVERT: A 3146 SER cc_start: 0.7916 (OUTLIER) cc_final: 0.7714 (p) outliers start: 58 outliers final: 47 residues processed: 284 average time/residue: 0.2525 time to fit residues: 116.6463 Evaluate side-chains 285 residues out of total 2482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 230 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 361 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1001 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1104 TYR Chi-restraints excluded: chain A residue 1147 MET Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1172 GLN Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1271 CYS Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1319 GLU Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1528 PHE Chi-restraints excluded: chain A residue 1627 ASP Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1824 CYS Chi-restraints excluded: chain A residue 2248 ILE Chi-restraints excluded: chain A residue 2257 TYR Chi-restraints excluded: chain A residue 2462 SER Chi-restraints excluded: chain A residue 2541 CYS Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2663 SER Chi-restraints excluded: chain A residue 2718 SER Chi-restraints excluded: chain A residue 2790 SER Chi-restraints excluded: chain A residue 2793 LEU Chi-restraints excluded: chain A residue 2925 TYR Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3165 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 78 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 220 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 770 ASN A2987 HIS ** A3030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.129267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.095671 restraints weight = 174563.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.099630 restraints weight = 84003.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.102156 restraints weight = 53852.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.103697 restraints weight = 40985.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.104607 restraints weight = 34848.763| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22087 Z= 0.133 Angle : 0.571 8.554 29905 Z= 0.304 Chirality : 0.037 0.380 3464 Planarity : 0.004 0.059 3777 Dihedral : 5.739 58.182 2947 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.25 % Favored : 84.57 % Rotamer: Outliers : 2.48 % Allowed : 22.03 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -1.69 (0.17), residues: 2689 helix: 0.42 (0.14), residues: 1464 sheet: -5.26 (0.71), residues: 9 loop : -3.20 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 37 TYR 0.027 0.001 TYR A 25 PHE 0.028 0.001 PHE A 635 TRP 0.009 0.001 TRP A1196 HIS 0.008 0.001 HIS A1786 Details of bonding type rmsd covalent geometry : bond 0.00293 (22087) covalent geometry : angle 0.57126 (29905) hydrogen bonds : bond 0.04082 ( 882) hydrogen bonds : angle 4.95500 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6373.37 seconds wall clock time: 109 minutes 31.59 seconds (6571.59 seconds total)