Starting phenix.real_space_refine on Sat Jul 20 01:48:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woo_37694/07_2024/8woo_37694_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woo_37694/07_2024/8woo_37694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woo_37694/07_2024/8woo_37694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woo_37694/07_2024/8woo_37694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woo_37694/07_2024/8woo_37694_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woo_37694/07_2024/8woo_37694_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 6007 2.51 5 N 1595 2.21 5 O 1764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9412 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1217, 9314 Classifications: {'peptide': 1217} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 30, 'TRANS': 1186} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 98 Unusual residues: {' MG': 2, 'ANP': 2, 'BLD': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.77, per 1000 atoms: 0.61 Number of scatterers: 9412 At special positions: 0 Unit cell: (73.7, 108.9, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 6 15.00 Mg 2 11.99 O 1764 8.00 N 1595 7.00 C 6007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.7 seconds 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 6 sheets defined 45.9% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 42 through 51 removed outlier: 4.398A pdb=" N ALA A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.511A pdb=" N PHE A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 82 removed outlier: 4.044A pdb=" N VAL A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 Processing helix chain 'A' and resid 93 through 98 Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.862A pdb=" N LYS A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.709A pdb=" N PHE A 135 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 161 through 177 removed outlier: 3.687A pdb=" N HIS A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 184 Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.545A pdb=" N VAL A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 221 removed outlier: 4.213A pdb=" N ALA A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.779A pdb=" N ASP A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 274 removed outlier: 3.764A pdb=" N LYS A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 282 through 289 removed outlier: 3.729A pdb=" N TYR A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.526A pdb=" N ILE A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 316 removed outlier: 3.661A pdb=" N THR A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 342 removed outlier: 3.927A pdb=" N LYS A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.617A pdb=" N ILE A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 414' Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.596A pdb=" N GLU A 474 " --> pdb=" O MET A 470 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 520 removed outlier: 4.012A pdb=" N ARG A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 548 removed outlier: 3.564A pdb=" N ILE A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 604 Processing helix chain 'A' and resid 622 through 632 removed outlier: 3.668A pdb=" N SER A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 680 removed outlier: 3.916A pdb=" N LEU A 677 " --> pdb=" O PHE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 684 through 696 removed outlier: 3.868A pdb=" N GLY A 690 " --> pdb=" O TYR A 686 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY A 693 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 696 " --> pdb=" O VAL A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 709 removed outlier: 3.939A pdb=" N VAL A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 715 Processing helix chain 'A' and resid 741 through 751 removed outlier: 4.761A pdb=" N ILE A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 772 removed outlier: 4.033A pdb=" N LEU A 768 " --> pdb=" O ARG A 764 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 779 Processing helix chain 'A' and resid 781 through 785 removed outlier: 3.792A pdb=" N ASN A 785 " --> pdb=" O ASP A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 824 through 829 removed outlier: 3.812A pdb=" N GLU A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 850 Proline residue: A 841 - end of helix removed outlier: 4.070A pdb=" N LEU A 845 " --> pdb=" O PRO A 841 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 removed outlier: 4.180A pdb=" N ALA A 864 " --> pdb=" O ASP A 860 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 860 through 865' Processing helix chain 'A' and resid 866 through 872 removed outlier: 3.863A pdb=" N MET A 870 " --> pdb=" O ALA A 866 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 871 " --> pdb=" O LYS A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 884 removed outlier: 3.683A pdb=" N VAL A 882 " --> pdb=" O ASN A 878 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 895 removed outlier: 3.660A pdb=" N PHE A 895 " --> pdb=" O LEU A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 905 removed outlier: 3.674A pdb=" N LYS A 904 " --> pdb=" O ARG A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 919 removed outlier: 4.451A pdb=" N PHE A 917 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 918 " --> pdb=" O GLY A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 926 removed outlier: 3.515A pdb=" N TYR A 925 " --> pdb=" O GLN A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 939 removed outlier: 3.661A pdb=" N LEU A 938 " --> pdb=" O TYR A 934 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 939 " --> pdb=" O GLY A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 942 No H-bonds generated for 'chain 'A' and resid 940 through 942' Processing helix chain 'A' and resid 949 through 954 Processing helix chain 'A' and resid 954 through 964 removed outlier: 3.587A pdb=" N ILE A 958 " --> pdb=" O VAL A 954 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER A 962 " --> pdb=" O ILE A 958 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 removed outlier: 4.191A pdb=" N SER A 968 " --> pdb=" O GLU A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 969 through 975 removed outlier: 3.507A pdb=" N ILE A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 removed outlier: 4.088A pdb=" N VAL A1054 " --> pdb=" O LYS A1051 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE A1055 " --> pdb=" O SER A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1079 No H-bonds generated for 'chain 'A' and resid 1077 through 1079' Processing helix chain 'A' and resid 1080 through 1085 Processing helix chain 'A' and resid 1086 through 1088 No H-bonds generated for 'chain 'A' and resid 1086 through 1088' Processing helix chain 'A' and resid 1115 through 1123 removed outlier: 3.979A pdb=" N ILE A1119 " --> pdb=" O GLU A1115 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP A1120 " --> pdb=" O SER A1116 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A1122 " --> pdb=" O VAL A1118 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG A1123 " --> pdb=" O ILE A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1133 Processing helix chain 'A' and resid 1150 through 1166 removed outlier: 3.912A pdb=" N ARG A1156 " --> pdb=" O GLY A1152 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A1157 " --> pdb=" O GLN A1153 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A1159 " --> pdb=" O GLN A1155 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A1160 " --> pdb=" O ARG A1156 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA A1162 " --> pdb=" O ALA A1158 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A1163 " --> pdb=" O ILE A1159 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A1164 " --> pdb=" O ALA A1160 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A1166 " --> pdb=" O ALA A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1247 removed outlier: 3.888A pdb=" N GLN A1246 " --> pdb=" O SER A1242 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A1247 " --> pdb=" O ARG A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1250 No H-bonds generated for 'chain 'A' and resid 1248 through 1250' Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 367 removed outlier: 3.673A pdb=" N GLU A 366 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 425 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 443 through 445 removed outlier: 6.177A pdb=" N GLY A 444 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA A 559 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA A 572 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ALA A 397 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 574 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL A 399 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 573 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 645 through 647 Processing sheet with id=AA4, first strand: chain 'A' and resid 1011 through 1012 removed outlier: 3.553A pdb=" N MET A1070 " --> pdb=" O GLU A1011 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1042 through 1043 Processing sheet with id=AA6, first strand: chain 'A' and resid 1217 through 1220 removed outlier: 7.464A pdb=" N VAL A1218 " --> pdb=" O VAL A1225 " (cutoff:3.500A) 226 hydrogen bonds defined for protein. 627 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: 2.72 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1529 1.31 - 1.44: 2558 1.44 - 1.56: 5424 1.56 - 1.68: 8 1.68 - 1.81: 71 Bond restraints: 9590 Sorted by residual: bond pdb=" C ALA A 126 " pdb=" N VAL A 127 " ideal model delta sigma weight residual 1.334 1.267 0.068 1.25e-02 6.40e+03 2.94e+01 bond pdb=" O3A ANP A1303 " pdb=" PB ANP A1303 " ideal model delta sigma weight residual 1.700 1.592 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" O3A ANP A1304 " pdb=" PB ANP A1304 " ideal model delta sigma weight residual 1.700 1.606 0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C VAL A 127 " pdb=" O VAL A 127 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.13e-02 7.83e+03 1.64e+01 bond pdb=" C4 ANP A1303 " pdb=" C5 ANP A1303 " ideal model delta sigma weight residual 1.387 1.464 -0.077 2.00e-02 2.50e+03 1.50e+01 ... (remaining 9585 not shown) Histogram of bond angle deviations from ideal: 88.12 - 97.75: 3 97.75 - 107.39: 307 107.39 - 117.03: 6244 117.03 - 126.67: 6353 126.67 - 136.31: 95 Bond angle restraints: 13002 Sorted by residual: angle pdb=" N GLN A 130 " pdb=" CA GLN A 130 " pdb=" C GLN A 130 " ideal model delta sigma weight residual 108.42 89.36 19.06 1.54e+00 4.22e-01 1.53e+02 angle pdb=" N GLN A 130 " pdb=" CA GLN A 130 " pdb=" CB GLN A 130 " ideal model delta sigma weight residual 111.56 129.54 -17.98 1.52e+00 4.33e-01 1.40e+02 angle pdb=" N ALA A1125 " pdb=" CA ALA A1125 " pdb=" C ALA A1125 " ideal model delta sigma weight residual 108.20 88.12 20.08 1.71e+00 3.42e-01 1.38e+02 angle pdb=" N TYR A 123 " pdb=" CA TYR A 123 " pdb=" C TYR A 123 " ideal model delta sigma weight residual 111.02 124.97 -13.95 1.22e+00 6.72e-01 1.31e+02 angle pdb=" C LYS A 122 " pdb=" CA LYS A 122 " pdb=" CB LYS A 122 " ideal model delta sigma weight residual 110.90 127.80 -16.90 1.58e+00 4.01e-01 1.14e+02 ... (remaining 12997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.77: 5660 31.77 - 63.55: 96 63.55 - 95.32: 22 95.32 - 127.09: 0 127.09 - 158.87: 2 Dihedral angle restraints: 5780 sinusoidal: 2292 harmonic: 3488 Sorted by residual: dihedral pdb=" C SER A 681 " pdb=" N SER A 681 " pdb=" CA SER A 681 " pdb=" CB SER A 681 " ideal model delta harmonic sigma weight residual -122.60 -162.82 40.22 0 2.50e+00 1.60e-01 2.59e+02 dihedral pdb=" N SER A 681 " pdb=" C SER A 681 " pdb=" CA SER A 681 " pdb=" CB SER A 681 " ideal model delta harmonic sigma weight residual 122.80 159.39 -36.59 0 2.50e+00 1.60e-01 2.14e+02 dihedral pdb=" C LYS A 122 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " pdb=" CB LYS A 122 " ideal model delta harmonic sigma weight residual -122.60 -148.01 25.41 0 2.50e+00 1.60e-01 1.03e+02 ... (remaining 5777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.339: 1491 0.339 - 0.677: 4 0.677 - 1.016: 4 1.016 - 1.355: 0 1.355 - 1.693: 1 Chirality restraints: 1500 Sorted by residual: chirality pdb=" CA SER A 681 " pdb=" N SER A 681 " pdb=" C SER A 681 " pdb=" CB SER A 681 " both_signs ideal model delta sigma weight residual False 2.51 0.82 1.69 2.00e-01 2.50e+01 7.17e+01 chirality pdb=" CA LYS A 122 " pdb=" N LYS A 122 " pdb=" C LYS A 122 " pdb=" CB LYS A 122 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" CA ALA A 118 " pdb=" N ALA A 118 " pdb=" C ALA A 118 " pdb=" CB ALA A 118 " both_signs ideal model delta sigma weight residual False 2.48 1.74 0.74 2.00e-01 2.50e+01 1.39e+01 ... (remaining 1497 not shown) Planarity restraints: 1642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 55 " 0.050 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO A 56 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 56 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 56 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 681 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO A 682 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 682 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 682 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 377 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO A 378 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " -0.036 5.00e-02 4.00e+02 ... (remaining 1639 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 34 2.48 - 3.08: 5810 3.08 - 3.69: 13352 3.69 - 4.29: 19165 4.29 - 4.90: 31008 Nonbonded interactions: 69369 Sorted by model distance: nonbonded pdb=" NZ LYS A 406 " pdb=" CG1 VAL A 558 " model vdw 1.870 3.540 nonbonded pdb=" N GLN A 130 " pdb=" O GLN A 130 " model vdw 2.237 2.496 nonbonded pdb=" O SER A 681 " pdb=" N GLU A 683 " model vdw 2.242 2.520 nonbonded pdb=" OH TYR A 644 " pdb=" O HIS A 865 " model vdw 2.280 2.440 nonbonded pdb=" OG SER A 697 " pdb=" O ALA A 744 " model vdw 2.290 2.440 ... (remaining 69364 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.870 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 0.005 0.108 9590 Z= 0.352 Angle : 1.136 20.084 13002 Z= 0.673 Chirality : 0.083 1.693 1500 Planarity : 0.007 0.074 1642 Dihedral : 13.301 158.867 3552 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.18 (0.16), residues: 1213 helix: -4.61 (0.09), residues: 623 sheet: -3.55 (0.48), residues: 89 loop : -3.26 (0.22), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 684 HIS 0.005 0.001 HIS A 51 PHE 0.024 0.002 PHE A1061 TYR 0.018 0.002 TYR A 463 ARG 0.006 0.001 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.8530 (mm110) cc_final: 0.8227 (mm110) REVERT: A 149 SER cc_start: 0.9054 (m) cc_final: 0.8751 (t) REVERT: A 157 ASP cc_start: 0.7757 (t0) cc_final: 0.7522 (t0) REVERT: A 266 MET cc_start: 0.8396 (ttp) cc_final: 0.8163 (ttm) REVERT: A 300 ASP cc_start: 0.7749 (p0) cc_final: 0.7061 (t0) REVERT: A 437 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8550 (mmmm) REVERT: A 646 TYR cc_start: 0.8832 (m-80) cc_final: 0.8424 (m-80) REVERT: A 708 MET cc_start: 0.8782 (tmm) cc_final: 0.8516 (tmm) REVERT: A 819 LEU cc_start: 0.9338 (tp) cc_final: 0.8937 (tt) REVERT: A 905 ARG cc_start: 0.8136 (tmt170) cc_final: 0.7759 (tmt170) REVERT: A 908 TYR cc_start: 0.8373 (m-10) cc_final: 0.8085 (m-10) REVERT: A 1041 GLN cc_start: 0.8412 (tp-100) cc_final: 0.8155 (tp40) REVERT: A 1060 ARG cc_start: 0.7788 (mtm180) cc_final: 0.7480 (mtm-85) REVERT: A 1079 LEU cc_start: 0.9199 (mt) cc_final: 0.8994 (mm) REVERT: A 1083 SER cc_start: 0.8689 (t) cc_final: 0.8312 (t) REVERT: A 1148 GLN cc_start: 0.8677 (tp-100) cc_final: 0.8436 (tp40) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2791 time to fit residues: 90.6316 Evaluate side-chains 128 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS A 483 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS A 602 GLN A 625 HIS A 748 GLN A 758 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9590 Z= 0.185 Angle : 0.644 12.321 13002 Z= 0.333 Chirality : 0.043 0.180 1500 Planarity : 0.005 0.053 1642 Dihedral : 10.447 136.260 1471 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.75 % Favored : 92.17 % Rotamer: Outliers : 2.04 % Allowed : 12.13 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.05 (0.19), residues: 1213 helix: -3.72 (0.14), residues: 624 sheet: -2.84 (0.66), residues: 57 loop : -2.77 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 684 HIS 0.003 0.001 HIS A 625 PHE 0.024 0.001 PHE A1031 TYR 0.026 0.001 TYR A1241 ARG 0.007 0.001 ARG A 992 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.8556 (mm110) cc_final: 0.8197 (mm110) REVERT: A 147 SER cc_start: 0.8963 (m) cc_final: 0.8489 (p) REVERT: A 149 SER cc_start: 0.8640 (m) cc_final: 0.8398 (p) REVERT: A 217 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7960 (mtm110) REVERT: A 680 ASN cc_start: 0.8700 (t0) cc_final: 0.8239 (t0) REVERT: A 799 ASP cc_start: 0.8363 (t0) cc_final: 0.8085 (t0) REVERT: A 905 ARG cc_start: 0.8147 (tmt170) cc_final: 0.7907 (tmt170) REVERT: A 975 ARG cc_start: 0.7889 (tmm-80) cc_final: 0.7448 (ttm170) REVERT: A 1041 GLN cc_start: 0.7784 (tp-100) cc_final: 0.7543 (tp40) REVERT: A 1063 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8376 (t0) REVERT: A 1216 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7726 (mt) outliers start: 20 outliers final: 7 residues processed: 157 average time/residue: 0.2286 time to fit residues: 49.6484 Evaluate side-chains 127 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 91 optimal weight: 0.0030 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9590 Z= 0.332 Angle : 0.697 14.749 13002 Z= 0.360 Chirality : 0.045 0.144 1500 Planarity : 0.004 0.052 1642 Dihedral : 9.684 145.855 1471 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 3.47 % Allowed : 12.74 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.21), residues: 1213 helix: -3.19 (0.16), residues: 631 sheet: -2.65 (0.60), residues: 67 loop : -2.37 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 684 HIS 0.006 0.001 HIS A 560 PHE 0.019 0.002 PHE A 386 TYR 0.018 0.002 TYR A1241 ARG 0.010 0.001 ARG A1223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 SER cc_start: 0.9046 (m) cc_final: 0.8734 (p) REVERT: A 518 MET cc_start: 0.8398 (mmm) cc_final: 0.8126 (mmm) REVERT: A 708 MET cc_start: 0.8505 (tmm) cc_final: 0.8199 (tmm) REVERT: A 905 ARG cc_start: 0.8292 (tmt170) cc_final: 0.8051 (tmt170) REVERT: A 975 ARG cc_start: 0.8104 (tmm-80) cc_final: 0.7490 (ttm170) REVERT: A 1041 GLN cc_start: 0.8038 (tp-100) cc_final: 0.7454 (tm-30) REVERT: A 1063 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8289 (t0) REVERT: A 1081 LEU cc_start: 0.9399 (tp) cc_final: 0.9143 (tp) REVERT: A 1123 ARG cc_start: 0.7153 (ptp-170) cc_final: 0.6148 (ptp-170) REVERT: A 1195 MET cc_start: 0.7258 (mmm) cc_final: 0.6526 (mmm) REVERT: A 1216 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7754 (mt) outliers start: 34 outliers final: 25 residues processed: 145 average time/residue: 0.2316 time to fit residues: 47.2047 Evaluate side-chains 139 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 0.0670 chunk 116 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 31 optimal weight: 0.0470 chunk 97 optimal weight: 9.9990 overall best weight: 0.4414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9590 Z= 0.128 Angle : 0.555 13.462 13002 Z= 0.288 Chirality : 0.041 0.197 1500 Planarity : 0.004 0.041 1642 Dihedral : 8.867 141.092 1471 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.04 % Allowed : 14.98 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.22), residues: 1213 helix: -2.66 (0.18), residues: 638 sheet: -2.41 (0.64), residues: 60 loop : -2.33 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 933 HIS 0.002 0.001 HIS A 749 PHE 0.019 0.001 PHE A 386 TYR 0.011 0.001 TYR A 220 ARG 0.004 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 SER cc_start: 0.9036 (m) cc_final: 0.8760 (p) REVERT: A 381 MET cc_start: 0.8084 (mmp) cc_final: 0.7870 (mmp) REVERT: A 549 VAL cc_start: 0.8493 (p) cc_final: 0.8177 (m) REVERT: A 689 MET cc_start: 0.7942 (tpp) cc_final: 0.7652 (tpp) REVERT: A 799 ASP cc_start: 0.8344 (t0) cc_final: 0.7977 (t0) REVERT: A 905 ARG cc_start: 0.8245 (tmt170) cc_final: 0.7989 (tmt170) REVERT: A 975 ARG cc_start: 0.8037 (tmm-80) cc_final: 0.7388 (tpp-160) REVERT: A 1028 PHE cc_start: 0.8559 (m-80) cc_final: 0.8246 (m-80) REVERT: A 1063 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8335 (t0) REVERT: A 1079 LEU cc_start: 0.9134 (mt) cc_final: 0.8700 (tt) REVERT: A 1195 MET cc_start: 0.7301 (mmm) cc_final: 0.6711 (mmt) REVERT: A 1216 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7819 (mt) outliers start: 20 outliers final: 9 residues processed: 150 average time/residue: 0.2148 time to fit residues: 45.3106 Evaluate side-chains 128 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9590 Z= 0.273 Angle : 0.636 14.973 13002 Z= 0.324 Chirality : 0.044 0.198 1500 Planarity : 0.004 0.045 1642 Dihedral : 8.857 146.906 1471 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.77 % Allowed : 14.07 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.22), residues: 1213 helix: -2.48 (0.18), residues: 636 sheet: -2.36 (0.60), residues: 71 loop : -2.22 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 933 HIS 0.004 0.001 HIS A 749 PHE 0.019 0.002 PHE A 386 TYR 0.013 0.002 TYR A 595 ARG 0.005 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 109 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 SER cc_start: 0.8991 (m) cc_final: 0.8754 (p) REVERT: A 381 MET cc_start: 0.8152 (mmp) cc_final: 0.7947 (mmp) REVERT: A 684 TRP cc_start: 0.6626 (p-90) cc_final: 0.6095 (p90) REVERT: A 975 ARG cc_start: 0.8103 (tmm-80) cc_final: 0.7399 (tpp-160) REVERT: A 1028 PHE cc_start: 0.8608 (m-80) cc_final: 0.8251 (m-80) REVERT: A 1063 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8447 (t0) REVERT: A 1079 LEU cc_start: 0.9177 (mt) cc_final: 0.8732 (tt) REVERT: A 1123 ARG cc_start: 0.7066 (ptp-170) cc_final: 0.5947 (ptp-170) REVERT: A 1195 MET cc_start: 0.7475 (mmm) cc_final: 0.6796 (mmm) REVERT: A 1216 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7911 (mt) outliers start: 37 outliers final: 26 residues processed: 136 average time/residue: 0.1931 time to fit residues: 37.8856 Evaluate side-chains 133 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 112 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9590 Z= 0.334 Angle : 0.675 15.436 13002 Z= 0.344 Chirality : 0.045 0.188 1500 Planarity : 0.004 0.048 1642 Dihedral : 8.984 150.474 1471 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 4.79 % Allowed : 14.17 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.22), residues: 1213 helix: -2.48 (0.18), residues: 643 sheet: -2.07 (0.64), residues: 67 loop : -2.22 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 108 HIS 0.004 0.001 HIS A 168 PHE 0.020 0.002 PHE A 287 TYR 0.012 0.002 TYR A 417 ARG 0.006 0.001 ARG A1060 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 115 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 SER cc_start: 0.8979 (m) cc_final: 0.8742 (p) REVERT: A 174 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8792 (tt) REVERT: A 518 MET cc_start: 0.8538 (mmm) cc_final: 0.8016 (mmm) REVERT: A 799 ASP cc_start: 0.8432 (t0) cc_final: 0.8136 (t0) REVERT: A 975 ARG cc_start: 0.8236 (tmm-80) cc_final: 0.7506 (tpp-160) REVERT: A 1022 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7738 (ttm170) REVERT: A 1028 PHE cc_start: 0.8591 (m-80) cc_final: 0.8289 (m-80) REVERT: A 1063 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8487 (t0) REVERT: A 1123 ARG cc_start: 0.6864 (ptp-170) cc_final: 0.5575 (ptp-170) REVERT: A 1216 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.8060 (tp) outliers start: 47 outliers final: 31 residues processed: 147 average time/residue: 0.2093 time to fit residues: 44.0249 Evaluate side-chains 144 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 109 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 207 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1022 ARG Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9590 Z= 0.205 Angle : 0.610 15.397 13002 Z= 0.309 Chirality : 0.042 0.195 1500 Planarity : 0.004 0.044 1642 Dihedral : 8.596 148.093 1471 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.36 % Allowed : 16.41 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.23), residues: 1213 helix: -2.19 (0.19), residues: 629 sheet: -1.83 (0.65), residues: 67 loop : -2.08 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 933 HIS 0.003 0.001 HIS A 749 PHE 0.014 0.001 PHE A 287 TYR 0.015 0.001 TYR A 595 ARG 0.006 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 112 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 MET cc_start: 0.8118 (mmp) cc_final: 0.7913 (mmp) REVERT: A 799 ASP cc_start: 0.8424 (t0) cc_final: 0.8087 (t0) REVERT: A 975 ARG cc_start: 0.8211 (tmm-80) cc_final: 0.7475 (tpp-160) REVERT: A 1022 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7705 (ttm170) REVERT: A 1028 PHE cc_start: 0.8572 (m-80) cc_final: 0.8307 (m-80) REVERT: A 1063 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8505 (t0) REVERT: A 1079 LEU cc_start: 0.9160 (mt) cc_final: 0.8833 (tt) REVERT: A 1123 ARG cc_start: 0.6930 (ptp-170) cc_final: 0.5576 (ptp-170) REVERT: A 1210 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8620 (mp) REVERT: A 1216 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8127 (tp) outliers start: 33 outliers final: 25 residues processed: 139 average time/residue: 0.2209 time to fit residues: 44.5390 Evaluate side-chains 138 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 833 SER Chi-restraints excluded: chain A residue 896 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 1022 ARG Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1140 THR Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9590 Z= 0.170 Angle : 0.576 9.577 13002 Z= 0.294 Chirality : 0.041 0.196 1500 Planarity : 0.003 0.039 1642 Dihedral : 8.257 146.903 1471 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.65 % Allowed : 17.64 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.23), residues: 1213 helix: -2.00 (0.20), residues: 629 sheet: -1.66 (0.63), residues: 71 loop : -1.99 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 778 HIS 0.002 0.001 HIS A 749 PHE 0.012 0.001 PHE A 386 TYR 0.009 0.001 TYR A 220 ARG 0.006 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 SER cc_start: 0.8999 (m) cc_final: 0.8748 (p) REVERT: A 381 MET cc_start: 0.8259 (mmp) cc_final: 0.8038 (mmp) REVERT: A 799 ASP cc_start: 0.8418 (t0) cc_final: 0.8041 (t0) REVERT: A 975 ARG cc_start: 0.8202 (tmm-80) cc_final: 0.7468 (tpp-160) REVERT: A 1022 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7574 (ttm170) REVERT: A 1063 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8481 (t70) REVERT: A 1123 ARG cc_start: 0.6998 (ptp-170) cc_final: 0.5636 (ptp-170) REVERT: A 1210 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8629 (mp) outliers start: 26 outliers final: 18 residues processed: 133 average time/residue: 0.2133 time to fit residues: 40.5769 Evaluate side-chains 128 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 896 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1022 ARG Chi-restraints excluded: chain A residue 1024 ASP Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1210 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 0.0010 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 0.0070 overall best weight: 0.9808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9590 Z= 0.176 Angle : 0.581 9.499 13002 Z= 0.296 Chirality : 0.042 0.196 1500 Planarity : 0.003 0.036 1642 Dihedral : 8.117 147.195 1471 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.75 % Allowed : 17.84 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.24), residues: 1213 helix: -1.85 (0.20), residues: 627 sheet: -1.40 (0.62), residues: 76 loop : -1.95 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 933 HIS 0.002 0.001 HIS A 749 PHE 0.011 0.001 PHE A 386 TYR 0.011 0.001 TYR A1241 ARG 0.007 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 147 SER cc_start: 0.9008 (m) cc_final: 0.8747 (p) REVERT: A 381 MET cc_start: 0.8265 (mmp) cc_final: 0.8029 (mmp) REVERT: A 799 ASP cc_start: 0.8315 (t0) cc_final: 0.8018 (t0) REVERT: A 975 ARG cc_start: 0.8203 (tmm-80) cc_final: 0.7480 (tpp-160) REVERT: A 1022 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7414 (ttm170) REVERT: A 1063 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8462 (t70) REVERT: A 1079 LEU cc_start: 0.9089 (mt) cc_final: 0.8711 (tt) REVERT: A 1123 ARG cc_start: 0.7009 (ptp-170) cc_final: 0.5600 (ptp-170) REVERT: A 1210 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8649 (mp) outliers start: 27 outliers final: 24 residues processed: 130 average time/residue: 0.1999 time to fit residues: 37.6976 Evaluate side-chains 131 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1022 ARG Chi-restraints excluded: chain A residue 1024 ASP Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1210 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 95 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 ASN ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9590 Z= 0.152 Angle : 0.570 9.303 13002 Z= 0.292 Chirality : 0.041 0.198 1500 Planarity : 0.003 0.037 1642 Dihedral : 7.861 146.608 1471 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.45 % Allowed : 18.35 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.24), residues: 1213 helix: -1.53 (0.21), residues: 611 sheet: -1.53 (0.58), residues: 86 loop : -2.00 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 778 HIS 0.002 0.000 HIS A 937 PHE 0.043 0.001 PHE A1031 TYR 0.009 0.001 TYR A 207 ARG 0.006 0.000 ARG A 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 489 LEU cc_start: 0.7903 (pp) cc_final: 0.7343 (mm) REVERT: A 799 ASP cc_start: 0.8249 (t0) cc_final: 0.8005 (t0) REVERT: A 815 MET cc_start: 0.7930 (mmt) cc_final: 0.7593 (mmt) REVERT: A 975 ARG cc_start: 0.8191 (tmm-80) cc_final: 0.7460 (tpp-160) REVERT: A 1022 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7399 (ttm170) REVERT: A 1057 MET cc_start: 0.7887 (mmt) cc_final: 0.7560 (mmt) REVERT: A 1063 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8442 (t70) REVERT: A 1102 ILE cc_start: 0.8296 (mt) cc_final: 0.8038 (tt) REVERT: A 1123 ARG cc_start: 0.7095 (ptp-170) cc_final: 0.5666 (ptp-170) REVERT: A 1210 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8669 (mp) outliers start: 24 outliers final: 21 residues processed: 131 average time/residue: 0.1981 time to fit residues: 37.4491 Evaluate side-chains 133 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 1022 ARG Chi-restraints excluded: chain A residue 1024 ASP Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1210 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.0030 chunk 40 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 ASN ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.166005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.117380 restraints weight = 15291.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.121042 restraints weight = 8760.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123425 restraints weight = 6012.141| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9590 Z= 0.148 Angle : 0.564 9.628 13002 Z= 0.289 Chirality : 0.041 0.198 1500 Planarity : 0.003 0.037 1642 Dihedral : 7.726 146.348 1471 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.45 % Allowed : 18.96 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.24), residues: 1213 helix: -1.40 (0.21), residues: 615 sheet: -1.51 (0.57), residues: 86 loop : -2.00 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.002 0.000 HIS A 937 PHE 0.039 0.001 PHE A1031 TYR 0.014 0.001 TYR A 646 ARG 0.007 0.000 ARG A 600 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1899.42 seconds wall clock time: 34 minutes 59.09 seconds (2099.09 seconds total)