Starting phenix.real_space_refine on Wed Apr 30 12:19:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8woo_37694/04_2025/8woo_37694_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8woo_37694/04_2025/8woo_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/cci-nas-00/data/ceres_data/8woo_37694/04_2025/8woo_37694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8woo_37694/04_2025/8woo_37694.map" model { file = "/net/cci-nas-00/data/ceres_data/8woo_37694/04_2025/8woo_37694_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8woo_37694/04_2025/8woo_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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.81, per 1000 atoms: 0.62 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.1 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: 1.49 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: 3.06 Time building geometry restraints manager: 2.85 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: 0.00 - 4.02: 12860 4.02 - 8.03: 113 8.03 - 12.05: 19 12.05 - 16.07: 5 16.07 - 20.08: 5 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: 2.24 - 2.77: 1860 2.77 - 3.30: 8303 3.30 - 3.83: 14099 3.83 - 4.37: 16958 4.37 - 4.90: 28146 Nonbonded interactions: 69366 Sorted by model distance: 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 3.120 nonbonded pdb=" OH TYR A 644 " pdb=" O HIS A 865 " model vdw 2.280 3.040 nonbonded pdb=" OG SER A 697 " pdb=" O ALA A 744 " model vdw 2.290 3.040 nonbonded pdb=" O THR A 395 " pdb=" OG SER A 570 " model vdw 2.295 3.040 ... (remaining 69361 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: 59.580 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.320 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.620 ------------------------------------------------------------------------------- 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 : 0.007 0.440 9591 Z= 0.530 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 : 2.237 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 Details of bonding type rmsd hydrogen bonds : bond 0.33114 ( 226) hydrogen bonds : angle 10.54072 ( 627) covalent geometry : bond 0.00537 ( 9590) covalent geometry : angle 1.13627 (13002) Misc. bond : bond 0.43985 ( 1) *********************** 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 to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.030 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: 0.2899 time to fit residues: 94.6811 Evaluate side-chains 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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: 0.7980 chunk 91 optimal weight: 0.3980 chunk 50 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 0.0970 chunk 109 optimal weight: 10.0000 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS A 585 HIS A 602 GLN A 625 HIS A 758 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.167257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120665 restraints weight = 15410.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124231 restraints weight = 9023.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.126618 restraints weight = 6203.441| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9591 Z= 0.124 Angle : 0.647 12.340 13002 Z= 0.336 Chirality : 0.043 0.161 1500 Planarity : 0.005 0.052 1642 Dihedral : 10.288 134.151 1471 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.25 % Favored : 92.66 % Rotamer: Outliers : 1.73 % Allowed : 11.82 % Favored : 86.44 % 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: -5.13 (0.18), residues: 1213 helix: -3.72 (0.14), residues: 632 sheet: -2.79 (0.63), residues: 60 loop : -2.87 (0.23), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 684 HIS 0.002 0.001 HIS A 560 PHE 0.024 0.001 PHE A1031 TYR 0.026 0.001 TYR A1241 ARG 0.007 0.001 ARG A 992 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 226) hydrogen bonds : angle 5.73304 ( 627) covalent geometry : bond 0.00258 ( 9590) covalent geometry : angle 0.64725 (13002) Misc. bond : bond 0.00238 ( 1) *********************** 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 180 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.8496 (mm110) cc_final: 0.8121 (mm110) REVERT: A 136 ASP cc_start: 0.8024 (p0) cc_final: 0.7685 (p0) REVERT: A 147 SER cc_start: 0.8983 (m) cc_final: 0.8520 (p) REVERT: A 157 ASP cc_start: 0.7546 (t0) cc_final: 0.7273 (t0) REVERT: A 217 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7938 (mtm110) REVERT: A 549 VAL cc_start: 0.8595 (p) cc_final: 0.8030 (m) REVERT: A 646 TYR cc_start: 0.8770 (m-80) cc_final: 0.8552 (m-80) REVERT: A 799 ASP cc_start: 0.8262 (t0) cc_final: 0.8037 (t0) REVERT: A 819 LEU cc_start: 0.9289 (tp) cc_final: 0.9086 (tt) REVERT: A 905 ARG cc_start: 0.8144 (tmt170) cc_final: 0.7840 (tmt170) REVERT: A 908 TYR cc_start: 0.8211 (m-10) cc_final: 0.7872 (m-10) REVERT: A 975 ARG cc_start: 0.7681 (tmm-80) cc_final: 0.7391 (ttm170) REVERT: A 1060 ARG cc_start: 0.7819 (mtm180) cc_final: 0.7432 (mtm-85) REVERT: A 1063 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8384 (t0) REVERT: A 1216 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7803 (mt) outliers start: 17 outliers final: 5 residues processed: 174 average time/residue: 0.2341 time to fit residues: 55.6648 Evaluate side-chains 130 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 106 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 94 optimal weight: 0.2980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 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 = 0.4024 r_free = 0.4024 target = 0.165019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.117566 restraints weight = 15394.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121135 restraints weight = 8858.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123605 restraints weight = 6098.948| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9591 Z= 0.124 Angle : 0.611 13.398 13002 Z= 0.316 Chirality : 0.042 0.144 1500 Planarity : 0.004 0.070 1642 Dihedral : 9.201 141.601 1471 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.06 % Allowed : 12.84 % Favored : 84.10 % 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: -4.35 (0.20), residues: 1213 helix: -3.03 (0.16), residues: 627 sheet: -2.74 (0.57), residues: 69 loop : -2.53 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 684 HIS 0.007 0.001 HIS A 560 PHE 0.022 0.001 PHE A 386 TYR 0.019 0.001 TYR A1241 ARG 0.011 0.001 ARG A1223 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 226) hydrogen bonds : angle 5.07522 ( 627) covalent geometry : bond 0.00275 ( 9590) covalent geometry : angle 0.61139 (13002) Misc. bond : bond 0.00003 ( 1) *********************** 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 163 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 SER cc_start: 0.9090 (m) cc_final: 0.8712 (p) REVERT: A 708 MET cc_start: 0.8593 (tmm) cc_final: 0.8271 (ttp) REVERT: A 799 ASP cc_start: 0.8320 (t0) cc_final: 0.8057 (t0) REVERT: A 905 ARG cc_start: 0.8221 (tmt170) cc_final: 0.7957 (tmt170) REVERT: A 908 TYR cc_start: 0.8240 (m-10) cc_final: 0.7889 (m-10) REVERT: A 975 ARG cc_start: 0.7698 (tmm-80) cc_final: 0.7352 (ttm170) REVERT: A 1063 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8366 (t0) REVERT: A 1070 MET cc_start: 0.6521 (mmp) cc_final: 0.5935 (mmt) REVERT: A 1079 LEU cc_start: 0.9074 (mt) cc_final: 0.8719 (tt) REVERT: A 1195 MET cc_start: 0.7090 (mmm) cc_final: 0.6768 (mmt) REVERT: A 1216 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7860 (mt) outliers start: 30 outliers final: 14 residues processed: 155 average time/residue: 0.3016 time to fit residues: 65.6060 Evaluate side-chains 126 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 342 ILE 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 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 920 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 76 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 48 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 117 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS A 560 HIS A1041 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.161511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112494 restraints weight = 15374.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115778 restraints weight = 9372.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117990 restraints weight = 6668.069| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9591 Z= 0.181 Angle : 0.655 14.977 13002 Z= 0.336 Chirality : 0.044 0.150 1500 Planarity : 0.004 0.045 1642 Dihedral : 9.146 144.315 1471 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.67 % Allowed : 14.07 % Favored : 82.26 % 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: -3.95 (0.21), residues: 1213 helix: -2.70 (0.18), residues: 615 sheet: -2.78 (0.55), residues: 68 loop : -2.32 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 684 HIS 0.007 0.001 HIS A 560 PHE 0.023 0.002 PHE A 386 TYR 0.014 0.002 TYR A 595 ARG 0.006 0.001 ARG A 561 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 226) hydrogen bonds : angle 5.03428 ( 627) covalent geometry : bond 0.00411 ( 9590) covalent geometry : angle 0.65462 (13002) Misc. bond : bond 0.00521 ( 1) *********************** 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 155 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 SER cc_start: 0.9009 (m) cc_final: 0.8731 (p) REVERT: A 217 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7931 (ptp-110) REVERT: A 708 MET cc_start: 0.8595 (tmm) cc_final: 0.8295 (ttp) REVERT: A 905 ARG cc_start: 0.8271 (tmt170) cc_final: 0.8061 (tmt170) REVERT: A 975 ARG cc_start: 0.7751 (tmm-80) cc_final: 0.7339 (tpp-160) REVERT: A 1022 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7674 (ttm170) REVERT: A 1028 PHE cc_start: 0.8633 (m-80) cc_final: 0.8283 (m-80) REVERT: A 1063 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8466 (t0) REVERT: A 1079 LEU cc_start: 0.9166 (mt) cc_final: 0.8704 (tt) REVERT: A 1102 ILE cc_start: 0.8341 (mt) cc_final: 0.8025 (tt) REVERT: A 1216 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7941 (mt) outliers start: 36 outliers final: 22 residues processed: 142 average time/residue: 0.2509 time to fit residues: 50.3797 Evaluate side-chains 132 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER 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 348 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 395 THR 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 625 HIS Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 683 GLU 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 912 THR Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 963 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 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 38 optimal weight: 0.0770 chunk 99 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 42 optimal weight: 0.0030 chunk 52 optimal weight: 7.9990 chunk 96 optimal weight: 0.0070 chunk 12 optimal weight: 2.9990 overall best weight: 0.3966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.165942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.119701 restraints weight = 15070.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.123301 restraints weight = 8370.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.125690 restraints weight = 5624.435| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9591 Z= 0.091 Angle : 0.551 14.518 13002 Z= 0.284 Chirality : 0.040 0.143 1500 Planarity : 0.003 0.039 1642 Dihedral : 8.536 136.996 1471 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.14 % Allowed : 15.80 % Favored : 82.06 % 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: -3.51 (0.22), residues: 1213 helix: -2.26 (0.19), residues: 623 sheet: -2.57 (0.58), residues: 59 loop : -2.24 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 933 HIS 0.002 0.001 HIS A 749 PHE 0.018 0.001 PHE A 386 TYR 0.011 0.001 TYR A 646 ARG 0.005 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.02572 ( 226) hydrogen bonds : angle 4.46330 ( 627) covalent geometry : bond 0.00200 ( 9590) covalent geometry : angle 0.55060 (13002) Misc. bond : bond 0.00293 ( 1) *********************** 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 150 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8803 (t80) cc_final: 0.8392 (t80) REVERT: A 147 SER cc_start: 0.9083 (m) cc_final: 0.8753 (p) REVERT: A 217 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7736 (ptp-110) REVERT: A 708 MET cc_start: 0.8512 (tmm) cc_final: 0.8104 (ttp) REVERT: A 799 ASP cc_start: 0.8088 (t0) cc_final: 0.7829 (t0) REVERT: A 898 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8623 (tm-30) REVERT: A 905 ARG cc_start: 0.8223 (tmt170) cc_final: 0.7980 (tmt170) REVERT: A 908 TYR cc_start: 0.8194 (m-10) cc_final: 0.7735 (m-80) REVERT: A 975 ARG cc_start: 0.7635 (tmm-80) cc_final: 0.7286 (tpp-160) REVERT: A 1022 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7638 (ttm170) REVERT: A 1028 PHE cc_start: 0.8483 (m-80) cc_final: 0.8237 (m-80) REVERT: A 1063 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8429 (t0) REVERT: A 1079 LEU cc_start: 0.9102 (mt) cc_final: 0.8660 (tt) REVERT: A 1195 MET cc_start: 0.7036 (mmm) cc_final: 0.6535 (mmt) REVERT: A 1216 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7919 (mt) outliers start: 21 outliers final: 11 residues processed: 142 average time/residue: 0.3527 time to fit residues: 70.8558 Evaluate side-chains 131 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 348 ILE 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 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 1022 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 97 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 51 optimal weight: 20.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.161933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111756 restraints weight = 15359.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.114929 restraints weight = 9360.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117078 restraints weight = 6722.917| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9591 Z= 0.211 Angle : 0.660 15.340 13002 Z= 0.335 Chirality : 0.044 0.136 1500 Planarity : 0.004 0.041 1642 Dihedral : 8.723 141.805 1471 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.08 % Allowed : 15.39 % Favored : 80.53 % 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: -3.45 (0.22), residues: 1213 helix: -2.22 (0.19), residues: 620 sheet: -2.50 (0.57), residues: 67 loop : -2.19 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 684 HIS 0.004 0.001 HIS A 749 PHE 0.019 0.002 PHE A 287 TYR 0.013 0.002 TYR A 417 ARG 0.007 0.000 ARG A1243 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 226) hydrogen bonds : angle 4.87098 ( 627) covalent geometry : bond 0.00484 ( 9590) covalent geometry : angle 0.65952 (13002) Misc. bond : bond 0.00486 ( 1) *********************** 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 153 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 SER cc_start: 0.8981 (m) cc_final: 0.8734 (p) REVERT: A 364 ASN cc_start: 0.7723 (t0) cc_final: 0.7290 (t0) REVERT: A 658 SER cc_start: 0.8958 (p) cc_final: 0.8085 (t) REVERT: A 708 MET cc_start: 0.8555 (tmm) cc_final: 0.8200 (ttp) REVERT: A 975 ARG cc_start: 0.7812 (tmm-80) cc_final: 0.7343 (tpp-160) REVERT: A 1022 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7635 (ttm170) REVERT: A 1063 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8471 (t0) REVERT: A 1079 LEU cc_start: 0.9196 (mt) cc_final: 0.8772 (tt) REVERT: A 1102 ILE cc_start: 0.8324 (mt) cc_final: 0.8094 (tt) REVERT: A 1195 MET cc_start: 0.7291 (mmm) cc_final: 0.6619 (mmm) REVERT: A 1216 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8043 (mt) outliers start: 40 outliers final: 31 residues processed: 140 average time/residue: 0.2156 time to fit residues: 43.0251 Evaluate side-chains 143 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 241 VAL Chi-restraints excluded: chain A residue 270 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 395 THR 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 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 844 VAL Chi-restraints excluded: chain A residue 896 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1022 ARG Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1199 THR 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 71 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 0.4980 chunk 81 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.165093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115288 restraints weight = 15286.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.118606 restraints weight = 9103.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120951 restraints weight = 6409.129| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9591 Z= 0.122 Angle : 0.586 16.059 13002 Z= 0.298 Chirality : 0.042 0.205 1500 Planarity : 0.003 0.041 1642 Dihedral : 8.451 138.958 1471 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.26 % Allowed : 16.92 % Favored : 79.82 % 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: -3.21 (0.23), residues: 1213 helix: -1.99 (0.20), residues: 623 sheet: -2.35 (0.58), residues: 66 loop : -2.12 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 108 HIS 0.003 0.001 HIS A 749 PHE 0.044 0.001 PHE A1031 TYR 0.014 0.001 TYR A 646 ARG 0.006 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.03066 ( 226) hydrogen bonds : angle 4.50266 ( 627) covalent geometry : bond 0.00283 ( 9590) covalent geometry : angle 0.58642 (13002) Misc. bond : bond 0.00532 ( 1) *********************** 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 149 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8781 (t80) cc_final: 0.8393 (t80) REVERT: A 147 SER cc_start: 0.9055 (m) cc_final: 0.8752 (p) REVERT: A 217 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7822 (ptp-110) REVERT: A 364 ASN cc_start: 0.7605 (t0) cc_final: 0.7228 (t0) REVERT: A 518 MET cc_start: 0.8288 (mmm) cc_final: 0.8066 (mmm) REVERT: A 655 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7278 (mm-30) REVERT: A 658 SER cc_start: 0.8951 (p) cc_final: 0.7941 (t) REVERT: A 708 MET cc_start: 0.8510 (tmm) cc_final: 0.7611 (tmm) REVERT: A 799 ASP cc_start: 0.8077 (t0) cc_final: 0.7838 (t0) REVERT: A 975 ARG cc_start: 0.7716 (tmm-80) cc_final: 0.7310 (tpp-160) REVERT: A 1011 GLU cc_start: 0.7072 (tp30) cc_final: 0.6522 (tp30) REVERT: A 1022 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7666 (ttm170) REVERT: A 1063 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8407 (t0) REVERT: A 1070 MET cc_start: 0.6997 (mmp) cc_final: 0.6072 (tpp) REVERT: A 1102 ILE cc_start: 0.8360 (mt) cc_final: 0.8129 (tt) REVERT: A 1195 MET cc_start: 0.7214 (mmm) cc_final: 0.6633 (mmt) REVERT: A 1216 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7909 (mt) outliers start: 32 outliers final: 21 residues processed: 139 average time/residue: 0.2387 time to fit residues: 46.9882 Evaluate side-chains 135 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 270 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 395 THR 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 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 896 CYS Chi-restraints excluded: chain A residue 952 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 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 80 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1105 ASN 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 = 0.165979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116593 restraints weight = 15566.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120058 restraints weight = 9092.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122408 restraints weight = 6317.432| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9591 Z= 0.111 Angle : 0.582 11.027 13002 Z= 0.294 Chirality : 0.041 0.200 1500 Planarity : 0.003 0.036 1642 Dihedral : 8.212 138.017 1471 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.85 % Allowed : 17.74 % 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: -2.98 (0.23), residues: 1213 helix: -1.73 (0.20), residues: 619 sheet: -2.41 (0.56), residues: 67 loop : -2.08 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.002 0.000 HIS A 749 PHE 0.026 0.001 PHE A1031 TYR 0.017 0.001 TYR A 595 ARG 0.011 0.000 ARG A1060 Details of bonding type rmsd hydrogen bonds : bond 0.02915 ( 226) hydrogen bonds : angle 4.39390 ( 627) covalent geometry : bond 0.00256 ( 9590) covalent geometry : angle 0.58162 (13002) Misc. bond : bond 0.00400 ( 1) *********************** 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 144 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8776 (t80) cc_final: 0.8350 (t80) REVERT: A 147 SER cc_start: 0.9053 (m) cc_final: 0.8761 (p) REVERT: A 217 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7777 (ptp-110) REVERT: A 364 ASN cc_start: 0.7638 (t0) cc_final: 0.7267 (t0) REVERT: A 518 MET cc_start: 0.8307 (mmm) cc_final: 0.8079 (mmm) REVERT: A 658 SER cc_start: 0.8920 (p) cc_final: 0.7922 (t) REVERT: A 684 TRP cc_start: 0.6754 (p-90) cc_final: 0.6136 (p90) REVERT: A 708 MET cc_start: 0.8536 (tmm) cc_final: 0.7620 (tmm) REVERT: A 799 ASP cc_start: 0.8112 (t0) cc_final: 0.7804 (t0) REVERT: A 898 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8585 (tm-30) REVERT: A 975 ARG cc_start: 0.7702 (tmm-80) cc_final: 0.7328 (tpp-160) REVERT: A 1011 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6552 (tp30) REVERT: A 1022 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7630 (ttm170) REVERT: A 1033 LEU cc_start: 0.8064 (tp) cc_final: 0.7852 (tt) REVERT: A 1070 MET cc_start: 0.6973 (mmp) cc_final: 0.6015 (tpp) REVERT: A 1079 LEU cc_start: 0.8971 (mt) cc_final: 0.8635 (tt) REVERT: A 1148 GLN cc_start: 0.8357 (tp-100) cc_final: 0.8109 (tp-100) REVERT: A 1195 MET cc_start: 0.7204 (mmm) cc_final: 0.6644 (mmt) REVERT: A 1216 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7909 (mt) outliers start: 28 outliers final: 19 residues processed: 136 average time/residue: 0.2016 time to fit residues: 39.5414 Evaluate side-chains 133 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 217 ARG Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 395 THR 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 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 896 CYS Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1022 ARG Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 75 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.162415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.113753 restraints weight = 15094.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.117134 restraints weight = 8575.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119373 restraints weight = 5875.780| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9591 Z= 0.167 Angle : 0.645 11.734 13002 Z= 0.326 Chirality : 0.043 0.192 1500 Planarity : 0.004 0.039 1642 Dihedral : 8.311 140.234 1471 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.47 % Allowed : 17.43 % Favored : 79.10 % 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: -2.97 (0.23), residues: 1213 helix: -1.73 (0.20), residues: 629 sheet: -2.47 (0.55), residues: 67 loop : -2.06 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 933 HIS 0.004 0.001 HIS A 749 PHE 0.021 0.002 PHE A1031 TYR 0.012 0.001 TYR A1241 ARG 0.010 0.000 ARG A1060 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 226) hydrogen bonds : angle 4.61538 ( 627) covalent geometry : bond 0.00387 ( 9590) covalent geometry : angle 0.64480 (13002) Misc. bond : bond 0.00342 ( 1) *********************** 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 150 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8888 (t80) cc_final: 0.8451 (t80) REVERT: A 147 SER cc_start: 0.9023 (m) cc_final: 0.8727 (p) REVERT: A 364 ASN cc_start: 0.7845 (t0) cc_final: 0.7456 (t0) REVERT: A 518 MET cc_start: 0.8391 (mmm) cc_final: 0.8114 (mmm) REVERT: A 658 SER cc_start: 0.8977 (p) cc_final: 0.8082 (t) REVERT: A 684 TRP cc_start: 0.6552 (p-90) cc_final: 0.5973 (p90) REVERT: A 708 MET cc_start: 0.8566 (tmm) cc_final: 0.7663 (tmm) REVERT: A 799 ASP cc_start: 0.8193 (t0) cc_final: 0.7982 (t0) REVERT: A 975 ARG cc_start: 0.7834 (tmm-80) cc_final: 0.7354 (tpp-160) REVERT: A 1011 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6574 (tp30) REVERT: A 1022 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7595 (ttm170) REVERT: A 1033 LEU cc_start: 0.8134 (tp) cc_final: 0.7890 (tt) REVERT: A 1070 MET cc_start: 0.6939 (mmp) cc_final: 0.5991 (tpp) REVERT: A 1079 LEU cc_start: 0.9061 (mt) cc_final: 0.8704 (tt) REVERT: A 1148 GLN cc_start: 0.8389 (tp-100) cc_final: 0.8126 (tp-100) REVERT: A 1216 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7976 (mt) outliers start: 34 outliers final: 27 residues processed: 139 average time/residue: 0.2063 time to fit residues: 41.1917 Evaluate side-chains 140 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 104 GLU 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 270 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 395 THR 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 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 952 VAL Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1022 ARG Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1140 THR Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1216 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 5 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A1128 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.164819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.116762 restraints weight = 15120.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120244 restraints weight = 8365.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.122562 restraints weight = 5652.933| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9591 Z= 0.113 Angle : 0.621 14.301 13002 Z= 0.312 Chirality : 0.041 0.198 1500 Planarity : 0.003 0.039 1642 Dihedral : 8.086 138.249 1471 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.65 % Allowed : 18.45 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.70 (0.23), residues: 1213 helix: -1.46 (0.21), residues: 626 sheet: -2.27 (0.56), residues: 67 loop : -2.01 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 108 HIS 0.003 0.001 HIS A 749 PHE 0.021 0.001 PHE A1031 TYR 0.015 0.001 TYR A 595 ARG 0.009 0.000 ARG A1060 Details of bonding type rmsd hydrogen bonds : bond 0.02961 ( 226) hydrogen bonds : angle 4.44371 ( 627) covalent geometry : bond 0.00257 ( 9590) covalent geometry : angle 0.62086 (13002) Misc. bond : bond 0.00621 ( 1) ********************** 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 142 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 79 MET cc_start: 0.7941 (tmm) cc_final: 0.7638 (tmm) REVERT: A 102 TYR cc_start: 0.8814 (t80) cc_final: 0.8398 (t80) REVERT: A 147 SER cc_start: 0.9059 (m) cc_final: 0.8724 (p) REVERT: A 364 ASN cc_start: 0.7868 (t0) cc_final: 0.7505 (t0) REVERT: A 489 LEU cc_start: 0.7593 (pp) cc_final: 0.6776 (mm) REVERT: A 518 MET cc_start: 0.8362 (mmm) cc_final: 0.8096 (mmm) REVERT: A 658 SER cc_start: 0.8956 (p) cc_final: 0.7957 (t) REVERT: A 799 ASP cc_start: 0.8108 (t0) cc_final: 0.7814 (t0) REVERT: A 898 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8580 (tm-30) REVERT: A 975 ARG cc_start: 0.7785 (tmm-80) cc_final: 0.7366 (tpp-160) REVERT: A 1011 GLU cc_start: 0.7019 (tp30) cc_final: 0.6525 (tp30) REVERT: A 1022 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7638 (ttm170) REVERT: A 1033 LEU cc_start: 0.8169 (tp) cc_final: 0.7956 (tt) REVERT: A 1079 LEU cc_start: 0.8972 (mt) cc_final: 0.8634 (tt) REVERT: A 1148 GLN cc_start: 0.8421 (tp-100) cc_final: 0.8149 (tp-100) outliers start: 26 outliers final: 19 residues processed: 135 average time/residue: 0.2051 time to fit residues: 39.9634 Evaluate side-chains 136 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 270 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 395 THR 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 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 896 CYS Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1022 ARG Chi-restraints excluded: chain A residue 1090 LEU 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 14 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 0.0030 chunk 40 optimal weight: 0.0770 chunk 106 optimal weight: 0.8980 overall best weight: 0.5348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.166916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118935 restraints weight = 15067.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122450 restraints weight = 8308.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124908 restraints weight = 5627.393| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9591 Z= 0.100 Angle : 0.608 13.617 13002 Z= 0.303 Chirality : 0.041 0.198 1500 Planarity : 0.004 0.085 1642 Dihedral : 7.673 136.125 1471 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.04 % Allowed : 19.37 % Favored : 78.59 % Cbeta Deviations : 0.00 % 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: -2.50 (0.24), residues: 1213 helix: -1.20 (0.21), residues: 616 sheet: -1.92 (0.58), residues: 62 loop : -2.10 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 108 HIS 0.002 0.000 HIS A 937 PHE 0.019 0.001 PHE A1031 TYR 0.013 0.001 TYR A1241 ARG 0.014 0.000 ARG A1193 Details of bonding type rmsd hydrogen bonds : bond 0.02675 ( 226) hydrogen bonds : angle 4.27298 ( 627) covalent geometry : bond 0.00229 ( 9590) covalent geometry : angle 0.60838 (13002) Misc. bond : bond 0.00575 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3444.31 seconds wall clock time: 62 minutes 4.62 seconds (3724.62 seconds total)