Starting phenix.real_space_refine on Tue May 13 00:41:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8woo_37694/05_2025/8woo_37694_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8woo_37694/05_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_37694/05_2025/8woo_37694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8woo_37694/05_2025/8woo_37694.map" model { file = "/net/cci-nas-00/data/ceres_data/8woo_37694/05_2025/8woo_37694_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8woo_37694/05_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-5687/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: 6.31, per 1000 atoms: 0.67 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: 2.27 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: 1.07 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: 3.05 Time building geometry restraints manager: 2.68 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: 0.930 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.470 Find NCS groups from input model: 0.090 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.820 ------------------------------------------------------------------------------- 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 : 0.933 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: 0.2772 time to fit residues: 90.1288 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 : 0.921 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.165970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120898 restraints weight = 15032.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.124359 restraints weight = 8501.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.126741 restraints weight = 5785.699| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 5.73303 ( 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 : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.8507 (mm110) cc_final: 0.8132 (mm110) REVERT: A 136 ASP cc_start: 0.8020 (p0) cc_final: 0.7683 (p0) REVERT: A 147 SER cc_start: 0.8987 (m) cc_final: 0.8520 (p) REVERT: A 157 ASP cc_start: 0.7555 (t0) cc_final: 0.7281 (t0) REVERT: A 217 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7929 (mtm110) REVERT: A 549 VAL cc_start: 0.8558 (p) cc_final: 0.8007 (m) REVERT: A 646 TYR cc_start: 0.8770 (m-80) cc_final: 0.8550 (m-80) REVERT: A 799 ASP cc_start: 0.8257 (t0) cc_final: 0.8031 (t0) REVERT: A 819 LEU cc_start: 0.9291 (tp) cc_final: 0.9086 (tt) REVERT: A 905 ARG cc_start: 0.8149 (tmt170) cc_final: 0.7839 (tmt170) REVERT: A 908 TYR cc_start: 0.8210 (m-10) cc_final: 0.7870 (m-10) REVERT: A 975 ARG cc_start: 0.7666 (tmm-80) cc_final: 0.7384 (ttm170) REVERT: A 1060 ARG cc_start: 0.7816 (mtm180) cc_final: 0.7434 (mtm-85) REVERT: A 1063 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8386 (t0) REVERT: A 1216 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7819 (mt) outliers start: 17 outliers final: 5 residues processed: 174 average time/residue: 0.2224 time to fit residues: 52.7612 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 : 0.913 ------------------------------------------------------------------------------- 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: 1.9990 chunk 2 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 94 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.164842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.117469 restraints weight = 15391.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.121001 restraints weight = 8835.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123462 restraints weight = 6095.302| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9591 Z= 0.126 Angle : 0.614 13.386 13002 Z= 0.317 Chirality : 0.042 0.144 1500 Planarity : 0.004 0.059 1642 Dihedral : 9.249 141.028 1471 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.96 % Allowed : 12.84 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.20), residues: 1213 helix: -3.07 (0.16), residues: 627 sheet: -2.77 (0.57), residues: 69 loop : -2.54 (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 0.021 0.001 PHE A 386 TYR 0.019 0.001 TYR A1241 ARG 0.009 0.001 ARG A1223 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 226) hydrogen bonds : angle 5.12457 ( 627) covalent geometry : bond 0.00282 ( 9590) covalent geometry : angle 0.61388 (13002) Misc. bond : bond 0.00148 ( 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 161 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 SER cc_start: 0.9080 (m) cc_final: 0.8694 (p) REVERT: A 381 MET cc_start: 0.8106 (mmp) cc_final: 0.7883 (mmp) REVERT: A 549 VAL cc_start: 0.8363 (p) cc_final: 0.7889 (m) REVERT: A 708 MET cc_start: 0.8580 (tmm) cc_final: 0.7833 (tmm) REVERT: A 799 ASP cc_start: 0.8311 (t0) cc_final: 0.8059 (t0) REVERT: A 905 ARG cc_start: 0.8218 (tmt170) cc_final: 0.7954 (tmt170) REVERT: A 908 TYR cc_start: 0.8258 (m-10) cc_final: 0.7897 (m-10) REVERT: A 975 ARG cc_start: 0.7711 (tmm-80) cc_final: 0.7355 (ttm170) REVERT: A 1063 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8337 (t0) REVERT: A 1070 MET cc_start: 0.6481 (mmp) cc_final: 0.5882 (mmt) REVERT: A 1079 LEU cc_start: 0.9071 (mt) cc_final: 0.8702 (tt) REVERT: A 1195 MET cc_start: 0.7078 (mmm) cc_final: 0.6729 (mmt) REVERT: A 1216 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7856 (mt) outliers start: 29 outliers final: 14 residues processed: 153 average time/residue: 0.2210 time to fit residues: 46.4859 Evaluate side-chains 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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: 3.9990 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 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: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS A1041 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.159897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.111508 restraints weight = 15420.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113204 restraints weight = 9737.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.114418 restraints weight = 7340.784| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9591 Z= 0.276 Angle : 0.741 15.493 13002 Z= 0.379 Chirality : 0.047 0.148 1500 Planarity : 0.004 0.051 1642 Dihedral : 9.462 143.534 1471 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.08 % Allowed : 13.25 % Favored : 82.67 % 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: -4.18 (0.21), residues: 1213 helix: -2.91 (0.17), residues: 625 sheet: -2.86 (0.56), residues: 70 loop : -2.39 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 684 HIS 0.005 0.001 HIS A 560 PHE 0.021 0.002 PHE A 386 TYR 0.015 0.002 TYR A 417 ARG 0.004 0.001 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 226) hydrogen bonds : angle 5.44579 ( 627) covalent geometry : bond 0.00626 ( 9590) covalent geometry : angle 0.74090 (13002) Misc. bond : bond 0.00396 ( 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 157 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 SER cc_start: 0.9002 (m) cc_final: 0.8747 (p) REVERT: A 549 VAL cc_start: 0.8356 (p) cc_final: 0.8125 (m) REVERT: A 560 HIS cc_start: 0.6972 (t-170) cc_final: 0.6700 (t70) REVERT: A 708 MET cc_start: 0.8578 (tmm) cc_final: 0.8268 (ttp) REVERT: A 975 ARG cc_start: 0.7994 (tmm-80) cc_final: 0.7392 (tpp-160) REVERT: A 1022 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7679 (ttm170) REVERT: A 1028 PHE cc_start: 0.8897 (m-80) cc_final: 0.8510 (m-80) REVERT: A 1195 MET cc_start: 0.7397 (mmm) cc_final: 0.6651 (mmm) REVERT: A 1216 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8006 (mt) outliers start: 40 outliers final: 30 residues processed: 143 average time/residue: 0.2069 time to fit residues: 41.3070 Evaluate side-chains 133 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 379 ASP 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 570 SER 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 742 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1022 ARG Chi-restraints excluded: chain A residue 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: 0.9980 chunk 99 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 42 optimal weight: 0.0370 chunk 52 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.165885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118308 restraints weight = 15255.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119977 restraints weight = 9511.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121340 restraints weight = 7150.266| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 9591 Z= 0.109 Angle : 0.583 14.753 13002 Z= 0.300 Chirality : 0.041 0.199 1500 Planarity : 0.004 0.043 1642 Dihedral : 8.875 139.762 1471 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.96 % Allowed : 14.88 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.22), residues: 1213 helix: -2.48 (0.18), residues: 627 sheet: -2.77 (0.55), residues: 68 loop : -2.29 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 933 HIS 0.005 0.001 HIS A 560 PHE 0.018 0.001 PHE A 386 TYR 0.011 0.001 TYR A1241 ARG 0.004 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.03002 ( 226) hydrogen bonds : angle 4.68067 ( 627) covalent geometry : bond 0.00250 ( 9590) covalent geometry : angle 0.58283 (13002) Misc. bond : bond 0.00536 ( 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 149 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8843 (t80) cc_final: 0.8420 (t80) REVERT: A 147 SER cc_start: 0.9042 (m) cc_final: 0.8758 (p) REVERT: A 217 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7899 (ptp-110) REVERT: A 549 VAL cc_start: 0.8318 (p) cc_final: 0.7975 (m) REVERT: A 560 HIS cc_start: 0.7104 (t-170) cc_final: 0.6890 (t70) REVERT: A 658 SER cc_start: 0.8868 (p) cc_final: 0.7933 (t) REVERT: A 689 MET cc_start: 0.7828 (tpp) cc_final: 0.7603 (tpp) REVERT: A 708 MET cc_start: 0.8556 (tmm) cc_final: 0.7657 (tmm) REVERT: A 799 ASP cc_start: 0.8199 (t0) cc_final: 0.7846 (t0) REVERT: A 975 ARG cc_start: 0.7880 (tmm-80) cc_final: 0.7395 (tpp-160) REVERT: A 1022 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7650 (ttm170) REVERT: A 1028 PHE cc_start: 0.8810 (m-80) cc_final: 0.8470 (m-80) REVERT: A 1031 PHE cc_start: 0.8527 (t80) cc_final: 0.8169 (t80) REVERT: A 1079 LEU cc_start: 0.9122 (mt) cc_final: 0.8771 (tt) REVERT: A 1195 MET cc_start: 0.7376 (mmm) cc_final: 0.6796 (mmt) REVERT: A 1216 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8013 (mt) outliers start: 29 outliers final: 17 residues processed: 140 average time/residue: 0.2169 time to fit residues: 42.9398 Evaluate side-chains 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 148 VAL 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 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 827 ILE Chi-restraints excluded: chain A residue 896 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1022 ARG Chi-restraints excluded: chain A residue 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: 3.9990 chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 82 optimal weight: 0.0980 chunk 114 optimal weight: 0.0970 chunk 51 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN A 784 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.166386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118201 restraints weight = 15174.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.121656 restraints weight = 8837.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123853 restraints weight = 6166.278| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9591 Z= 0.094 Angle : 0.564 15.548 13002 Z= 0.289 Chirality : 0.040 0.208 1500 Planarity : 0.004 0.084 1642 Dihedral : 8.343 136.916 1471 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.55 % Allowed : 15.90 % Favored : 81.55 % 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: -3.27 (0.23), residues: 1213 helix: -2.05 (0.20), residues: 628 sheet: -2.63 (0.59), residues: 58 loop : -2.13 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 933 HIS 0.002 0.001 HIS A 560 PHE 0.014 0.001 PHE A 386 TYR 0.019 0.001 TYR A 595 ARG 0.006 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.02630 ( 226) hydrogen bonds : angle 4.36722 ( 627) covalent geometry : bond 0.00211 ( 9590) covalent geometry : angle 0.56442 (13002) Misc. bond : bond 0.00438 ( 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 143 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8741 (t80) cc_final: 0.8371 (t80) REVERT: A 147 SER cc_start: 0.9047 (m) cc_final: 0.8775 (p) REVERT: A 217 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7781 (ptp-110) REVERT: A 364 ASN cc_start: 0.7583 (t0) cc_final: 0.7069 (t0) REVERT: A 658 SER cc_start: 0.8736 (p) cc_final: 0.7790 (t) REVERT: A 684 TRP cc_start: 0.6566 (p-90) cc_final: 0.6065 (p90) REVERT: A 708 MET cc_start: 0.8521 (tmm) cc_final: 0.7630 (tmm) REVERT: A 799 ASP cc_start: 0.8147 (t0) cc_final: 0.7796 (t0) REVERT: A 908 TYR cc_start: 0.8111 (m-10) cc_final: 0.7761 (m-80) REVERT: A 975 ARG cc_start: 0.7694 (tmm-80) cc_final: 0.7275 (tpp-160) REVERT: A 1022 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7520 (ttm170) REVERT: A 1028 PHE cc_start: 0.8528 (m-80) cc_final: 0.8317 (m-80) REVERT: A 1031 PHE cc_start: 0.8434 (t80) cc_final: 0.8109 (t80) REVERT: A 1195 MET cc_start: 0.7091 (mmm) cc_final: 0.6585 (mmt) outliers start: 25 outliers final: 15 residues processed: 134 average time/residue: 0.2196 time to fit residues: 40.9737 Evaluate side-chains 124 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET 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 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 896 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 913 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.161317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113504 restraints weight = 15461.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114188 restraints weight = 9595.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.115556 restraints weight = 7271.972| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9591 Z= 0.224 Angle : 0.662 8.893 13002 Z= 0.341 Chirality : 0.045 0.194 1500 Planarity : 0.004 0.058 1642 Dihedral : 8.645 141.981 1471 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.77 % Allowed : 16.31 % Favored : 79.92 % 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: -3.43 (0.22), residues: 1213 helix: -2.16 (0.19), residues: 636 sheet: -2.46 (0.53), residues: 82 loop : -2.21 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 778 HIS 0.005 0.001 HIS A 168 PHE 0.018 0.002 PHE A 287 TYR 0.015 0.002 TYR A 646 ARG 0.007 0.001 ARG A1243 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 226) hydrogen bonds : angle 4.88047 ( 627) covalent geometry : bond 0.00515 ( 9590) covalent geometry : angle 0.66153 (13002) Misc. bond : bond 0.00248 ( 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 146 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8870 (t80) cc_final: 0.8456 (t80) REVERT: A 147 SER cc_start: 0.8975 (m) cc_final: 0.8735 (p) REVERT: A 364 ASN cc_start: 0.8052 (t0) cc_final: 0.7619 (t0) REVERT: A 658 SER cc_start: 0.8956 (p) cc_final: 0.8157 (t) REVERT: A 684 TRP cc_start: 0.6608 (p-90) cc_final: 0.6173 (p90) REVERT: A 708 MET cc_start: 0.8557 (tmm) cc_final: 0.8198 (ttp) REVERT: A 975 ARG cc_start: 0.7959 (tmm-80) cc_final: 0.7428 (ttm170) REVERT: A 1022 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7732 (ttm170) REVERT: A 1028 PHE cc_start: 0.8762 (m-80) cc_final: 0.8429 (m-80) REVERT: A 1031 PHE cc_start: 0.8535 (t80) cc_final: 0.8271 (t80) outliers start: 37 outliers final: 28 residues processed: 136 average time/residue: 0.2174 time to fit residues: 42.2256 Evaluate side-chains 138 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 207 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 896 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 1022 ARG Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1210 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 80 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.165567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115415 restraints weight = 15614.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.118861 restraints weight = 9167.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121151 restraints weight = 6452.750| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9591 Z= 0.112 Angle : 0.588 10.133 13002 Z= 0.299 Chirality : 0.041 0.197 1500 Planarity : 0.004 0.040 1642 Dihedral : 8.347 138.937 1471 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.96 % Allowed : 17.33 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.23), residues: 1213 helix: -1.83 (0.20), residues: 630 sheet: -2.23 (0.56), residues: 72 loop : -2.05 (0.27), residues: 511 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 0.011 0.001 PHE A 287 TYR 0.013 0.001 TYR A 646 ARG 0.007 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.02945 ( 226) hydrogen bonds : angle 4.51351 ( 627) covalent geometry : bond 0.00256 ( 9590) covalent geometry : angle 0.58763 (13002) Misc. bond : bond 0.00239 ( 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: 29 poor density : 115 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8822 (t80) cc_final: 0.8380 (t80) REVERT: A 147 SER cc_start: 0.9043 (m) cc_final: 0.8723 (p) REVERT: A 364 ASN cc_start: 0.7778 (t0) cc_final: 0.7368 (t0) REVERT: A 518 MET cc_start: 0.8584 (mmm) cc_final: 0.7949 (mmm) REVERT: A 658 SER cc_start: 0.8965 (p) cc_final: 0.8019 (t) REVERT: A 708 MET cc_start: 0.8516 (tmm) cc_final: 0.7600 (tmm) REVERT: A 799 ASP cc_start: 0.8114 (t0) cc_final: 0.7870 (t0) REVERT: A 975 ARG cc_start: 0.7839 (tmm-80) cc_final: 0.7373 (tpp-160) REVERT: A 993 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8186 (mt) REVERT: A 1011 GLU cc_start: 0.7082 (tp30) cc_final: 0.6669 (tp30) REVERT: A 1022 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7676 (ttm170) REVERT: A 1057 MET cc_start: 0.7899 (mmt) cc_final: 0.7549 (mmt) REVERT: A 1070 MET cc_start: 0.6760 (mmp) cc_final: 0.5967 (mmm) REVERT: A 1079 LEU cc_start: 0.9159 (mt) cc_final: 0.8682 (tt) REVERT: A 1148 GLN cc_start: 0.8404 (tp-100) cc_final: 0.8145 (tp-100) outliers start: 29 outliers final: 23 residues processed: 135 average time/residue: 0.1957 time to fit residues: 37.5040 Evaluate side-chains 133 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 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 993 ILE Chi-restraints excluded: chain A residue 1022 ARG Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1210 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 75 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 58 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.165658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.117772 restraints weight = 14988.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121250 restraints weight = 8314.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.123683 restraints weight = 5643.679| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9591 Z= 0.101 Angle : 0.584 9.375 13002 Z= 0.294 Chirality : 0.041 0.200 1500 Planarity : 0.004 0.039 1642 Dihedral : 8.073 137.310 1471 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.45 % Allowed : 18.04 % Favored : 79.51 % 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: -2.84 (0.23), residues: 1213 helix: -1.59 (0.20), residues: 626 sheet: -2.19 (0.56), residues: 72 loop : -2.07 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 933 HIS 0.002 0.000 HIS A 749 PHE 0.051 0.001 PHE A1031 TYR 0.016 0.001 TYR A 595 ARG 0.008 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.02702 ( 226) hydrogen bonds : angle 4.39852 ( 627) covalent geometry : bond 0.00231 ( 9590) covalent geometry : angle 0.58365 (13002) Misc. bond : bond 0.00216 ( 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 139 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8826 (t80) cc_final: 0.8420 (t80) REVERT: A 147 SER cc_start: 0.9046 (m) cc_final: 0.8725 (p) REVERT: A 364 ASN cc_start: 0.7842 (t0) cc_final: 0.7468 (t0) REVERT: A 489 LEU cc_start: 0.7479 (pp) cc_final: 0.7278 (pp) REVERT: A 518 MET cc_start: 0.8537 (mmm) cc_final: 0.7964 (mmm) REVERT: A 658 SER cc_start: 0.8849 (p) cc_final: 0.7939 (t) REVERT: A 708 MET cc_start: 0.8499 (tmm) cc_final: 0.7630 (tmm) REVERT: A 898 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8603 (tm-30) REVERT: A 975 ARG cc_start: 0.7837 (tmm-80) cc_final: 0.7368 (tpp-160) REVERT: A 1011 GLU cc_start: 0.6749 (tp30) cc_final: 0.6396 (tp30) REVERT: A 1022 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7634 (ttm170) REVERT: A 1057 MET cc_start: 0.7863 (mmt) cc_final: 0.7533 (mmt) REVERT: A 1079 LEU cc_start: 0.9096 (mt) cc_final: 0.8663 (tt) REVERT: A 1123 ARG cc_start: 0.7588 (mtt180) cc_final: 0.6714 (ptp-170) REVERT: A 1148 GLN cc_start: 0.8437 (tp-100) cc_final: 0.8164 (tp-100) REVERT: A 1210 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8451 (mp) outliers start: 24 outliers final: 19 residues processed: 133 average time/residue: 0.1955 time to fit residues: 37.6620 Evaluate side-chains 135 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 177 LEU 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 406 LYS Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 896 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1022 ARG Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1210 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 5 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 15 optimal weight: 0.0670 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.165210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.116922 restraints weight = 15263.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120438 restraints weight = 8516.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122868 restraints weight = 5750.559| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9591 Z= 0.108 Angle : 0.608 12.569 13002 Z= 0.303 Chirality : 0.041 0.200 1500 Planarity : 0.003 0.036 1642 Dihedral : 7.928 137.715 1471 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.45 % Allowed : 18.55 % Favored : 79.00 % 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: -2.67 (0.23), residues: 1213 helix: -1.37 (0.21), residues: 621 sheet: -2.09 (0.56), residues: 72 loop : -2.11 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.002 0.001 HIS A 749 PHE 0.034 0.001 PHE A1031 TYR 0.010 0.001 TYR A 207 ARG 0.006 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.02725 ( 226) hydrogen bonds : angle 4.35337 ( 627) covalent geometry : bond 0.00248 ( 9590) covalent geometry : angle 0.60841 (13002) Misc. bond : bond 0.00209 ( 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 143 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8795 (t80) cc_final: 0.8359 (t80) REVERT: A 147 SER cc_start: 0.9060 (m) cc_final: 0.8735 (p) REVERT: A 364 ASN cc_start: 0.7993 (t0) cc_final: 0.7621 (t0) REVERT: A 489 LEU cc_start: 0.7508 (pp) cc_final: 0.7304 (pp) REVERT: A 518 MET cc_start: 0.8522 (mmm) cc_final: 0.8099 (mmm) REVERT: A 658 SER cc_start: 0.8922 (p) cc_final: 0.7943 (t) REVERT: A 708 MET cc_start: 0.8527 (tmm) cc_final: 0.8154 (ttp) REVERT: A 898 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8591 (tm-30) REVERT: A 975 ARG cc_start: 0.7829 (tmm-80) cc_final: 0.7356 (tpp-160) REVERT: A 993 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8011 (mt) REVERT: A 1011 GLU cc_start: 0.6752 (tp30) cc_final: 0.6390 (tp30) REVERT: A 1022 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7648 (ttm170) REVERT: A 1026 MET cc_start: 0.7317 (mmp) cc_final: 0.7037 (mmp) REVERT: A 1070 MET cc_start: 0.6625 (mmp) cc_final: 0.5917 (mmm) REVERT: A 1079 LEU cc_start: 0.9086 (mt) cc_final: 0.8760 (mp) REVERT: A 1123 ARG cc_start: 0.7614 (mtt180) cc_final: 0.6696 (ptp-170) REVERT: A 1148 GLN cc_start: 0.8448 (tp-100) cc_final: 0.8175 (tp-100) REVERT: A 1210 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8482 (mp) outliers start: 24 outliers final: 19 residues processed: 137 average time/residue: 0.1882 time to fit residues: 38.0961 Evaluate side-chains 135 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 896 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 993 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 14 optimal weight: 0.2980 chunk 24 optimal weight: 5.9990 chunk 58 optimal weight: 0.0470 chunk 55 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 40 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 overall best weight: 0.4280 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.168117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.119441 restraints weight = 15448.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122946 restraints weight = 8867.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125395 restraints weight = 6118.460| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9591 Z= 0.095 Angle : 0.596 8.949 13002 Z= 0.296 Chirality : 0.041 0.200 1500 Planarity : 0.003 0.037 1642 Dihedral : 7.734 136.466 1471 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.14 % Allowed : 19.27 % 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: -2.46 (0.24), residues: 1213 helix: -1.15 (0.21), residues: 615 sheet: -1.88 (0.58), residues: 72 loop : -2.09 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 778 HIS 0.002 0.000 HIS A 937 PHE 0.036 0.001 PHE A1031 TYR 0.014 0.001 TYR A1241 ARG 0.007 0.000 ARG A 992 Details of bonding type rmsd hydrogen bonds : bond 0.02525 ( 226) hydrogen bonds : angle 4.22529 ( 627) covalent geometry : bond 0.00216 ( 9590) covalent geometry : angle 0.59554 (13002) Misc. bond : bond 0.00195 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2889.09 seconds wall clock time: 51 minutes 21.03 seconds (3081.03 seconds total)