Starting phenix.real_space_refine on Sun Sep 13 05:04:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qk7_4571/09_2026/6qk7_4571.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qk7_4571/09_2026/6qk7_4571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qk7_4571/09_2026/6qk7_4571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qk7_4571/09_2026/6qk7_4571.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6qk7_4571/09_2026/6qk7_4571.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qk7_4571/09_2026/6qk7_4571.cif" model { file = "/net/cci-nas-00/data/ceres_data/6qk7_4571/09_2026/6qk7_4571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qk7_4571/09_2026/6qk7_4571.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 95 5.16 5 C 13221 2.51 5 N 3506 2.21 5 O 3964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20790 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1161, 9267 Classifications: {'peptide': 1161} Link IDs: {'PTRANS': 37, 'TRANS': 1123} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Chain: "B" Number of atoms: 6019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6019 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 24, 'TRANS': 724} Chain breaks: 2 Chain: "C" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3560 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 424} Chain breaks: 2 Chain: "D" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1918 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 4, 'TRANS': 233} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'5AD': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15392 SG CYS C 108 67.358 91.522 59.590 1.00 58.12 S ATOM 15467 SG CYS C 118 62.700 89.053 63.757 1.00 65.28 S ATOM 15492 SG CYS C 121 68.032 92.046 65.725 1.00 61.72 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLU C 162 " occ=0.43 ... (7 atoms not shown) pdb=" OE2 GLU C 162 " occ=0.43 Time building chain proxies: 4.68, per 1000 atoms: 0.23 Number of scatterers: 20790 At special positions: 0 Unit cell: (179.55, 147.15, 170.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 95 16.00 O 3964 8.00 N 3506 7.00 C 13221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 955.7 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 601 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 108 " pdb="FE4 SF4 C 601 " - pdb=" SG CYS C 121 " pdb="FE3 SF4 C 601 " - pdb=" SG CYS C 118 " Number of angles added : 9 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4910 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 32 sheets defined 30.7% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.594A pdb=" N LYS A 507 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 755 removed outlier: 3.632A pdb=" N ALA A 747 " --> pdb=" O ILE A 743 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET A 754 " --> pdb=" O ARG A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 768 removed outlier: 3.752A pdb=" N VAL A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS A 768 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 778 Processing helix chain 'A' and resid 779 through 786 removed outlier: 4.378A pdb=" N ILE A 784 " --> pdb=" O PRO A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 794 removed outlier: 3.591A pdb=" N PHE A 790 " --> pdb=" O ASN A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 806 removed outlier: 3.734A pdb=" N LEU A 800 " --> pdb=" O ARG A 796 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 802 " --> pdb=" O ASP A 798 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 805 " --> pdb=" O ASN A 801 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS A 806 " --> pdb=" O LEU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 843 removed outlier: 3.593A pdb=" N TYR A 842 " --> pdb=" O GLU A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 866 removed outlier: 3.560A pdb=" N ILE A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 860 " --> pdb=" O ASN A 856 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 865 " --> pdb=" O ALA A 861 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 866 " --> pdb=" O VAL A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 876 removed outlier: 3.617A pdb=" N LYS A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 885 removed outlier: 3.697A pdb=" N ILE A 880 " --> pdb=" O TYR A 876 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 882 " --> pdb=" O GLN A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 899 removed outlier: 3.871A pdb=" N ALA A 895 " --> pdb=" O ASN A 891 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 898 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 899 " --> pdb=" O ALA A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 916 removed outlier: 3.718A pdb=" N SER A 910 " --> pdb=" O GLU A 906 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 929 Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.766A pdb=" N ALA A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 939 " --> pdb=" O SER A 935 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 960 removed outlier: 3.965A pdb=" N TYR A 951 " --> pdb=" O ASP A 947 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 952 " --> pdb=" O PRO A 948 " (cutoff:3.500A) Proline residue: A 953 - end of helix removed outlier: 3.658A pdb=" N LEU A 958 " --> pdb=" O PHE A 954 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP A 960 " --> pdb=" O GLN A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 973 removed outlier: 3.706A pdb=" N PHE A 968 " --> pdb=" O LEU A 964 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP A 971 " --> pdb=" O LYS A 967 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A 972 " --> pdb=" O PHE A 968 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 986 removed outlier: 3.831A pdb=" N HIS A 983 " --> pdb=" O LYS A 979 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.629A pdb=" N HIS A1004 " --> pdb=" O TYR A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1013 removed outlier: 3.678A pdb=" N LEU A1013 " --> pdb=" O HIS A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1035 removed outlier: 4.657A pdb=" N VAL A1023 " --> pdb=" O GLU A1019 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE A1024 " --> pdb=" O LYS A1020 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A1025 " --> pdb=" O GLN A1021 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN A1026 " --> pdb=" O ASN A1022 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A1027 " --> pdb=" O VAL A1023 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A1029 " --> pdb=" O TYR A1025 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS A1030 " --> pdb=" O ASN A1026 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS A1031 " --> pdb=" O ILE A1027 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A1034 " --> pdb=" O LYS A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1049 removed outlier: 3.966A pdb=" N ALA A1044 " --> pdb=" O ASP A1040 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A1046 " --> pdb=" O ALA A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1062 removed outlier: 3.528A pdb=" N GLN A1059 " --> pdb=" O MET A1055 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER A1060 " --> pdb=" O GLY A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1074 removed outlier: 3.657A pdb=" N ALA A1067 " --> pdb=" O ARG A1063 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A1068 " --> pdb=" O TRP A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1077 No H-bonds generated for 'chain 'A' and resid 1075 through 1077' Processing helix chain 'A' and resid 1078 through 1092 removed outlier: 3.794A pdb=" N GLU A1085 " --> pdb=" O SER A1081 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER A1088 " --> pdb=" O GLU A1084 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER A1089 " --> pdb=" O GLU A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1106 removed outlier: 3.834A pdb=" N ILE A1102 " --> pdb=" O ASP A1098 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A1103 " --> pdb=" O ALA A1099 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A1105 " --> pdb=" O ASP A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1120 removed outlier: 3.685A pdb=" N ALA A1113 " --> pdb=" O ASN A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1133 removed outlier: 3.814A pdb=" N LEU A1128 " --> pdb=" O ASP A1124 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A1130 " --> pdb=" O ALA A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1142 Processing helix chain 'A' and resid 1142 through 1172 removed outlier: 3.620A pdb=" N GLY A1148 " --> pdb=" O ASP A1144 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A1159 " --> pdb=" O ALA A1155 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A1163 " --> pdb=" O ALA A1159 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A1164 " --> pdb=" O ASP A1160 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A1166 " --> pdb=" O LYS A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1255 No H-bonds generated for 'chain 'A' and resid 1253 through 1255' Processing helix chain 'A' and resid 1256 through 1283 removed outlier: 4.197A pdb=" N GLY A1260 " --> pdb=" O VAL A1256 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A1262 " --> pdb=" O SER A1258 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A1265 " --> pdb=" O ARG A1261 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A1267 " --> pdb=" O ILE A1263 " (cutoff:3.500A) Proline residue: A1271 - end of helix removed outlier: 3.757A pdb=" N ARG A1275 " --> pdb=" O PRO A1271 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A1276 " --> pdb=" O ASP A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1303 removed outlier: 3.559A pdb=" N LEU A1303 " --> pdb=" O VAL A1299 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.537A pdb=" N LYS B 257 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 478 removed outlier: 4.084A pdb=" N MET B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 545 removed outlier: 3.715A pdb=" N ARG B 544 " --> pdb=" O ASP B 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.675A pdb=" N THR C 114 " --> pdb=" O HIS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 150 removed outlier: 3.723A pdb=" N ARG C 145 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 147 " --> pdb=" O SER C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 164 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 187 through 204 removed outlier: 4.194A pdb=" N ASP C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 201 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 217 removed outlier: 3.874A pdb=" N ILE C 214 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 removed outlier: 4.067A pdb=" N ASP C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 267 removed outlier: 3.732A pdb=" N ALA C 264 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.558A pdb=" N CYS C 277 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA C 281 " --> pdb=" O CYS C 277 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.689A pdb=" N GLU C 308 " --> pdb=" O GLU C 304 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE C 310 " --> pdb=" O ASP C 306 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C 314 " --> pdb=" O PHE C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 352 through 362 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 391 through 400 Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.655A pdb=" N THR C 476 " --> pdb=" O LYS C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 523 removed outlier: 3.521A pdb=" N GLU C 517 " --> pdb=" O MET C 513 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 520 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 522 " --> pdb=" O ARG C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 543 removed outlier: 4.209A pdb=" N TYR C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 542 " --> pdb=" O ARG C 538 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS C 543 " --> pdb=" O ASN C 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 537 through 543' Processing helix chain 'D' and resid 1007 through 1013 removed outlier: 3.565A pdb=" N ALA D1012 " --> pdb=" O LYS D1008 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D1013 " --> pdb=" O HIS D1009 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1035 removed outlier: 3.587A pdb=" N GLN D1021 " --> pdb=" O ASP D1017 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN D1022 " --> pdb=" O SER D1018 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL D1023 " --> pdb=" O GLU D1019 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE D1024 " --> pdb=" O LYS D1020 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D1025 " --> pdb=" O GLN D1021 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN D1026 " --> pdb=" O ASN D1022 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER D1034 " --> pdb=" O LYS D1030 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN D1035 " --> pdb=" O HIS D1031 " (cutoff:3.500A) Processing helix chain 'D' and resid 1037 through 1047 removed outlier: 3.582A pdb=" N ALA D1044 " --> pdb=" O ASP D1040 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET D1047 " --> pdb=" O VAL D1043 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1061 removed outlier: 4.069A pdb=" N GLY D1056 " --> pdb=" O LYS D1052 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA D1057 " --> pdb=" O GLU D1053 " (cutoff:3.500A) Processing helix chain 'D' and resid 1063 through 1075 removed outlier: 3.608A pdb=" N ILE D1070 " --> pdb=" O GLU D1066 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN D1073 " --> pdb=" O SER D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1078 through 1093 removed outlier: 3.773A pdb=" N ALA D1083 " --> pdb=" O VAL D1079 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU D1084 " --> pdb=" O GLU D1080 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D1088 " --> pdb=" O GLU D1084 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE D1092 " --> pdb=" O SER D1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 1095 through 1106 removed outlier: 3.860A pdb=" N GLU D1105 " --> pdb=" O ASP D1101 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1120 removed outlier: 3.568A pdb=" N ALA D1115 " --> pdb=" O LYS D1111 " (cutoff:3.500A) Processing helix chain 'D' and resid 1122 through 1133 removed outlier: 3.621A pdb=" N ILE D1131 " --> pdb=" O SER D1127 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1142 Processing helix chain 'D' and resid 1142 through 1169 removed outlier: 3.538A pdb=" N GLY D1152 " --> pdb=" O GLY D1148 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE D1165 " --> pdb=" O CYS D1161 " (cutoff:3.500A) Processing helix chain 'D' and resid 1253 through 1283 removed outlier: 3.520A pdb=" N GLN D1257 " --> pdb=" O GLU D1253 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D1262 " --> pdb=" O SER D1258 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D1263 " --> pdb=" O VAL D1259 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU D1264 " --> pdb=" O GLY D1260 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D1265 " --> pdb=" O ARG D1261 " (cutoff:3.500A) Proline residue: D1271 - end of helix removed outlier: 3.591A pdb=" N VAL D1274 " --> pdb=" O LYS D1270 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG D1275 " --> pdb=" O PRO D1271 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL D1276 " --> pdb=" O ASP D1272 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY D1279 " --> pdb=" O ARG D1275 " (cutoff:3.500A) Processing helix chain 'D' and resid 1285 through 1310 removed outlier: 3.642A pdb=" N GLU D1298 " --> pdb=" O LYS D1294 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA D1305 " --> pdb=" O ASP D1301 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN D1306 " --> pdb=" O LEU D1302 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D1307 " --> pdb=" O LEU D1303 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS D1308 " --> pdb=" O LYS D1304 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D1309 " --> pdb=" O ALA D1305 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 29 removed outlier: 6.830A pdb=" N ASP A 423 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS A 26 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 421 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS A 28 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE A 419 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 413 " --> pdb=" O ASN A 420 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 414 " --> pdb=" O TYR A 400 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TYR A 400 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 53 removed outlier: 5.472A pdb=" N LEU A 47 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY A 64 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A 49 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 58 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 73 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 99 removed outlier: 7.099A pdb=" N VAL A 112 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.801A pdb=" N ASN A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 166 " --> pdb=" O TYR A 179 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 168 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER A 177 " --> pdb=" O VAL A 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 253 through 255 removed outlier: 3.755A pdb=" N SER A 296 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER A 289 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU A 294 " --> pdb=" O SER A 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 332 through 337 removed outlier: 4.501A pdb=" N VAL A 332 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY A 345 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 removed outlier: 4.206A pdb=" N GLN A 391 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR A 381 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU A 389 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 429 through 430 removed outlier: 4.256A pdb=" N ALA A 429 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 469 " --> pdb=" O VAL A 450 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 478 through 480 removed outlier: 4.074A pdb=" N CYS A 516 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA A 499 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE A 514 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 529 through 536 removed outlier: 5.859A pdb=" N LEU A 530 " --> pdb=" O ASP A 546 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASP A 546 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 532 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG A 552 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A 555 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 529 through 536 removed outlier: 5.859A pdb=" N LEU A 530 " --> pdb=" O ASP A 546 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASP A 546 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 532 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG A 552 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER A 551 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 572 " --> pdb=" O SER A 551 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 576 through 581 removed outlier: 6.717A pdb=" N GLU A 591 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU A 579 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL A 589 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS A 598 " --> pdb=" O TYR A 590 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLN A 599 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLU A 608 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 616 through 625 removed outlier: 3.859A pdb=" N ASP A 618 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 624 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 641 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 666 through 670 removed outlier: 4.386A pdb=" N SER A 666 " --> pdb=" O THR A 677 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 676 " --> pdb=" O GLN A 684 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 709 " --> pdb=" O LEU A 683 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 716 through 721 removed outlier: 5.790A pdb=" N LEU A 717 " --> pdb=" O GLN A 730 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLN A 730 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER A 719 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG C 433 " --> pdb=" O THR A 738 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP C 442 " --> pdb=" O ARG C 463 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG C 463 " --> pdb=" O TRP C 442 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR C 444 " --> pdb=" O ARG C 461 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG C 461 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU C 446 " --> pdb=" O LEU C 459 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU C 459 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR C 448 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 455 " --> pdb=" O ASP C 450 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ILE C 457 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL C 488 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU C 459 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU C 486 " --> pdb=" O LEU C 459 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARG C 461 " --> pdb=" O ARG C 484 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR C 552 " --> pdb=" O ASP C 549 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 5 through 11 removed outlier: 6.811A pdb=" N ILE B 782 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE B 10 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR B 780 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 774 " --> pdb=" O ARG B 757 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 21 through 23 removed outlier: 3.613A pdb=" N ALA B 31 " --> pdb=" O ASP B 22 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 53 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 62 through 67 removed outlier: 4.060A pdb=" N GLN B 98 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS B 87 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N CYS B 96 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 107 through 113 removed outlier: 4.087A pdb=" N THR B 125 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU B 143 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE B 128 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 155 through 161 removed outlier: 3.610A pdb=" N SER B 157 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS B 165 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 182 " --> pdb=" O TYR B 166 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B 179 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N SER B 181 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL B 194 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ILE B 183 " --> pdb=" O CYS B 192 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N CYS B 192 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 207 through 210 removed outlier: 3.675A pdb=" N GLY B 270 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE B 261 " --> pdb=" O VAL B 269 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 284 through 289 removed outlier: 6.560A pdb=" N ALA B 299 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 287 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 297 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 321 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU B 309 " --> pdb=" O CYS B 319 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N CYS B 319 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 344 through 348 removed outlier: 3.536A pdb=" N LEU B 345 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU B 356 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE B 347 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP B 353 " --> pdb=" O THR B 369 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR B 369 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N MET B 366 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 370 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 388 through 393 removed outlier: 3.943A pdb=" N ASP B 390 " --> pdb=" O THR B 403 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 412 through 417 removed outlier: 9.902A pdb=" N PHE B 412 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 11.117A pdb=" N THR B 428 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 11.556A pdb=" N ILE B 426 " --> pdb=" O PRO B 414 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE B 416 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 444 through 447 removed outlier: 6.982A pdb=" N LEU B 462 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LYS B 553 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N SER B 464 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 561 through 566 removed outlier: 3.638A pdb=" N CYS B 563 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 609 through 614 removed outlier: 3.741A pdb=" N LYS B 613 " --> pdb=" O LEU B 622 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 643 " --> pdb=" O GLU B 634 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 656 through 661 removed outlier: 3.718A pdb=" N ASP B 658 " --> pdb=" O ALA B 673 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 670 " --> pdb=" O TRP B 682 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 674 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR B 678 " --> pdb=" O SER B 674 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 679 " --> pdb=" O SER B 697 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER B 697 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 681 " --> pdb=" O GLU B 695 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 685 " --> pdb=" O ASP B 691 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP B 691 " --> pdb=" O GLN B 685 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 704 through 709 removed outlier: 6.830A pdb=" N GLY B 723 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 707 " --> pdb=" O SER B 721 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER B 721 " --> pdb=" O ILE B 707 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE B 709 " --> pdb=" O LEU B 719 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU B 719 " --> pdb=" O ILE B 709 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 718 " --> pdb=" O TYR B 734 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE B 729 " --> pdb=" O GLN B 744 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLN B 744 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU B 731 " --> pdb=" O ILE B 742 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 742 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 97 through 102 removed outlier: 6.223A pdb=" N ALA C 97 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL C 177 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL C 99 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N MET C 179 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL C 101 " --> pdb=" O MET C 179 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL C 174 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLY C 226 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU C 230 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG C 251 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY C 255 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS C 289 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLU C 253 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL C 291 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLY C 255 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N HIS C 293 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY C 323 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU C 324 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG C 373 " --> pdb=" O LEU C 324 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 1926 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: 5.10 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 8584 1.39 - 1.58: 12475 1.58 - 1.76: 0 1.76 - 1.95: 141 1.95 - 2.13: 12 Bond restraints: 21212 Sorted by residual: bond pdb=" S4 SF4 C 601 " pdb="FE2 SF4 C 601 " ideal model delta sigma weight residual 2.280 2.118 0.162 3.00e-02 1.11e+03 2.92e+01 bond pdb=" S1 SF4 C 601 " pdb="FE2 SF4 C 601 " ideal model delta sigma weight residual 2.280 2.118 0.162 3.00e-02 1.11e+03 2.91e+01 bond pdb=" S3 SF4 C 601 " pdb="FE2 SF4 C 601 " ideal model delta sigma weight residual 2.280 2.119 0.161 3.00e-02 1.11e+03 2.89e+01 bond pdb=" S2 SF4 C 601 " pdb="FE1 SF4 C 601 " ideal model delta sigma weight residual 2.280 2.119 0.161 3.00e-02 1.11e+03 2.89e+01 bond pdb=" S2 SF4 C 601 " pdb="FE3 SF4 C 601 " ideal model delta sigma weight residual 2.280 2.120 0.160 3.00e-02 1.11e+03 2.86e+01 ... (remaining 21207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 28601 3.73 - 7.46: 89 7.46 - 11.19: 6 11.19 - 14.92: 10 14.92 - 18.65: 14 Bond angle restraints: 28720 Sorted by residual: angle pdb="FE2 SF4 C 601 " pdb=" S3 SF4 C 601 " pdb="FE4 SF4 C 601 " ideal model delta sigma weight residual 73.70 92.35 -18.65 1.50e+00 4.44e-01 1.55e+02 angle pdb="FE2 SF4 C 601 " pdb=" S1 SF4 C 601 " pdb="FE4 SF4 C 601 " ideal model delta sigma weight residual 73.70 92.10 -18.40 1.50e+00 4.44e-01 1.51e+02 angle pdb="FE1 SF4 C 601 " pdb=" S2 SF4 C 601 " pdb="FE3 SF4 C 601 " ideal model delta sigma weight residual 73.70 91.18 -17.48 1.50e+00 4.44e-01 1.36e+02 angle pdb="FE2 SF4 C 601 " pdb=" S4 SF4 C 601 " pdb="FE3 SF4 C 601 " ideal model delta sigma weight residual 73.70 91.03 -17.33 1.50e+00 4.44e-01 1.33e+02 angle pdb="FE1 SF4 C 601 " pdb=" S4 SF4 C 601 " pdb="FE3 SF4 C 601 " ideal model delta sigma weight residual 73.70 91.00 -17.30 1.50e+00 4.44e-01 1.33e+02 ... (remaining 28715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 12012 15.87 - 31.74: 611 31.74 - 47.60: 122 47.60 - 63.47: 10 63.47 - 79.34: 16 Dihedral angle restraints: 12771 sinusoidal: 5175 harmonic: 7596 Sorted by residual: dihedral pdb=" CA LEU B 251 " pdb=" C LEU B 251 " pdb=" N THR B 252 " pdb=" CA THR B 252 " ideal model delta harmonic sigma weight residual -180.00 -150.03 -29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA LEU A1086 " pdb=" C LEU A1086 " pdb=" N ILE A1087 " pdb=" CA ILE A1087 " ideal model delta harmonic sigma weight residual -180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA ALA A 679 " pdb=" C ALA A 679 " pdb=" N GLN A 680 " pdb=" CA GLN A 680 " ideal model delta harmonic sigma weight residual 180.00 150.80 29.20 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 12768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 3208 0.213 - 0.425: 6 0.425 - 0.638: 0 0.638 - 0.851: 0 0.851 - 1.063: 4 Chirality restraints: 3218 Sorted by residual: chirality pdb="FE2 SF4 C 601 " pdb=" S1 SF4 C 601 " pdb=" S3 SF4 C 601 " pdb=" S4 SF4 C 601 " both_signs ideal model delta sigma weight residual False 10.55 9.49 1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb="FE1 SF4 C 601 " pdb=" S2 SF4 C 601 " pdb=" S3 SF4 C 601 " pdb=" S4 SF4 C 601 " both_signs ideal model delta sigma weight residual False -10.55 -9.54 -1.02 2.00e-01 2.50e+01 2.58e+01 chirality pdb="FE3 SF4 C 601 " pdb=" S1 SF4 C 601 " pdb=" S2 SF4 C 601 " pdb=" S4 SF4 C 601 " both_signs ideal model delta sigma weight residual False -10.55 -9.56 -1.00 2.00e-01 2.50e+01 2.49e+01 ... (remaining 3215 not shown) Planarity restraints: 3679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 303 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C GLY A 303 " -0.055 2.00e-02 2.50e+03 pdb=" O GLY A 303 " 0.020 2.00e-02 2.50e+03 pdb=" N MET A 304 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 108 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO C 109 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 109 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 109 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 750 " 0.041 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO B 751 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 751 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 751 " 0.034 5.00e-02 4.00e+02 ... (remaining 3676 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 158 2.57 - 3.16: 16263 3.16 - 3.74: 30106 3.74 - 4.32: 42821 4.32 - 4.90: 70305 Nonbonded interactions: 159653 Sorted by model distance: nonbonded pdb=" NE2 GLN A 307 " pdb=" O VAL A 357 " model vdw 1.993 3.120 nonbonded pdb=" OH TYR C 120 " pdb=" OE1 GLN C 257 " model vdw 2.102 3.040 nonbonded pdb=" N GLN A 307 " pdb=" OE1 GLN A 307 " model vdw 2.188 3.120 nonbonded pdb=" OG SER B 674 " pdb=" OD1 ASP B 676 " model vdw 2.199 3.040 nonbonded pdb=" O ILE B 749 " pdb=" OH TYR B 783 " model vdw 2.200 3.040 ... (remaining 159648 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.380 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.004 0.162 21215 Z= 0.175 Angle : 0.807 34.969 28729 Z= 0.454 Chirality : 0.057 1.063 3218 Planarity : 0.006 0.075 3679 Dihedral : 10.672 79.341 7861 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.44 % Allowed : 4.42 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.70 (0.13), residues: 2564 helix: -3.81 (0.11), residues: 696 sheet: -2.07 (0.20), residues: 573 loop : -3.22 (0.13), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 19 TYR 0.013 0.001 TYR D1058 PHE 0.011 0.001 PHE A 347 TRP 0.017 0.001 TRP C 368 HIS 0.005 0.000 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.17 (21212) covalent geometry : angle 0.75028 / 0.45 (28720) hydrogen bonds : bond 0.31693 / 20.96 ( 666) hydrogen bonds : angle 10.09626 / 6.84 ( 1926) metal coordination : bond 0.02783 / 1.34 ( 3) metal coordination : angle 16.77957 / 7.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 214 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.8986 (mt) cc_final: 0.8612 (mt) REVERT: A 306 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.7001 (p-80) REVERT: A 1055 MET cc_start: 0.6010 (ttp) cc_final: 0.5573 (ttp) REVERT: A 1255 LEU cc_start: 0.6726 (tp) cc_final: 0.6173 (pp) REVERT: B 442 MET cc_start: 0.8242 (mmp) cc_final: 0.7986 (mmp) REVERT: B 578 ARG cc_start: 0.8527 (ttm170) cc_final: 0.8287 (ttm170) REVERT: C 144 MET cc_start: 0.8165 (mtm) cc_final: 0.7946 (mtp) REVERT: D 1161 CYS cc_start: 0.7481 (m) cc_final: 0.7153 (p) outliers start: 10 outliers final: 5 residues processed: 223 average time/residue: 0.1656 time to fit residues: 56.0370 Evaluate side-chains 103 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain C residue 116 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN A 563 GLN A 890 GLN ** A1031 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN C 524 HIS D1295 ASN D1345 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.102194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.068854 restraints weight = 55409.414| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.41 r_work: 0.2971 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21215 Z= 0.178 Angle : 0.679 9.924 28729 Z= 0.361 Chirality : 0.047 0.201 3218 Planarity : 0.005 0.057 3679 Dihedral : 6.192 59.653 2833 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.06 % Allowed : 7.83 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.14), residues: 2564 helix: -2.14 (0.15), residues: 731 sheet: -1.68 (0.20), residues: 632 loop : -2.97 (0.15), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1095 TYR 0.027 0.002 TYR A1058 PHE 0.017 0.002 PHE B 670 TRP 0.013 0.002 TRP D1064 HIS 0.008 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (21212) covalent geometry : angle 0.67197 / 0.36 (28720) hydrogen bonds : bond 0.05048 / 3.34 ( 666) hydrogen bonds : angle 5.79006 / 3.88 ( 1926) metal coordination : bond 0.01775 / 0.86 ( 3) metal coordination : angle 5.46118 / 2.58 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 102 time to evaluate : 0.795 Fit side-chains TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.8598 (mmm) cc_final: 0.8229 (mmm) REVERT: A 328 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8823 (tm-30) REVERT: A 433 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8235 (m) REVERT: A 563 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: A 831 MET cc_start: 0.8656 (mmp) cc_final: 0.8013 (mmm) REVERT: A 839 MET cc_start: 0.8257 (mtt) cc_final: 0.8007 (tmm) REVERT: A 847 MET cc_start: 0.8767 (ttm) cc_final: 0.8529 (pmm) REVERT: A 1264 GLU cc_start: 0.7480 (tt0) cc_final: 0.7007 (tm-30) REVERT: B 637 MET cc_start: 0.8735 (mmm) cc_final: 0.8059 (mmt) REVERT: B 724 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8949 (pp) REVERT: D 1134 LYS cc_start: 0.5593 (mptt) cc_final: 0.5264 (mmmt) REVERT: D 1291 GLN cc_start: 0.9174 (tt0) cc_final: 0.8624 (tp40) outliers start: 47 outliers final: 23 residues processed: 143 average time/residue: 0.1501 time to fit residues: 33.9613 Evaluate side-chains 115 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 521 LYS Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1151 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 25 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 204 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 243 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 233 optimal weight: 0.0870 chunk 166 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 430 GLN A 771 ASN A 956 GLN ** A1031 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1021 GLN D1094 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.101333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.066882 restraints weight = 55743.743| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.81 r_work: 0.2993 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21215 Z= 0.161 Angle : 0.639 14.495 28729 Z= 0.333 Chirality : 0.046 0.180 3218 Planarity : 0.004 0.053 3679 Dihedral : 5.682 54.843 2829 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.27 % Allowed : 8.14 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.15), residues: 2564 helix: -1.14 (0.18), residues: 742 sheet: -1.41 (0.20), residues: 634 loop : -2.69 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 479 TYR 0.027 0.002 TYR A1058 PHE 0.020 0.002 PHE C 310 TRP 0.019 0.002 TRP A 635 HIS 0.009 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (21212) covalent geometry : angle 0.62788 / 0.33 (28720) hydrogen bonds : bond 0.03994 / 2.64 ( 666) hydrogen bonds : angle 5.18588 / 3.47 ( 1926) metal coordination : bond 0.00925 / 0.47 ( 3) metal coordination : angle 6.63357 / 2.99 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 91 time to evaluate : 0.750 Fit side-chains TARDY: cannot create tardy model for: "VAL A1307 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8774 (tm-30) REVERT: A 433 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8445 (m) REVERT: A 771 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8342 (t0) REVERT: A 831 MET cc_start: 0.8654 (mmp) cc_final: 0.7838 (mmm) REVERT: A 847 MET cc_start: 0.8836 (ttm) cc_final: 0.8595 (pmm) REVERT: B 346 TRP cc_start: 0.8452 (OUTLIER) cc_final: 0.7426 (m-10) REVERT: B 381 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8980 (pp) REVERT: B 724 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8943 (pp) REVERT: D 1068 MET cc_start: 0.1965 (mmp) cc_final: 0.1411 (mtm) REVERT: D 1134 LYS cc_start: 0.5522 (mptt) cc_final: 0.5153 (mmmt) REVERT: D 1291 GLN cc_start: 0.9125 (tt0) cc_final: 0.8646 (tp40) outliers start: 52 outliers final: 23 residues processed: 135 average time/residue: 0.1340 time to fit residues: 29.3008 Evaluate side-chains 113 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1151 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 21 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 chunk 255 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 217 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 HIS A 614 GLN A 942 GLN ** A1031 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.096575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061949 restraints weight = 55138.146| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.72 r_work: 0.2842 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 21215 Z= 0.263 Angle : 0.717 20.728 28729 Z= 0.372 Chirality : 0.048 0.187 3218 Planarity : 0.005 0.060 3679 Dihedral : 5.626 24.854 2822 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.84 % Allowed : 9.10 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.16), residues: 2564 helix: -0.57 (0.18), residues: 744 sheet: -1.35 (0.20), residues: 656 loop : -2.63 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 757 TYR 0.027 0.002 TYR A1058 PHE 0.030 0.002 PHE C 310 TRP 0.020 0.002 TRP C 442 HIS 0.006 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.26 (21212) covalent geometry : angle 0.69992 / 0.37 (28720) hydrogen bonds : bond 0.03907 / 2.57 ( 666) hydrogen bonds : angle 5.09374 / 3.40 ( 1926) metal coordination : bond 0.01727 / 0.87 ( 3) metal coordination : angle 8.70372 / 3.87 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 89 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8849 (tm-30) REVERT: A 433 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8734 (m) REVERT: A 506 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8518 (ttt) REVERT: A 520 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8674 (tmmm) REVERT: A 599 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: A 771 ASN cc_start: 0.9106 (OUTLIER) cc_final: 0.8669 (t0) REVERT: A 831 MET cc_start: 0.8724 (mmp) cc_final: 0.7978 (mmm) REVERT: A 847 MET cc_start: 0.9003 (ttm) cc_final: 0.8592 (pmm) REVERT: A 1278 GLU cc_start: 0.5731 (tt0) cc_final: 0.5418 (mm-30) REVERT: B 173 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.9095 (t) REVERT: B 346 TRP cc_start: 0.8892 (OUTLIER) cc_final: 0.7959 (m-10) REVERT: B 381 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9033 (pp) REVERT: B 687 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8536 (pp20) REVERT: B 713 MET cc_start: 0.8527 (mtp) cc_final: 0.7975 (mtm) REVERT: B 724 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8978 (pp) REVERT: C 308 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8477 (mp0) REVERT: D 1055 MET cc_start: -0.0829 (mmp) cc_final: -0.1100 (mmp) REVERT: D 1068 MET cc_start: 0.1922 (mmp) cc_final: 0.1484 (mtm) REVERT: D 1134 LYS cc_start: 0.5661 (mptt) cc_final: 0.5279 (mmmt) REVERT: D 1291 GLN cc_start: 0.9102 (tt0) cc_final: 0.8529 (tp40) REVERT: D 1295 ASN cc_start: 0.8735 (m-40) cc_final: 0.8429 (m-40) outliers start: 65 outliers final: 30 residues processed: 149 average time/residue: 0.1323 time to fit residues: 31.9299 Evaluate side-chains 123 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 82 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 599 GLN Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1151 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 92 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 170 optimal weight: 0.2980 chunk 158 optimal weight: 0.9980 chunk 232 optimal weight: 0.0770 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 614 GLN A 771 ASN ** A1031 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1059 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.099362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.065097 restraints weight = 55239.580| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.73 r_work: 0.2950 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21215 Z= 0.135 Angle : 0.632 20.767 28729 Z= 0.322 Chirality : 0.045 0.159 3218 Planarity : 0.004 0.051 3679 Dihedral : 5.290 25.701 2821 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.19 % Allowed : 10.63 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.16), residues: 2564 helix: -0.21 (0.19), residues: 750 sheet: -1.16 (0.20), residues: 642 loop : -2.51 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 283 TYR 0.021 0.001 TYR A1058 PHE 0.015 0.001 PHE C 310 TRP 0.009 0.001 TRP C 442 HIS 0.008 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (21212) covalent geometry : angle 0.61252 / 0.32 (28720) hydrogen bonds : bond 0.03250 / 2.14 ( 666) hydrogen bonds : angle 4.84210 / 3.22 ( 1926) metal coordination : bond 0.00949 / 0.49 ( 3) metal coordination : angle 8.74274 / 3.86 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 86 time to evaluate : 0.726 Fit side-chains REVERT: A 328 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8726 (tm-30) REVERT: A 433 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8620 (m) REVERT: A 506 MET cc_start: 0.8706 (tpp) cc_final: 0.8420 (ttt) REVERT: A 831 MET cc_start: 0.8696 (mmp) cc_final: 0.7882 (mmm) REVERT: A 847 MET cc_start: 0.8820 (ttm) cc_final: 0.8483 (pmm) REVERT: A 1278 GLU cc_start: 0.6148 (tt0) cc_final: 0.5727 (mm-30) REVERT: B 173 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.9037 (t) REVERT: B 346 TRP cc_start: 0.8660 (OUTLIER) cc_final: 0.7702 (m-10) REVERT: B 381 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8949 (pp) REVERT: B 687 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8453 (pp20) REVERT: B 713 MET cc_start: 0.8292 (mtp) cc_final: 0.7767 (mtm) REVERT: B 724 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8946 (pp) REVERT: C 308 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: D 1068 MET cc_start: 0.1891 (mmp) cc_final: 0.1662 (mtm) REVERT: D 1134 LYS cc_start: 0.5649 (mptt) cc_final: 0.5298 (mmmt) REVERT: D 1291 GLN cc_start: 0.9063 (tt0) cc_final: 0.8558 (tp40) REVERT: D 1295 ASN cc_start: 0.8734 (m-40) cc_final: 0.8441 (m-40) outliers start: 50 outliers final: 31 residues processed: 131 average time/residue: 0.1442 time to fit residues: 30.6530 Evaluate side-chains 122 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 84 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1151 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 139 optimal weight: 0.0980 chunk 185 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 134 optimal weight: 0.4980 chunk 194 optimal weight: 0.0270 chunk 232 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 614 GLN ** A1031 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1345 HIS ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.099933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.065602 restraints weight = 55138.225| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.78 r_work: 0.2965 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21215 Z= 0.122 Angle : 0.611 19.406 28729 Z= 0.310 Chirality : 0.044 0.158 3218 Planarity : 0.004 0.050 3679 Dihedral : 5.061 25.986 2821 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.36 % Allowed : 10.72 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.16), residues: 2564 helix: 0.05 (0.19), residues: 757 sheet: -1.05 (0.21), residues: 637 loop : -2.44 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.018 0.001 TYR A1058 PHE 0.014 0.001 PHE A 347 TRP 0.008 0.001 TRP B 630 HIS 0.007 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (21212) covalent geometry : angle 0.59200 / 0.31 (28720) hydrogen bonds : bond 0.03008 / 1.99 ( 666) hydrogen bonds : angle 4.65904 / 3.09 ( 1926) metal coordination : bond 0.00891 / 0.45 ( 3) metal coordination : angle 8.49909 / 3.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 89 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8692 (tm-30) REVERT: A 433 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8584 (m) REVERT: A 506 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8434 (ttt) REVERT: A 599 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8608 (tt0) REVERT: A 831 MET cc_start: 0.8725 (mmp) cc_final: 0.7917 (mmm) REVERT: A 1278 GLU cc_start: 0.6027 (tt0) cc_final: 0.5464 (mm-30) REVERT: B 173 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.9008 (t) REVERT: B 254 LEU cc_start: 0.8743 (tp) cc_final: 0.8459 (mp) REVERT: B 346 TRP cc_start: 0.8594 (OUTLIER) cc_final: 0.7655 (m-10) REVERT: B 381 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8943 (pp) REVERT: B 687 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8459 (pp20) REVERT: B 713 MET cc_start: 0.8273 (mtp) cc_final: 0.7744 (mtm) REVERT: B 724 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8947 (pp) REVERT: C 308 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: D 1068 MET cc_start: 0.2076 (mmp) cc_final: 0.1826 (mtm) REVERT: D 1134 LYS cc_start: 0.5795 (mptt) cc_final: 0.5451 (mmmt) REVERT: D 1291 GLN cc_start: 0.8985 (tt0) cc_final: 0.8553 (tp40) outliers start: 54 outliers final: 32 residues processed: 136 average time/residue: 0.1311 time to fit residues: 29.2822 Evaluate side-chains 125 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 84 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 599 GLN Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1151 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 153 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 614 GLN A 959 GLN ** A1031 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.096310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.062014 restraints weight = 55775.050| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.74 r_work: 0.2865 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 21215 Z= 0.294 Angle : 0.727 23.241 28729 Z= 0.373 Chirality : 0.049 0.189 3218 Planarity : 0.004 0.063 3679 Dihedral : 5.484 25.416 2821 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.45 % Allowed : 10.76 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.16), residues: 2564 helix: 0.00 (0.19), residues: 746 sheet: -1.13 (0.20), residues: 652 loop : -2.47 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 484 TYR 0.026 0.002 TYR B 259 PHE 0.021 0.002 PHE B 670 TRP 0.015 0.002 TRP C 442 HIS 0.009 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.29 (21212) covalent geometry : angle 0.70582 / 0.37 (28720) hydrogen bonds : bond 0.03715 / 2.43 ( 666) hydrogen bonds : angle 4.95018 / 3.30 ( 1926) metal coordination : bond 0.02396 / 1.19 ( 3) metal coordination : angle 9.80821 / 4.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 89 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8789 (tm-30) REVERT: A 433 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8769 (m) REVERT: A 506 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8524 (ttt) REVERT: A 599 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8461 (tt0) REVERT: A 1278 GLU cc_start: 0.6009 (tt0) cc_final: 0.5346 (mm-30) REVERT: B 173 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9035 (t) REVERT: B 254 LEU cc_start: 0.8797 (tp) cc_final: 0.8480 (mp) REVERT: B 346 TRP cc_start: 0.8906 (OUTLIER) cc_final: 0.8243 (m-10) REVERT: B 381 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.8939 (pp) REVERT: B 503 LYS cc_start: 0.8179 (pttm) cc_final: 0.7889 (tptp) REVERT: B 687 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8534 (pp20) REVERT: B 713 MET cc_start: 0.8428 (mtp) cc_final: 0.7982 (mtm) REVERT: B 724 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8946 (pp) REVERT: C 308 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8161 (mp0) REVERT: D 1068 MET cc_start: 0.1993 (mmp) cc_final: 0.1630 (mtm) REVERT: D 1134 LYS cc_start: 0.5824 (mptt) cc_final: 0.5491 (mmmt) REVERT: D 1291 GLN cc_start: 0.9091 (tt0) cc_final: 0.8748 (tp40) outliers start: 56 outliers final: 39 residues processed: 139 average time/residue: 0.1299 time to fit residues: 29.8149 Evaluate side-chains 130 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 82 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 599 GLN Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 400 MET Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1095 ARG Chi-restraints excluded: chain D residue 1151 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 7 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 186 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 614 GLN ** A1031 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.098334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.064130 restraints weight = 55218.017| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.74 r_work: 0.2932 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21215 Z= 0.147 Angle : 0.639 22.661 28729 Z= 0.325 Chirality : 0.045 0.160 3218 Planarity : 0.004 0.055 3679 Dihedral : 5.216 25.923 2821 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.27 % Allowed : 11.29 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.16), residues: 2564 helix: 0.17 (0.19), residues: 755 sheet: -1.01 (0.20), residues: 644 loop : -2.44 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 283 TYR 0.018 0.001 TYR A1058 PHE 0.015 0.001 PHE A 347 TRP 0.010 0.001 TRP B 630 HIS 0.007 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (21212) covalent geometry : angle 0.61727 / 0.32 (28720) hydrogen bonds : bond 0.03104 / 2.04 ( 666) hydrogen bonds : angle 4.73580 / 3.15 ( 1926) metal coordination : bond 0.01069 / 0.54 ( 3) metal coordination : angle 9.28742 / 4.08 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 84 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8747 (tm-30) REVERT: A 433 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8696 (m) REVERT: A 506 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8362 (ttt) REVERT: A 599 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8535 (tt0) REVERT: A 717 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9212 (mm) REVERT: A 1278 GLU cc_start: 0.6472 (tt0) cc_final: 0.5540 (mm-30) REVERT: B 173 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9073 (t) REVERT: B 254 LEU cc_start: 0.8864 (tp) cc_final: 0.8533 (mp) REVERT: B 346 TRP cc_start: 0.8789 (OUTLIER) cc_final: 0.7912 (m-10) REVERT: B 381 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8920 (pp) REVERT: B 687 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8552 (pp20) REVERT: B 713 MET cc_start: 0.8289 (mtp) cc_final: 0.7781 (mtm) REVERT: B 724 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8937 (pp) REVERT: C 308 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: D 1068 MET cc_start: 0.1895 (mmp) cc_final: 0.1597 (mtm) REVERT: D 1134 LYS cc_start: 0.5863 (mptt) cc_final: 0.5514 (mmmt) REVERT: D 1291 GLN cc_start: 0.9047 (tt0) cc_final: 0.8680 (tp40) outliers start: 52 outliers final: 33 residues processed: 130 average time/residue: 0.1323 time to fit residues: 28.3397 Evaluate side-chains 125 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 82 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 599 GLN Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1095 ARG Chi-restraints excluded: chain D residue 1151 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 102 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 246 optimal weight: 9.9990 chunk 243 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 614 GLN A1021 GLN ** A1031 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.097072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.063930 restraints weight = 54953.648| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.38 r_work: 0.2854 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21215 Z= 0.168 Angle : 0.645 21.639 28729 Z= 0.329 Chirality : 0.046 0.172 3218 Planarity : 0.004 0.051 3679 Dihedral : 5.140 26.022 2821 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.10 % Allowed : 11.59 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.16), residues: 2564 helix: 0.27 (0.19), residues: 753 sheet: -0.98 (0.20), residues: 646 loop : -2.38 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 283 TYR 0.018 0.001 TYR A1058 PHE 0.017 0.001 PHE A 347 TRP 0.011 0.001 TRP C 442 HIS 0.006 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (21212) covalent geometry : angle 0.62504 / 0.33 (28720) hydrogen bonds : bond 0.03164 / 2.08 ( 666) hydrogen bonds : angle 4.70515 / 3.12 ( 1926) metal coordination : bond 0.01407 / 0.71 ( 3) metal coordination : angle 9.05211 / 4.00 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 84 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8809 (tm-30) REVERT: A 433 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8675 (m) REVERT: A 506 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8362 (ttt) REVERT: A 599 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8564 (tt0) REVERT: A 717 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9230 (mm) REVERT: A 1278 GLU cc_start: 0.6644 (tt0) cc_final: 0.5659 (mm-30) REVERT: B 173 THR cc_start: 0.9333 (OUTLIER) cc_final: 0.9098 (t) REVERT: B 254 LEU cc_start: 0.8860 (tp) cc_final: 0.8549 (mp) REVERT: B 346 TRP cc_start: 0.8857 (OUTLIER) cc_final: 0.7977 (m-10) REVERT: B 381 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8906 (pp) REVERT: B 687 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8591 (pp20) REVERT: B 713 MET cc_start: 0.8391 (mtp) cc_final: 0.7856 (mtm) REVERT: B 724 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8893 (pp) REVERT: C 308 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: D 1068 MET cc_start: 0.2035 (mmp) cc_final: 0.1717 (mtm) REVERT: D 1134 LYS cc_start: 0.5439 (mptt) cc_final: 0.5080 (mmmt) REVERT: D 1291 GLN cc_start: 0.9040 (tt0) cc_final: 0.8708 (tp40) outliers start: 48 outliers final: 33 residues processed: 127 average time/residue: 0.1341 time to fit residues: 27.8799 Evaluate side-chains 124 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 81 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 599 GLN Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1151 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 85 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 255 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 614 GLN ** A1031 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1021 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.097012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.063075 restraints weight = 55448.850| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.41 r_work: 0.2854 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21215 Z= 0.174 Angle : 0.649 21.781 28729 Z= 0.331 Chirality : 0.046 0.167 3218 Planarity : 0.004 0.054 3679 Dihedral : 5.144 25.994 2821 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.06 % Allowed : 11.81 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.16), residues: 2564 helix: 0.31 (0.19), residues: 754 sheet: -1.00 (0.20), residues: 645 loop : -2.36 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 283 TYR 0.018 0.001 TYR A1058 PHE 0.017 0.001 PHE A 347 TRP 0.021 0.001 TRP D1064 HIS 0.009 0.001 HIS D1290 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (21212) covalent geometry : angle 0.62843 / 0.33 (28720) hydrogen bonds : bond 0.03189 / 2.10 ( 666) hydrogen bonds : angle 4.71296 / 3.13 ( 1926) metal coordination : bond 0.01383 / 0.70 ( 3) metal coordination : angle 9.09702 / 4.02 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 83 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8793 (tm-30) REVERT: A 433 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8682 (m) REVERT: A 506 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8368 (ttt) REVERT: A 599 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8574 (tt0) REVERT: A 667 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9346 (pp) REVERT: B 173 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.9077 (t) REVERT: B 254 LEU cc_start: 0.8846 (tp) cc_final: 0.8543 (mp) REVERT: B 346 TRP cc_start: 0.8850 (OUTLIER) cc_final: 0.8038 (m-10) REVERT: B 381 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.8889 (pp) REVERT: B 687 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8600 (pp20) REVERT: B 713 MET cc_start: 0.8363 (mtp) cc_final: 0.7879 (mtm) REVERT: B 724 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8904 (pp) REVERT: C 308 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: D 1068 MET cc_start: 0.2052 (mmp) cc_final: 0.1724 (mtm) REVERT: D 1134 LYS cc_start: 0.5349 (mptt) cc_final: 0.4986 (mmmt) REVERT: D 1291 GLN cc_start: 0.8985 (tt0) cc_final: 0.8637 (tp40) outliers start: 47 outliers final: 35 residues processed: 125 average time/residue: 0.1369 time to fit residues: 27.9918 Evaluate side-chains 125 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 80 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 599 GLN Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 771 ASN Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1151 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 84 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 255 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 256 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 247 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 614 GLN ** A1031 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 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 = 0.3705 r_free = 0.3705 target = 0.097492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.063653 restraints weight = 54991.184| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.40 r_work: 0.2869 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21215 Z= 0.133 Angle : 0.635 21.809 28729 Z= 0.323 Chirality : 0.045 0.172 3218 Planarity : 0.004 0.054 3679 Dihedral : 5.085 26.211 2821 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.19 % Allowed : 11.81 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.16), residues: 2564 helix: 0.37 (0.19), residues: 754 sheet: -0.96 (0.20), residues: 644 loop : -2.32 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 283 TYR 0.017 0.001 TYR A1058 PHE 0.015 0.001 PHE A 347 TRP 0.019 0.001 TRP D1064 HIS 0.006 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (21212) covalent geometry : angle 0.61398 / 0.32 (28720) hydrogen bonds : bond 0.03058 / 2.02 ( 666) hydrogen bonds : angle 4.68239 / 3.11 ( 1926) metal coordination : bond 0.01070 / 0.54 ( 3) metal coordination : angle 9.14723 / 4.05 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5567.35 seconds wall clock time: 96 minutes 17.78 seconds (5777.78 seconds total)