Starting phenix.real_space_refine on Tue Aug 26 14:59:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yqu_39506/08_2025/8yqu_39506.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yqu_39506/08_2025/8yqu_39506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yqu_39506/08_2025/8yqu_39506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yqu_39506/08_2025/8yqu_39506.map" model { file = "/net/cci-nas-00/data/ceres_data/8yqu_39506/08_2025/8yqu_39506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yqu_39506/08_2025/8yqu_39506.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 9 6.06 5 Mg 1 5.21 5 S 210 5.16 5 C 24386 2.51 5 N 6532 2.21 5 O 7101 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38239 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 11201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 11201 Classifications: {'peptide': 1407} Link IDs: {'PCIS': 2, 'PTRANS': 63, 'TRANS': 1341} Chain breaks: 2 Chain: "E" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 853 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "B" Number of atoms: 9553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1207, 9553 Classifications: {'peptide': 1207} Link IDs: {'PTRANS': 53, 'TRANS': 1153} Chain breaks: 4 Chain: "C" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2897 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 19, 'TRANS': 337} Chain: "D" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1668 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "H" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 630 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 5, 'TRANS': 74} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 815 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "F" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2694 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "J" Number of atoms: 7918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7918 Classifications: {'peptide': 972} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 442 SG CYS A 59 107.858 77.033 68.586 1.00 63.57 S ATOM 463 SG CYS A 62 105.598 75.883 65.762 1.00 49.39 S ATOM 523 SG CYS A 69 104.688 78.954 67.790 1.00 54.37 S ATOM 767 SG CYS A 99 91.892 60.347 110.442 1.00 87.13 S ATOM 789 SG CYS A 102 92.287 57.048 108.755 1.00 86.15 S ATOM 1041 SG CYS A 134 89.617 57.186 110.835 1.00 98.16 S ATOM 1066 SG CYS A 137 93.232 57.403 112.459 1.00100.92 S ATOM 21127 SG CYS B1180 97.370 62.049 69.243 1.00 57.15 S ATOM 21152 SG CYS B1183 97.322 62.664 72.956 1.00 61.57 S ATOM 21268 SG CYS B1198 99.917 64.225 71.079 1.00 67.07 S ATOM 21290 SG CYS B1201 100.131 60.360 71.236 1.00 71.16 S ATOM 26223 SG CYS H 7 71.288 135.772 47.846 1.00 38.01 S ATOM 26247 SG CYS H 10 70.021 135.905 44.196 1.00 43.38 S ATOM 26666 SG CYS H 65 67.642 135.638 47.232 1.00 30.16 S ATOM 26672 SG CYS H 66 69.534 138.860 46.221 1.00 46.95 S ATOM 27369 SG CYS G 73 36.575 133.367 110.348 1.00 67.48 S ATOM 27390 SG CYS G 76 38.008 136.895 110.765 1.00 72.67 S ATOM 27547 SG CYS G 96 40.274 134.124 109.684 1.00 71.61 S ATOM 27564 SG CYS G 98 38.892 134.149 113.232 1.00 69.72 S ATOM 26833 SG CYS G 4 67.279 101.248 140.015 1.00 72.79 S ATOM 26853 SG CYS G 7 70.672 101.817 138.280 1.00 77.80 S ATOM 26987 SG CYS G 24 68.704 98.788 137.426 1.00 77.30 S ATOM 26999 SG CYS G 26 70.220 99.070 140.917 1.00 88.67 S ATOM 35940 SG CYS J 937 21.405 95.935 102.864 1.00 77.95 S ATOM 36042 SG CYS J 950 19.199 93.694 100.528 1.00 90.10 S ATOM 36064 SG CYS J 953 18.318 97.353 101.097 1.00 88.99 S ATOM 35624 SG CYS J 898 21.660 115.922 74.887 1.00 71.30 S ATOM 35643 SG CYS J 901 19.077 118.314 76.009 1.00 70.41 S ATOM 32937 SG CYS J 401 112.346 73.169 29.682 1.00 90.48 S ATOM 33276 SG CYS J 442 115.007 76.028 30.765 1.00102.27 S Time building chain proxies: 9.58, per 1000 atoms: 0.25 Number of scatterers: 38239 At special positions: 0 Unit cell: (150.288, 173.72, 175.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 9 29.99 S 210 16.00 Mg 1 11.99 O 7101 8.00 N 6532 7.00 C 24386 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: 3.26 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" NE2 HIS A 72 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 62 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 59 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 69 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 102 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 134 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 99 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 137 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1198 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1180 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1183 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1201 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 76 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 96 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 98 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 73 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 24 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 7 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 26 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 4 " pdb=" ZN H 101 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 10 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 66 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 65 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 7 " pdb=" ZN J1301 " pdb="ZN ZN J1301 " - pdb=" ND1 HIS J 943 " pdb="ZN ZN J1301 " - pdb=" SG CYS J 953 " pdb="ZN ZN J1301 " - pdb=" SG CYS J 950 " pdb="ZN ZN J1301 " - pdb=" SG CYS J 937 " pdb=" ZN J1302 " pdb="ZN ZN J1302 " - pdb=" SG CYS J 901 " pdb="ZN ZN J1302 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1302 " - pdb=" ND1 HIS J 857 " pdb=" ZN J1303 " pdb="ZN ZN J1303 " - pdb=" ND1 HIS J 403 " pdb="ZN ZN J1303 " - pdb=" SG CYS J 442 " pdb="ZN ZN J1303 " - pdb=" SG CYS J 401 " Number of angles added : 36 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9056 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 51 sheets defined 44.9% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 116 through 126 removed outlier: 4.829A pdb=" N LEU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.857A pdb=" N ARG A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.703A pdb=" N HIS A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.656A pdb=" N LEU A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 273 removed outlier: 3.527A pdb=" N ASP A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 358 through 369 Proline residue: A 364 - end of helix removed outlier: 3.578A pdb=" N GLY A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 455 removed outlier: 4.317A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 552 through 561 removed outlier: 3.797A pdb=" N LEU A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 625 through 648 removed outlier: 3.528A pdb=" N LEU A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASN A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 659 through 686 Processing helix chain 'A' and resid 696 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 715 through 722 removed outlier: 3.765A pdb=" N ILE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 741 through 750 removed outlier: 3.518A pdb=" N MET A 745 " --> pdb=" O SER A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 785 Processing helix chain 'A' and resid 797 through 834 removed outlier: 3.691A pdb=" N PHE A 810 " --> pdb=" O MET A 806 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 811 " --> pdb=" O ASN A 807 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 819 " --> pdb=" O LYS A 815 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR A 822 " --> pdb=" O SER A 818 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 861 through 865 removed outlier: 4.035A pdb=" N LEU A 865 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 885 Processing helix chain 'A' and resid 891 through 918 removed outlier: 3.752A pdb=" N GLU A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 945 Processing helix chain 'A' and resid 953 through 970 Processing helix chain 'A' and resid 971 through 976 Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.875A pdb=" N GLU A 981 " --> pdb=" O ASN A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 995 removed outlier: 3.616A pdb=" N ALA A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1006 Processing helix chain 'A' and resid 1015 through 1033 Processing helix chain 'A' and resid 1040 through 1051 Processing helix chain 'A' and resid 1052 through 1059 Processing helix chain 'A' and resid 1060 through 1063 removed outlier: 3.689A pdb=" N ARG A1063 " --> pdb=" O SER A1060 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1060 through 1063' Processing helix chain 'A' and resid 1075 through 1082 Processing helix chain 'A' and resid 1085 through 1089 Processing helix chain 'A' and resid 1102 through 1105 Processing helix chain 'A' and resid 1106 through 1117 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 5.210A pdb=" N SER A1150 " --> pdb=" O ASP A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1162 removed outlier: 3.962A pdb=" N ASP A1157 " --> pdb=" O GLU A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1188 Processing helix chain 'A' and resid 1191 through 1203 Processing helix chain 'A' and resid 1229 through 1234 Processing helix chain 'A' and resid 1242 through 1256 Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1310 through 1314 removed outlier: 4.028A pdb=" N ILE A1314 " --> pdb=" O PRO A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1326 Processing helix chain 'A' and resid 1327 through 1344 Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 3.878A pdb=" N LEU A1353 " --> pdb=" O ASN A1349 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A1355 " --> pdb=" O ARG A1351 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A1356 " --> pdb=" O HIS A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1378 Processing helix chain 'A' and resid 1381 through 1389 removed outlier: 3.980A pdb=" N SER A1389 " --> pdb=" O ARG A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1402 Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1422 through 1426 Processing helix chain 'A' and resid 1432 through 1440 removed outlier: 3.747A pdb=" N GLU A1438 " --> pdb=" O LYS A1434 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.529A pdb=" N ARG E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 90 Processing helix chain 'E' and resid 101 through 112 Processing helix chain 'B' and resid 12 through 16 removed outlier: 3.631A pdb=" N VAL B 16 " --> pdb=" O ILE B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 38 removed outlier: 4.411A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 30 " --> pdb=" O MET B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.566A pdb=" N ILE B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.965A pdb=" N PHE B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 removed outlier: 3.865A pdb=" N LEU B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.808A pdb=" N PHE B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 removed outlier: 4.024A pdb=" N VAL B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 314 removed outlier: 3.988A pdb=" N HIS B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 Processing helix chain 'B' and resid 353 through 372 removed outlier: 3.567A pdb=" N VAL B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 382 through 402 removed outlier: 3.521A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 420 through 437 removed outlier: 3.641A pdb=" N ALA B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 452 Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.597A pdb=" N LEU B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 489 Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 535 through 542 removed outlier: 3.501A pdb=" N ASP B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 592 removed outlier: 3.925A pdb=" N LEU B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 602 No H-bonds generated for 'chain 'B' and resid 600 through 602' Processing helix chain 'B' and resid 603 through 609 removed outlier: 3.554A pdb=" N VAL B 608 " --> pdb=" O ASN B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 642 removed outlier: 3.517A pdb=" N ARG B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU B 641 " --> pdb=" O MET B 637 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 642 " --> pdb=" O LEU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 696 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 715 through 724 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.550A pdb=" N GLU B 747 " --> pdb=" O GLU B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'B' and resid 774 through 779 removed outlier: 3.564A pdb=" N ILE B 778 " --> pdb=" O PRO B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 805 removed outlier: 3.611A pdb=" N ARG B 805 " --> pdb=" O THR B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 818 Processing helix chain 'B' and resid 836 through 841 removed outlier: 3.565A pdb=" N HIS B 839 " --> pdb=" O THR B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 874 Processing helix chain 'B' and resid 1032 through 1037 removed outlier: 4.155A pdb=" N ARG B1036 " --> pdb=" O SER B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1055 removed outlier: 3.841A pdb=" N MET B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B1050 " --> pdb=" O THR B1046 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B1053 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1078 removed outlier: 3.711A pdb=" N ALA B1076 " --> pdb=" O SER B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1119 Processing helix chain 'B' and resid 1148 through 1159 Processing helix chain 'B' and resid 1160 through 1169 removed outlier: 3.678A pdb=" N ILE B1164 " --> pdb=" O ALA B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1214 through 1226 Processing helix chain 'C' and resid 19 through 30 Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 89 through 99 removed outlier: 3.660A pdb=" N PHE C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 230 through 258 removed outlier: 3.560A pdb=" N ARG C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 302 removed outlier: 3.646A pdb=" N GLY C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 358 removed outlier: 3.535A pdb=" N ILE C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 17 removed outlier: 3.552A pdb=" N THR D 8 " --> pdb=" O GLN D 4 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR D 11 " --> pdb=" O PHE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 38 Processing helix chain 'D' and resid 62 through 67 removed outlier: 3.789A pdb=" N HIS D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.595A pdb=" N MET D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 98 removed outlier: 3.663A pdb=" N LEU D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 98' Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.673A pdb=" N LEU D 125 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS D 127 " --> pdb=" O HIS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'H' and resid 14 through 16 No H-bonds generated for 'chain 'H' and resid 14 through 16' Processing helix chain 'H' and resid 17 through 33 removed outlier: 3.600A pdb=" N GLU H 27 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 44 Proline residue: H 42 - end of helix Processing helix chain 'H' and resid 51 through 58 Processing helix chain 'H' and resid 63 through 73 Processing helix chain 'H' and resid 75 through 79 Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 22 through 36 Processing helix chain 'F' and resid 171 through 194 removed outlier: 3.843A pdb=" N LEU F 178 " --> pdb=" O GLN F 174 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 207 removed outlier: 4.015A pdb=" N ILE F 200 " --> pdb=" O ASP F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 248 Processing helix chain 'F' and resid 288 through 314 removed outlier: 3.844A pdb=" N MET F 292 " --> pdb=" O SER F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 323 removed outlier: 3.653A pdb=" N ILE F 320 " --> pdb=" O ASN F 316 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS F 323 " --> pdb=" O LEU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 332 Processing helix chain 'J' and resid 75 through 84 removed outlier: 3.834A pdb=" N ILE J 79 " --> pdb=" O ILE J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 149 removed outlier: 3.706A pdb=" N PHE J 142 " --> pdb=" O SER J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 163 Processing helix chain 'J' and resid 168 through 173 Processing helix chain 'J' and resid 194 through 212 Processing helix chain 'J' and resid 215 through 236 removed outlier: 3.501A pdb=" N ILE J 219 " --> pdb=" O HIS J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 267 removed outlier: 4.327A pdb=" N THR J 267 " --> pdb=" O LYS J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 289 Processing helix chain 'J' and resid 299 through 343 removed outlier: 3.975A pdb=" N PHE J 303 " --> pdb=" O VAL J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 356 Processing helix chain 'J' and resid 364 through 371 Processing helix chain 'J' and resid 375 through 398 removed outlier: 3.772A pdb=" N ALA J 379 " --> pdb=" O GLY J 375 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE J 382 " --> pdb=" O GLU J 378 " (cutoff:3.500A) Processing helix chain 'J' and resid 401 through 411 removed outlier: 4.375A pdb=" N LYS J 405 " --> pdb=" O CYS J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 415 through 428 removed outlier: 3.531A pdb=" N LEU J 419 " --> pdb=" O GLN J 415 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS J 421 " --> pdb=" O ALA J 417 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL J 428 " --> pdb=" O GLU J 424 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 463 Processing helix chain 'J' and resid 466 through 474 removed outlier: 3.784A pdb=" N LYS J 473 " --> pdb=" O THR J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 673 through 683 removed outlier: 3.536A pdb=" N LEU J 683 " --> pdb=" O THR J 679 " (cutoff:3.500A) Processing helix chain 'J' and resid 684 through 697 removed outlier: 3.737A pdb=" N ASP J 697 " --> pdb=" O VAL J 693 " (cutoff:3.500A) Processing helix chain 'J' and resid 707 through 720 Processing helix chain 'J' and resid 722 through 727 removed outlier: 3.582A pdb=" N LEU J 727 " --> pdb=" O PRO J 723 " (cutoff:3.500A) Processing helix chain 'J' and resid 744 through 748 Processing helix chain 'J' and resid 769 through 791 Processing helix chain 'J' and resid 795 through 816 Processing helix chain 'J' and resid 845 through 849 Processing helix chain 'J' and resid 879 through 881 No H-bonds generated for 'chain 'J' and resid 879 through 881' Processing helix chain 'J' and resid 882 through 887 Processing helix chain 'J' and resid 907 through 911 removed outlier: 3.628A pdb=" N GLN J 910 " --> pdb=" O GLU J 907 " (cutoff:3.500A) Processing helix chain 'J' and resid 912 through 933 Processing helix chain 'J' and resid 956 through 960 removed outlier: 3.572A pdb=" N ILE J 960 " --> pdb=" O THR J 957 " (cutoff:3.500A) Processing helix chain 'J' and resid 966 through 977 removed outlier: 3.826A pdb=" N TYR J 973 " --> pdb=" O LEU J 969 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR J 974 " --> pdb=" O VAL J 970 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN J 975 " --> pdb=" O HIS J 971 " (cutoff:3.500A) Processing helix chain 'J' and resid 977 through 989 Processing helix chain 'J' and resid 1017 through 1028 Processing helix chain 'J' and resid 1030 through 1036 removed outlier: 3.903A pdb=" N ILE J1034 " --> pdb=" O SER J1030 " (cutoff:3.500A) Processing helix chain 'J' and resid 1044 through 1051 Processing helix chain 'J' and resid 1063 through 1085 removed outlier: 4.040A pdb=" N MET J1067 " --> pdb=" O ASP J1063 " (cutoff:3.500A) Processing helix chain 'J' and resid 1086 through 1089 Processing helix chain 'J' and resid 1093 through 1098 removed outlier: 3.992A pdb=" N ARG J1098 " --> pdb=" O ILE J1094 " (cutoff:3.500A) Processing helix chain 'J' and resid 1104 through 1109 Processing helix chain 'J' and resid 1121 through 1133 removed outlier: 3.694A pdb=" N THR J1125 " --> pdb=" O GLU J1121 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL J1131 " --> pdb=" O LYS J1127 " (cutoff:3.500A) Processing helix chain 'J' and resid 1133 through 1154 removed outlier: 3.771A pdb=" N LEU J1139 " --> pdb=" O ALA J1135 " (cutoff:3.500A) Processing helix chain 'J' and resid 1161 through 1182 removed outlier: 4.032A pdb=" N GLU J1167 " --> pdb=" O ASN J1163 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE J1168 " --> pdb=" O ILE J1164 " (cutoff:3.500A) Processing helix chain 'J' and resid 1190 through 1195 removed outlier: 3.628A pdb=" N ILE J1193 " --> pdb=" O ASN J1190 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE J1194 " --> pdb=" O PHE J1191 " (cutoff:3.500A) Processing helix chain 'J' and resid 1209 through 1213 Processing helix chain 'J' and resid 1242 through 1247 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.250A pdb=" N GLY A 4 " --> pdb=" O MET B1209 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASP B1211 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1404 through 1406 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.896A pdb=" N LEU A 39 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 83 removed outlier: 10.300A pdb=" N MET A 78 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 10.787A pdb=" N GLN A 202 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 10.803A pdb=" N ALA A 80 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA A 200 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 146 Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 319 Processing sheet with id=AA7, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 3.554A pdb=" N SER A 325 " --> pdb=" O MET A 463 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 338 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 436 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR A 340 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE A 444 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR A 326 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N MET A 446 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N CYS A 328 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 349 through 353 removed outlier: 3.979A pdb=" N ARG A 378 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP A 408 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N CYS A 376 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 514 through 515 Processing sheet with id=AB1, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AB2, first strand: chain 'A' and resid 566 through 569 removed outlier: 3.622A pdb=" N GLU A 600 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ARG A 594 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 753 through 754 Processing sheet with id=AB4, first strand: chain 'A' and resid 837 through 838 removed outlier: 3.542A pdb=" N SER A 845 " --> pdb=" O ILE A 837 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 844 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 866 through 869 Processing sheet with id=AB6, first strand: chain 'A' and resid 1267 through 1278 removed outlier: 6.600A pdb=" N ASN A1267 " --> pdb=" O THR A1295 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR A1295 " --> pdb=" O ASN A1267 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASN A1269 " --> pdb=" O ILE A1293 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE A1293 " --> pdb=" O ASN A1269 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A1271 " --> pdb=" O TYR A1291 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR A1291 " --> pdb=" O VAL A1271 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU A1273 " --> pdb=" O ASN A1289 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN A1289 " --> pdb=" O LEU A1273 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 3.662A pdb=" N ILE A1120 " --> pdb=" O ILE A1259 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1206 through 1210 removed outlier: 6.507A pdb=" N ILE A1223 " --> pdb=" O ILE A1176 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A1176 " --> pdb=" O ILE A1223 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE A1225 " --> pdb=" O TRP A1174 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TRP A1174 " --> pdb=" O ILE A1225 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU A1227 " --> pdb=" O ALA A1172 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A1128 " --> pdb=" O GLU A1179 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER G 40 " --> pdb=" O LEU A1131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1428 through 1431 removed outlier: 3.841A pdb=" N ASP A1428 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE E 132 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL E 125 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLN E 130 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR E 56 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL E 133 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL E 58 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE E 135 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 145 through 161 removed outlier: 3.762A pdb=" N ALA B 132 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B 130 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN B 156 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B 128 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N SER B 158 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY B 126 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE B 96 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN B 129 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B 94 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA B 131 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 84 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC3, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC4, first strand: chain 'B' and resid 416 through 419 removed outlier: 6.198A pdb=" N LEU B 204 " --> pdb=" O ASN B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 213 through 217 removed outlier: 6.851A pdb=" N TYR B 250 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG B 229 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 248 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU B 231 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 246 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE B 233 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER B 244 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AC7, first strand: chain 'B' and resid 710 through 712 removed outlier: 3.539A pdb=" N LEU B 674 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 596 through 598 removed outlier: 5.569A pdb=" N TRP B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 617 " --> pdb=" O TRP B 621 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY B 623 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 823 through 826 removed outlier: 7.146A pdb=" N LEU B 981 " --> pdb=" O VAL B 968 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL B 968 " --> pdb=" O LEU B 981 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG B 983 " --> pdb=" O ASP B 966 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 834 through 835 Processing sheet with id=AD2, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 6.098A pdb=" N VAL B 865 " --> pdb=" O ALA B1006 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B1008 " --> pdb=" O VAL B 865 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE B1102 " --> pdb=" O TYR B 853 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 894 through 896 removed outlier: 3.710A pdb=" N ASP B 952 " --> pdb=" O LYS B 905 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 932 through 934 Processing sheet with id=AD5, first strand: chain 'B' and resid 1017 through 1018 Processing sheet with id=AD6, first strand: chain 'B' and resid 1188 through 1190 Processing sheet with id=AD7, first strand: chain 'C' and resid 5 through 12 removed outlier: 5.123A pdb=" N PHE C 5 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS C 48 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASN C 7 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP C 46 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL C 39 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA C 225 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N CYS C 222 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LYS C 181 " --> pdb=" O CYS C 222 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 67 through 73 removed outlier: 5.094A pdb=" N ILE C 159 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N SER C 115 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLU C 161 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 113 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C 110 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 123 through 126 Processing sheet with id=AE1, first strand: chain 'C' and resid 267 through 271 Processing sheet with id=AE2, first strand: chain 'C' and resid 267 through 271 removed outlier: 3.745A pdb=" N GLU C 318 " --> pdb=" O VAL C 313 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 20 through 21 removed outlier: 5.141A pdb=" N ILE D 52 " --> pdb=" O TYR D 85 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU D 87 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLU D 86 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ASN D 119 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU D 88 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N TYR D 121 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU D 90 " --> pdb=" O TYR D 121 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 138 through 142 removed outlier: 4.473A pdb=" N PHE D 181 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N MET D 162 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N THR D 201 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE D 164 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 12 through 16 Processing sheet with id=AE6, first strand: chain 'G' and resid 68 through 69 Processing sheet with id=AE7, first strand: chain 'F' and resid 3 through 13 removed outlier: 6.241A pdb=" N SER F 75 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL F 51 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL F 77 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR F 49 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N SER F 79 " --> pdb=" O ASN F 47 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N ASN F 47 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 3 through 13 Processing sheet with id=AE9, first strand: chain 'F' and resid 86 through 95 removed outlier: 6.581A pdb=" N LEU F 101 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE F 100 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL F 110 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL F 130 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA F 89 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 237 through 238 removed outlier: 6.940A pdb=" N VAL F 163 " --> pdb=" O ILE F 285 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N CYS F 287 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N HIS F 165 " --> pdb=" O CYS F 287 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 117 through 119 removed outlier: 5.662A pdb=" N ILE J 91 " --> pdb=" O PHE J 110 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL J 92 " --> pdb=" O GLY J 129 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY J 129 " --> pdb=" O VAL J 92 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 440 through 441 removed outlier: 6.780A pdb=" N ASN J 440 " --> pdb=" O LEU J 449 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 493 through 495 removed outlier: 3.810A pdb=" N ALA J 504 " --> pdb=" O TYR J 494 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 875 through 878 removed outlier: 6.474A pdb=" N TRP J 859 " --> pdb=" O CYS J 898 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N CYS J 898 " --> pdb=" O TRP J 859 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE J 861 " --> pdb=" O LEU J 896 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU J 896 " --> pdb=" O ILE J 861 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL J 863 " --> pdb=" O ALA J 894 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 945 through 946 1698 hydrogen bonds defined for protein. 4716 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: 10.71 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6857 1.32 - 1.45: 9572 1.45 - 1.57: 22230 1.57 - 1.69: 0 1.69 - 1.81: 340 Bond restraints: 38999 Sorted by residual: bond pdb=" CA TYR J 733 " pdb=" C TYR J 733 " ideal model delta sigma weight residual 1.522 1.452 0.070 1.31e-02 5.83e+03 2.84e+01 bond pdb=" N THR J 738 " pdb=" CA THR J 738 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.22e-02 6.72e+03 1.26e+01 bond pdb=" CA LYS J 740 " pdb=" C LYS J 740 " ideal model delta sigma weight residual 1.525 1.481 0.044 1.25e-02 6.40e+03 1.24e+01 bond pdb=" CA THR J 738 " pdb=" C THR J 738 " ideal model delta sigma weight residual 1.520 1.480 0.040 1.16e-02 7.43e+03 1.17e+01 bond pdb=" N ASP J 734 " pdb=" CA ASP J 734 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.28e-02 6.10e+03 1.12e+01 ... (remaining 38994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 52488 2.84 - 5.67: 259 5.67 - 8.51: 9 8.51 - 11.34: 4 11.34 - 14.18: 4 Bond angle restraints: 52764 Sorted by residual: angle pdb=" N GLN J 747 " pdb=" CA GLN J 747 " pdb=" C GLN J 747 " ideal model delta sigma weight residual 113.30 100.66 12.64 1.34e+00 5.57e-01 8.89e+01 angle pdb=" N LEU J 748 " pdb=" CA LEU J 748 " pdb=" C LEU J 748 " ideal model delta sigma weight residual 113.20 102.05 11.15 1.21e+00 6.83e-01 8.49e+01 angle pdb=" C ARG J 750 " pdb=" CA ARG J 750 " pdb=" CB ARG J 750 " ideal model delta sigma weight residual 110.42 121.77 -11.35 1.99e+00 2.53e-01 3.25e+01 angle pdb=" N THR J 738 " pdb=" CA THR J 738 " pdb=" C THR J 738 " ideal model delta sigma weight residual 108.26 99.99 8.27 1.66e+00 3.63e-01 2.48e+01 angle pdb=" N ASN B1200 " pdb=" CA ASN B1200 " pdb=" C ASN B1200 " ideal model delta sigma weight residual 114.62 109.70 4.92 1.14e+00 7.69e-01 1.86e+01 ... (remaining 52759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 22161 17.11 - 34.22: 1364 34.22 - 51.33: 198 51.33 - 68.43: 38 68.43 - 85.54: 27 Dihedral angle restraints: 23788 sinusoidal: 9780 harmonic: 14008 Sorted by residual: dihedral pdb=" CA GLY A1073 " pdb=" C GLY A1073 " pdb=" N ILE A1074 " pdb=" CA ILE A1074 " ideal model delta harmonic sigma weight residual 180.00 -142.98 -37.02 0 5.00e+00 4.00e-02 5.48e+01 dihedral pdb=" CA ILE J 371 " pdb=" C ILE J 371 " pdb=" N LYS J 372 " pdb=" CA LYS J 372 " ideal model delta harmonic sigma weight residual 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA LEU A 303 " pdb=" C LEU A 303 " pdb=" N PRO A 304 " pdb=" CA PRO A 304 " ideal model delta harmonic sigma weight residual 180.00 -153.56 -26.44 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 23785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 5508 0.085 - 0.170: 441 0.170 - 0.254: 3 0.254 - 0.339: 0 0.339 - 0.424: 2 Chirality restraints: 5954 Sorted by residual: chirality pdb=" CA ARG J 750 " pdb=" N ARG J 750 " pdb=" C ARG J 750 " pdb=" CB ARG J 750 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" CA LEU J 751 " pdb=" N LEU J 751 " pdb=" C LEU J 751 " pdb=" CB LEU J 751 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA TYR J 741 " pdb=" N TYR J 741 " pdb=" C TYR J 741 " pdb=" CB TYR J 741 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 5951 not shown) Planarity restraints: 6780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 728 " -0.020 2.00e-02 2.50e+03 3.96e-02 1.56e+01 pdb=" C SER J 728 " 0.068 2.00e-02 2.50e+03 pdb=" O SER J 728 " -0.026 2.00e-02 2.50e+03 pdb=" N GLN J 729 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 235 " 0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO F 236 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO F 236 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 236 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 117 " 0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A 118 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " 0.036 5.00e-02 4.00e+02 ... (remaining 6777 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 322 2.60 - 3.17: 31992 3.17 - 3.75: 58894 3.75 - 4.32: 86029 4.32 - 4.90: 142540 Nonbonded interactions: 319777 Sorted by model distance: nonbonded pdb=" OD2 ASP A 459 " pdb="MG MG A2001 " model vdw 2.019 2.170 nonbonded pdb=" OG1 THR A1135 " pdb=" OD1 ASN A1173 " model vdw 2.118 3.040 nonbonded pdb=" OD1 ASP A 461 " pdb="MG MG A2001 " model vdw 2.158 2.170 nonbonded pdb=" O ILE B 486 " pdb=" OG1 THR B 506 " model vdw 2.171 3.040 nonbonded pdb=" O PHE D 58 " pdb=" OH TYR D 123 " model vdw 2.196 3.040 ... (remaining 319772 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=1.00 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: 3.240 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: 0.050 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 44.130 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 39033 Z= 0.144 Angle : 0.565 15.320 52800 Z= 0.304 Chirality : 0.044 0.424 5954 Planarity : 0.004 0.082 6780 Dihedral : 11.565 85.543 14732 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.31 % Allowed : 0.16 % Favored : 99.53 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.44 (0.12), residues: 4737 helix: -0.00 (0.12), residues: 1875 sheet: 0.06 (0.21), residues: 621 loop : -0.52 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 176 TYR 0.038 0.001 TYR J 689 PHE 0.036 0.001 PHE A 417 TRP 0.015 0.002 TRP J 439 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00269 (38999) covalent geometry : angle 0.55350 (52764) hydrogen bonds : bond 0.21167 ( 1674) hydrogen bonds : angle 7.27383 ( 4716) metal coordination : bond 0.00732 ( 34) metal coordination : angle 4.43397 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 751 time to evaluate : 1.481 Fit side-chains REVERT: A 394 LYS cc_start: 0.7889 (mtpt) cc_final: 0.7296 (mmpt) REVERT: A 1093 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7735 (mt-10) REVERT: A 1111 GLN cc_start: 0.8196 (tp-100) cc_final: 0.7979 (tp-100) REVERT: A 1209 MET cc_start: 0.7780 (mtp) cc_final: 0.7548 (mtp) REVERT: B 51 MET cc_start: 0.8982 (mmp) cc_final: 0.8698 (mmp) REVERT: B 93 ASP cc_start: 0.7865 (t0) cc_final: 0.6933 (m-30) REVERT: B 336 LEU cc_start: 0.8749 (tp) cc_final: 0.8543 (tm) REVERT: B 1019 GLU cc_start: 0.8454 (tt0) cc_final: 0.8233 (tt0) REVERT: C 354 VAL cc_start: 0.8818 (t) cc_final: 0.8489 (t) REVERT: D 50 HIS cc_start: 0.7753 (m90) cc_final: 0.7338 (m90) REVERT: J 182 LYS cc_start: 0.7549 (pttp) cc_final: 0.6913 (pptt) REVERT: J 228 HIS cc_start: 0.6107 (t-170) cc_final: 0.5734 (t-170) REVERT: J 380 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6372 (mm-30) REVERT: J 735 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7499 (mmmt) REVERT: J 946 GLN cc_start: 0.6616 (pt0) cc_final: 0.6209 (mp10) outliers start: 13 outliers final: 8 residues processed: 763 average time/residue: 0.8037 time to fit residues: 726.3104 Evaluate side-chains 491 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 482 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain J residue 730 LYS Chi-restraints excluded: chain J residue 735 LYS Chi-restraints excluded: chain J residue 739 SER Chi-restraints excluded: chain J residue 741 TYR Chi-restraints excluded: chain J residue 747 GLN Chi-restraints excluded: chain J residue 750 ARG Chi-restraints excluded: chain J residue 964 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 470 optimal weight: 0.2980 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 228 ASN A 265 GLN A 269 ASN A 382 GLN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN A 663 HIS A 744 ASN A 814 ASN A 834 GLN A1203 HIS A1256 ASN A1267 ASN A1350 HIS A1405 ASN E 130 GLN B 108 ASN B 484 GLN B 507 GLN B 516 ASN B 527 HIS B1077 GLN B1200 ASN B1227 ASN B1240 GLN D 80 ASN H 39 GLN F 133 GLN J 164 ASN J 487 ASN J 834 GLN J 917 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.150070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.111881 restraints weight = 47763.247| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.84 r_work: 0.3139 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 39033 Z= 0.192 Angle : 0.612 16.738 52800 Z= 0.317 Chirality : 0.047 0.204 5954 Planarity : 0.005 0.056 6780 Dihedral : 4.991 53.108 5217 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.82 % Favored : 96.16 % Rotamer: Outliers : 1.88 % Allowed : 9.42 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.01 (0.12), residues: 4737 helix: 0.62 (0.12), residues: 1896 sheet: -0.04 (0.20), residues: 635 loop : -0.42 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 301 TYR 0.035 0.002 TYR J 689 PHE 0.034 0.002 PHE A 417 TRP 0.018 0.002 TRP A 466 HIS 0.008 0.001 HIS B1033 Details of bonding type rmsd covalent geometry : bond 0.00460 (38999) covalent geometry : angle 0.60459 (52764) hydrogen bonds : bond 0.04845 ( 1674) hydrogen bonds : angle 5.20207 ( 4716) metal coordination : bond 0.00790 ( 34) metal coordination : angle 3.72327 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 518 time to evaluate : 1.623 Fit side-chains revert: symmetry clash REVERT: A 382 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7425 (pt0) REVERT: A 394 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7151 (mmpt) REVERT: A 424 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8447 (mt-10) REVERT: A 890 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7811 (mp10) REVERT: A 926 ASP cc_start: 0.8756 (p0) cc_final: 0.8542 (p0) REVERT: A 1093 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7981 (mt-10) REVERT: A 1094 MET cc_start: 0.9018 (ttp) cc_final: 0.8773 (ttp) REVERT: A 1209 MET cc_start: 0.7986 (mtp) cc_final: 0.7742 (mtp) REVERT: B 20 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: B 51 MET cc_start: 0.9079 (mmp) cc_final: 0.8762 (mmp) REVERT: B 93 ASP cc_start: 0.7993 (t0) cc_final: 0.6996 (m-30) REVERT: B 300 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7168 (mp) REVERT: B 302 ASN cc_start: 0.8402 (m-40) cc_final: 0.7942 (t0) REVERT: B 307 GLU cc_start: 0.8217 (tt0) cc_final: 0.7742 (mt-10) REVERT: B 317 ASP cc_start: 0.7479 (t0) cc_final: 0.7258 (t0) REVERT: B 451 GLN cc_start: 0.7827 (mt0) cc_final: 0.7599 (mm-40) REVERT: B 1019 GLU cc_start: 0.8746 (tt0) cc_final: 0.8515 (tt0) REVERT: B 1193 HIS cc_start: 0.8425 (t-170) cc_final: 0.8169 (t-170) REVERT: C 354 VAL cc_start: 0.8747 (t) cc_final: 0.8407 (t) REVERT: D 1 MET cc_start: 0.5639 (ttt) cc_final: 0.4773 (tpt) REVERT: D 50 HIS cc_start: 0.7904 (m90) cc_final: 0.7363 (m90) REVERT: G 1 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.5280 (pmt) REVERT: F 103 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6522 (mp0) REVERT: F 120 GLN cc_start: 0.6904 (tp40) cc_final: 0.6617 (tp40) REVERT: F 248 LYS cc_start: 0.6639 (mmmm) cc_final: 0.6404 (mmmm) REVERT: J 182 LYS cc_start: 0.7596 (pttp) cc_final: 0.6741 (pptt) REVERT: J 228 HIS cc_start: 0.5647 (t-170) cc_final: 0.5326 (t-170) REVERT: J 233 ARG cc_start: 0.5937 (OUTLIER) cc_final: 0.5391 (mpt-90) REVERT: J 324 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7826 (tm) REVERT: J 409 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6459 (mp10) REVERT: J 730 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7421 (tttt) REVERT: J 742 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7696 (mmt-90) REVERT: J 946 GLN cc_start: 0.6544 (pt0) cc_final: 0.6062 (mp10) REVERT: J 972 ASP cc_start: 0.7586 (m-30) cc_final: 0.7227 (m-30) REVERT: J 1101 LYS cc_start: 0.7506 (tttp) cc_final: 0.7166 (tptp) REVERT: J 1155 ILE cc_start: 0.7592 (tt) cc_final: 0.7189 (pp) outliers start: 80 outliers final: 31 residues processed: 564 average time/residue: 0.6777 time to fit residues: 459.2631 Evaluate side-chains 499 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 458 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain J residue 233 ARG Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 355 THR Chi-restraints excluded: chain J residue 409 GLN Chi-restraints excluded: chain J residue 425 SER Chi-restraints excluded: chain J residue 730 LYS Chi-restraints excluded: chain J residue 741 TYR Chi-restraints excluded: chain J residue 742 ARG Chi-restraints excluded: chain J residue 750 ARG Chi-restraints excluded: chain J residue 990 SER Chi-restraints excluded: chain J residue 1211 SER Chi-restraints excluded: chain J residue 1215 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 265 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 357 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 472 optimal weight: 2.9990 chunk 335 optimal weight: 9.9990 chunk 420 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 273 optimal weight: 1.9990 chunk 237 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 HIS A1166 GLN E 130 GLN B 57 GLN B 507 GLN B1240 GLN D 66 HIS D 80 ASN H 39 GLN G 89 GLN F 174 GLN J 164 ASN J 729 GLN J 905 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.151073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.112374 restraints weight = 47630.007| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.81 r_work: 0.3166 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 39033 Z= 0.135 Angle : 0.544 16.786 52800 Z= 0.281 Chirality : 0.045 0.189 5954 Planarity : 0.004 0.056 6780 Dihedral : 4.712 59.848 5203 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.04 % Allowed : 10.97 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.22 (0.12), residues: 4737 helix: 0.90 (0.12), residues: 1904 sheet: -0.03 (0.20), residues: 631 loop : -0.37 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 301 TYR 0.032 0.001 TYR J 689 PHE 0.023 0.001 PHE A 417 TRP 0.015 0.001 TRP A 466 HIS 0.007 0.001 HIS B1033 Details of bonding type rmsd covalent geometry : bond 0.00313 (38999) covalent geometry : angle 0.53792 (52764) hydrogen bonds : bond 0.04284 ( 1674) hydrogen bonds : angle 4.90139 ( 4716) metal coordination : bond 0.00649 ( 34) metal coordination : angle 3.12653 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 481 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: A 394 LYS cc_start: 0.7900 (mtpt) cc_final: 0.7201 (mmpt) REVERT: A 424 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8474 (mt-10) REVERT: A 668 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7703 (tt0) REVERT: A 890 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7799 (mp10) REVERT: A 1093 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8018 (mt-10) REVERT: A 1109 TYR cc_start: 0.8172 (m-80) cc_final: 0.7971 (m-80) REVERT: B 51 MET cc_start: 0.9028 (mmp) cc_final: 0.8724 (mmp) REVERT: B 93 ASP cc_start: 0.8026 (t0) cc_final: 0.7073 (m-30) REVERT: B 302 ASN cc_start: 0.8374 (m-40) cc_final: 0.7966 (t0) REVERT: B 307 GLU cc_start: 0.8247 (tt0) cc_final: 0.7778 (mt-10) REVERT: B 317 ASP cc_start: 0.7485 (t0) cc_final: 0.7272 (t0) REVERT: B 1019 GLU cc_start: 0.8704 (tt0) cc_final: 0.8486 (tt0) REVERT: B 1193 HIS cc_start: 0.8434 (t-170) cc_final: 0.8224 (t-170) REVERT: C 244 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7330 (mtp180) REVERT: C 245 ILE cc_start: 0.9107 (mm) cc_final: 0.8869 (mp) REVERT: C 354 VAL cc_start: 0.8783 (t) cc_final: 0.8415 (t) REVERT: D 1 MET cc_start: 0.5764 (ttt) cc_final: 0.4940 (tpt) REVERT: D 50 HIS cc_start: 0.7899 (m90) cc_final: 0.7400 (m90) REVERT: H 27 GLU cc_start: 0.8420 (mp0) cc_final: 0.7995 (mt-10) REVERT: G 1 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.5332 (pmt) REVERT: F 103 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6480 (mp0) REVERT: F 120 GLN cc_start: 0.6955 (tp40) cc_final: 0.6670 (tp40) REVERT: F 145 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.6946 (mtt180) REVERT: F 248 LYS cc_start: 0.6592 (mmmm) cc_final: 0.6348 (mmmm) REVERT: J 182 LYS cc_start: 0.7626 (pttp) cc_final: 0.6761 (pptt) REVERT: J 228 HIS cc_start: 0.5744 (t-170) cc_final: 0.5457 (t-170) REVERT: J 233 ARG cc_start: 0.6046 (OUTLIER) cc_final: 0.5236 (mpt-90) REVERT: J 324 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7928 (tm) REVERT: J 409 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6488 (mp10) REVERT: J 742 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7477 (mmm-85) REVERT: J 946 GLN cc_start: 0.6495 (pt0) cc_final: 0.6036 (mp10) REVERT: J 1101 LYS cc_start: 0.7501 (tttp) cc_final: 0.7185 (tptp) REVERT: J 1155 ILE cc_start: 0.7545 (tt) cc_final: 0.7263 (pp) REVERT: J 1181 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7730 (tttm) outliers start: 87 outliers final: 36 residues processed: 532 average time/residue: 0.7036 time to fit residues: 449.2662 Evaluate side-chains 491 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 445 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 233 ARG Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 409 GLN Chi-restraints excluded: chain J residue 741 TYR Chi-restraints excluded: chain J residue 742 ARG Chi-restraints excluded: chain J residue 799 LEU Chi-restraints excluded: chain J residue 964 LEU Chi-restraints excluded: chain J residue 990 SER Chi-restraints excluded: chain J residue 1161 VAL Chi-restraints excluded: chain J residue 1181 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 1 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 309 optimal weight: 6.9990 chunk 315 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 325 optimal weight: 0.0980 chunk 353 optimal weight: 0.9980 chunk 407 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN E 130 GLN B 43 ASN B 108 ASN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN C 19 ASN H 39 GLN G 89 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 ASN J 905 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111065 restraints weight = 46448.870| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.77 r_work: 0.3199 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 39033 Z= 0.176 Angle : 0.566 15.534 52800 Z= 0.291 Chirality : 0.046 0.197 5954 Planarity : 0.004 0.058 6780 Dihedral : 4.560 35.260 5195 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.86 % Favored : 96.12 % Rotamer: Outliers : 2.42 % Allowed : 12.05 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.26 (0.12), residues: 4737 helix: 0.98 (0.12), residues: 1894 sheet: -0.10 (0.20), residues: 631 loop : -0.36 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 66 TYR 0.028 0.002 TYR J 689 PHE 0.024 0.001 PHE A 417 TRP 0.016 0.001 TRP A 466 HIS 0.010 0.001 HIS B1033 Details of bonding type rmsd covalent geometry : bond 0.00425 (38999) covalent geometry : angle 0.55970 (52764) hydrogen bonds : bond 0.04255 ( 1674) hydrogen bonds : angle 4.82429 ( 4716) metal coordination : bond 0.00742 ( 34) metal coordination : angle 3.21989 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 469 time to evaluate : 1.654 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7806 (mt0) REVERT: A 239 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8253 (mp) REVERT: A 382 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7544 (pt0) REVERT: A 668 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7664 (tt0) REVERT: A 765 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: A 806 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8762 (mtt) REVERT: A 866 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8141 (tp30) REVERT: A 890 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7806 (mp10) REVERT: A 1093 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7991 (mt-10) REVERT: A 1286 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8102 (mtm-85) REVERT: B 51 MET cc_start: 0.9016 (mmp) cc_final: 0.8703 (mmp) REVERT: B 93 ASP cc_start: 0.8042 (t0) cc_final: 0.7137 (m-30) REVERT: B 302 ASN cc_start: 0.8353 (m-40) cc_final: 0.8000 (t0) REVERT: B 307 GLU cc_start: 0.8231 (tt0) cc_final: 0.7793 (mt-10) REVERT: B 336 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8150 (tm) REVERT: B 542 MET cc_start: 0.8674 (ptp) cc_final: 0.8353 (ptm) REVERT: B 1019 GLU cc_start: 0.8676 (tt0) cc_final: 0.8430 (tt0) REVERT: B 1193 HIS cc_start: 0.8451 (t-170) cc_final: 0.8230 (t-170) REVERT: C 244 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7286 (mtp180) REVERT: C 354 VAL cc_start: 0.8831 (t) cc_final: 0.8459 (t) REVERT: D 1 MET cc_start: 0.5832 (ttt) cc_final: 0.5354 (tpt) REVERT: D 50 HIS cc_start: 0.7944 (m90) cc_final: 0.7449 (m90) REVERT: G 1 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.5255 (pmt) REVERT: F 1 MET cc_start: 0.7833 (ttp) cc_final: 0.7415 (ttp) REVERT: F 103 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6673 (mp0) REVERT: F 120 GLN cc_start: 0.6835 (tp40) cc_final: 0.6598 (tp40) REVERT: F 145 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.6892 (mtt180) REVERT: F 204 GLU cc_start: 0.6971 (tp30) cc_final: 0.6433 (mt-10) REVERT: F 248 LYS cc_start: 0.6484 (mmmm) cc_final: 0.6188 (mmmm) REVERT: F 327 TRP cc_start: 0.7447 (m100) cc_final: 0.7239 (m100) REVERT: J 182 LYS cc_start: 0.7702 (pttp) cc_final: 0.6807 (pptt) REVERT: J 228 HIS cc_start: 0.5729 (t-170) cc_final: 0.5518 (t-170) REVERT: J 229 ARG cc_start: 0.6864 (mtm-85) cc_final: 0.6244 (mtt-85) REVERT: J 233 ARG cc_start: 0.5801 (OUTLIER) cc_final: 0.5296 (mpt-90) REVERT: J 324 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7878 (tm) REVERT: J 398 LYS cc_start: 0.7386 (mtpp) cc_final: 0.7003 (mmmt) REVERT: J 409 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6497 (mp10) REVERT: J 742 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7625 (mmt-90) REVERT: J 1101 LYS cc_start: 0.7472 (tttp) cc_final: 0.7145 (tptp) REVERT: J 1130 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7145 (ttm170) REVERT: J 1155 ILE cc_start: 0.7555 (tt) cc_final: 0.7317 (pp) outliers start: 103 outliers final: 47 residues processed: 529 average time/residue: 0.7217 time to fit residues: 460.4930 Evaluate side-chains 513 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 451 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1190 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1286 ARG Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 233 ARG Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 409 GLN Chi-restraints excluded: chain J residue 425 SER Chi-restraints excluded: chain J residue 741 TYR Chi-restraints excluded: chain J residue 742 ARG Chi-restraints excluded: chain J residue 964 LEU Chi-restraints excluded: chain J residue 990 SER Chi-restraints excluded: chain J residue 1130 ARG Chi-restraints excluded: chain J residue 1161 VAL Chi-restraints excluded: chain J residue 1211 SER Chi-restraints excluded: chain J residue 1215 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 142 optimal weight: 5.9990 chunk 441 optimal weight: 8.9990 chunk 234 optimal weight: 3.9990 chunk 358 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 185 optimal weight: 10.0000 chunk 417 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 chunk 243 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 209 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN B 507 GLN C 19 ASN D 4 GLN H 39 GLN G 89 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 ASN J 905 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.152086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.114475 restraints weight = 46286.120| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.74 r_work: 0.3213 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 39033 Z= 0.104 Angle : 0.509 16.521 52800 Z= 0.262 Chirality : 0.043 0.220 5954 Planarity : 0.004 0.057 6780 Dihedral : 4.355 37.199 5195 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.14 % Allowed : 13.35 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.48 (0.12), residues: 4737 helix: 1.21 (0.12), residues: 1902 sheet: -0.09 (0.20), residues: 641 loop : -0.26 (0.13), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 92 TYR 0.026 0.001 TYR C 310 PHE 0.017 0.001 PHE A 918 TRP 0.015 0.001 TRP A 466 HIS 0.004 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00232 (38999) covalent geometry : angle 0.50474 (52764) hydrogen bonds : bond 0.03547 ( 1674) hydrogen bonds : angle 4.61532 ( 4716) metal coordination : bond 0.00547 ( 34) metal coordination : angle 2.65340 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 496 time to evaluate : 1.235 Fit side-chains REVERT: A 24 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: A 239 LEU cc_start: 0.8669 (mp) cc_final: 0.8226 (mp) REVERT: A 382 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7438 (pt0) REVERT: A 394 LYS cc_start: 0.7921 (mtpt) cc_final: 0.7168 (mmpt) REVERT: A 656 MET cc_start: 0.9107 (mtt) cc_final: 0.8899 (mtm) REVERT: A 668 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7528 (tt0) REVERT: A 806 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8702 (mtt) REVERT: A 866 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8120 (tp30) REVERT: A 904 ASP cc_start: 0.8331 (m-30) cc_final: 0.7892 (t0) REVERT: A 1093 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7852 (mt-10) REVERT: B 93 ASP cc_start: 0.7997 (t0) cc_final: 0.7042 (m-30) REVERT: B 302 ASN cc_start: 0.8268 (m-40) cc_final: 0.7911 (t0) REVERT: B 307 GLU cc_start: 0.8101 (tt0) cc_final: 0.7623 (mt-10) REVERT: B 317 ASP cc_start: 0.7281 (t0) cc_final: 0.7072 (t0) REVERT: B 324 GLN cc_start: 0.8545 (tt0) cc_final: 0.8328 (mt0) REVERT: B 336 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8099 (tm) REVERT: B 371 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7787 (tt) REVERT: B 773 ASP cc_start: 0.8292 (t0) cc_final: 0.8020 (t70) REVERT: B 1019 GLU cc_start: 0.8649 (tt0) cc_final: 0.8425 (tt0) REVERT: B 1173 ASP cc_start: 0.8410 (p0) cc_final: 0.8141 (p0) REVERT: C 210 MET cc_start: 0.8380 (mmm) cc_final: 0.8023 (mmt) REVERT: C 244 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7061 (mtp180) REVERT: C 272 MET cc_start: 0.8278 (mtm) cc_final: 0.8062 (mtp) REVERT: C 354 VAL cc_start: 0.8642 (t) cc_final: 0.8260 (t) REVERT: D 1 MET cc_start: 0.5622 (ttt) cc_final: 0.4936 (tpt) REVERT: D 50 HIS cc_start: 0.7876 (m90) cc_final: 0.7344 (m90) REVERT: D 83 LYS cc_start: 0.7473 (mtmp) cc_final: 0.7264 (mtmm) REVERT: H 27 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: F 103 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6498 (mp0) REVERT: F 120 GLN cc_start: 0.6889 (tp40) cc_final: 0.6638 (tp40) REVERT: F 204 GLU cc_start: 0.6955 (tp30) cc_final: 0.6310 (mt-10) REVERT: F 248 LYS cc_start: 0.6532 (mmmm) cc_final: 0.6191 (mmmm) REVERT: F 328 MET cc_start: 0.7178 (ttt) cc_final: 0.6539 (tmt) REVERT: J 182 LYS cc_start: 0.7672 (pttp) cc_final: 0.6790 (pptt) REVERT: J 229 ARG cc_start: 0.6722 (mtm-85) cc_final: 0.5923 (mmt180) REVERT: J 233 ARG cc_start: 0.5707 (OUTLIER) cc_final: 0.5239 (mpt-90) REVERT: J 324 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7741 (tm) REVERT: J 409 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6439 (mp10) REVERT: J 742 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7441 (mmt-90) REVERT: J 972 ASP cc_start: 0.7804 (m-30) cc_final: 0.7334 (m-30) REVERT: J 1101 LYS cc_start: 0.7492 (tttp) cc_final: 0.7122 (tptp) REVERT: J 1130 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7017 (ttm170) outliers start: 91 outliers final: 36 residues processed: 549 average time/residue: 0.7312 time to fit residues: 486.1701 Evaluate side-chains 502 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 454 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 233 ARG Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 376 LYS Chi-restraints excluded: chain J residue 409 GLN Chi-restraints excluded: chain J residue 425 SER Chi-restraints excluded: chain J residue 741 TYR Chi-restraints excluded: chain J residue 742 ARG Chi-restraints excluded: chain J residue 964 LEU Chi-restraints excluded: chain J residue 990 SER Chi-restraints excluded: chain J residue 1130 ARG Chi-restraints excluded: chain J residue 1161 VAL Chi-restraints excluded: chain J residue 1211 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 39 optimal weight: 4.9990 chunk 392 optimal weight: 20.0000 chunk 409 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 0.0970 chunk 389 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 339 optimal weight: 7.9990 chunk 306 optimal weight: 5.9990 chunk 334 optimal weight: 10.0000 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A 318 GLN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 507 GLN C 19 ASN H 39 GLN G 45 HIS G 89 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 ASN ** J 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 917 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106606 restraints weight = 46919.522| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.85 r_work: 0.3118 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 39033 Z= 0.357 Angle : 0.706 13.142 52800 Z= 0.362 Chirality : 0.052 0.216 5954 Planarity : 0.005 0.059 6780 Dihedral : 4.965 36.684 5195 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.44 % Rotamer: Outliers : 2.98 % Allowed : 13.89 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.00 (0.12), residues: 4737 helix: 0.73 (0.12), residues: 1892 sheet: -0.24 (0.20), residues: 654 loop : -0.48 (0.13), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 96 TYR 0.027 0.002 TYR J 689 PHE 0.029 0.002 PHE A 918 TRP 0.016 0.002 TRP A 466 HIS 0.012 0.002 HIS J 215 Details of bonding type rmsd covalent geometry : bond 0.00879 (38999) covalent geometry : angle 0.69748 (52764) hydrogen bonds : bond 0.05277 ( 1674) hydrogen bonds : angle 5.04764 ( 4716) metal coordination : bond 0.01405 ( 34) metal coordination : angle 4.33192 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 456 time to evaluate : 1.679 Fit side-chains REVERT: A 23 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7754 (mtm-85) REVERT: A 24 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7869 (mt0) REVERT: A 382 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7687 (pt0) REVERT: A 765 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: A 806 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8862 (mtt) REVERT: A 866 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7974 (tp30) REVERT: A 890 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7864 (mp10) REVERT: A 1093 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8244 (mt-10) REVERT: A 1179 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: B 93 ASP cc_start: 0.8072 (t0) cc_final: 0.7191 (m-30) REVERT: B 302 ASN cc_start: 0.8482 (m-40) cc_final: 0.8255 (t0) REVERT: B 307 GLU cc_start: 0.8346 (tt0) cc_final: 0.7959 (mt-10) REVERT: B 317 ASP cc_start: 0.7413 (t0) cc_final: 0.7193 (t0) REVERT: B 336 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8197 (tm) REVERT: B 727 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8858 (tp) REVERT: B 1019 GLU cc_start: 0.8737 (tt0) cc_final: 0.8524 (tt0) REVERT: C 20 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8164 (mm) REVERT: C 244 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7437 (mtp180) REVERT: D 1 MET cc_start: 0.6259 (ttt) cc_final: 0.4707 (tpp) REVERT: D 34 MET cc_start: 0.7740 (mtt) cc_final: 0.7366 (mtp) REVERT: D 50 HIS cc_start: 0.8062 (m90) cc_final: 0.7605 (m90) REVERT: G 1 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.5576 (pmt) REVERT: F 103 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6535 (mp0) REVERT: F 120 GLN cc_start: 0.6889 (tp40) cc_final: 0.6646 (tp40) REVERT: F 204 GLU cc_start: 0.7046 (tp30) cc_final: 0.6684 (tt0) REVERT: F 248 LYS cc_start: 0.6552 (mmmm) cc_final: 0.6276 (mmmm) REVERT: F 328 MET cc_start: 0.7208 (ttt) cc_final: 0.6561 (tmt) REVERT: J 229 ARG cc_start: 0.6979 (mtm-85) cc_final: 0.6186 (mtt-85) REVERT: J 233 ARG cc_start: 0.5888 (OUTLIER) cc_final: 0.5245 (mpt-90) REVERT: J 313 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6224 (mp0) REVERT: J 324 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8016 (tm) REVERT: J 398 LYS cc_start: 0.7460 (mtpp) cc_final: 0.7074 (mmmt) REVERT: J 409 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6621 (mp10) REVERT: J 742 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7573 (mmt-90) REVERT: J 972 ASP cc_start: 0.8061 (m-30) cc_final: 0.7562 (m-30) REVERT: J 1101 LYS cc_start: 0.7504 (tttp) cc_final: 0.7178 (tptp) outliers start: 127 outliers final: 59 residues processed: 538 average time/residue: 0.7030 time to fit residues: 460.4858 Evaluate side-chains 515 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 440 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1190 ILE Chi-restraints excluded: chain A residue 1281 GLN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 233 ARG Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 313 GLU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 409 GLN Chi-restraints excluded: chain J residue 425 SER Chi-restraints excluded: chain J residue 741 TYR Chi-restraints excluded: chain J residue 742 ARG Chi-restraints excluded: chain J residue 964 LEU Chi-restraints excluded: chain J residue 990 SER Chi-restraints excluded: chain J residue 1161 VAL Chi-restraints excluded: chain J residue 1211 SER Chi-restraints excluded: chain J residue 1215 SER Chi-restraints excluded: chain J residue 1242 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 421 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 465 optimal weight: 1.9990 chunk 316 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 458 optimal weight: 0.0030 chunk 199 optimal weight: 0.8980 chunk 302 optimal weight: 8.9990 chunk 407 optimal weight: 10.0000 chunk 432 optimal weight: 0.8980 chunk 296 optimal weight: 9.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 ASN E 130 GLN B 108 ASN B 507 GLN B1200 ASN H 39 GLN G 89 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 ASN J 167 ASN J 917 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109308 restraints weight = 46786.315| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.83 r_work: 0.3156 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39033 Z= 0.132 Angle : 0.548 16.149 52800 Z= 0.282 Chirality : 0.044 0.233 5954 Planarity : 0.004 0.058 6780 Dihedral : 4.595 37.584 5195 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.16 % Allowed : 14.80 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.29 (0.12), residues: 4737 helix: 1.06 (0.12), residues: 1902 sheet: -0.21 (0.20), residues: 636 loop : -0.36 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 92 TYR 0.015 0.001 TYR J 974 PHE 0.020 0.001 PHE A 918 TRP 0.018 0.001 TRP A1154 HIS 0.008 0.001 HIS B1033 Details of bonding type rmsd covalent geometry : bond 0.00305 (38999) covalent geometry : angle 0.54266 (52764) hydrogen bonds : bond 0.03849 ( 1674) hydrogen bonds : angle 4.73585 ( 4716) metal coordination : bond 0.00684 ( 34) metal coordination : angle 2.96674 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 483 time to evaluate : 1.443 Fit side-chains REVERT: A 24 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7791 (mt0) REVERT: A 176 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.6332 (mtp180) REVERT: A 382 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7541 (pt0) REVERT: A 394 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7140 (mmpt) REVERT: A 806 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8716 (mtt) REVERT: A 866 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8064 (tp30) REVERT: A 890 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7806 (mp10) REVERT: A 950 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8153 (mp) REVERT: A 1093 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8055 (mt-10) REVERT: A 1441 LYS cc_start: 0.7602 (mmtm) cc_final: 0.6432 (ptpt) REVERT: B 93 ASP cc_start: 0.7976 (t0) cc_final: 0.7083 (m-30) REVERT: B 302 ASN cc_start: 0.8333 (m-40) cc_final: 0.8034 (t0) REVERT: B 307 GLU cc_start: 0.8175 (tt0) cc_final: 0.7745 (mt-10) REVERT: B 317 ASP cc_start: 0.7422 (t0) cc_final: 0.7213 (t0) REVERT: B 336 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8166 (tm) REVERT: B 727 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8770 (tp) REVERT: B 1019 GLU cc_start: 0.8657 (tt0) cc_final: 0.8445 (tt0) REVERT: C 244 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7159 (mtp180) REVERT: C 354 VAL cc_start: 0.8795 (t) cc_final: 0.8409 (t) REVERT: D 1 MET cc_start: 0.5688 (ttt) cc_final: 0.5054 (tpt) REVERT: D 50 HIS cc_start: 0.7993 (m90) cc_final: 0.7476 (m90) REVERT: H 27 GLU cc_start: 0.8428 (mp0) cc_final: 0.7873 (mt-10) REVERT: G 1 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.5659 (pmt) REVERT: F 103 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6551 (mp0) REVERT: F 120 GLN cc_start: 0.6823 (tp40) cc_final: 0.6572 (tp40) REVERT: F 204 GLU cc_start: 0.6983 (tp30) cc_final: 0.6390 (mt-10) REVERT: F 248 LYS cc_start: 0.6523 (mmmm) cc_final: 0.6213 (mmmm) REVERT: F 328 MET cc_start: 0.7189 (ttt) cc_final: 0.6552 (tmt) REVERT: J 229 ARG cc_start: 0.6815 (mtm-85) cc_final: 0.6000 (mmt180) REVERT: J 233 ARG cc_start: 0.5799 (OUTLIER) cc_final: 0.5292 (mpt-90) REVERT: J 313 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6181 (mp0) REVERT: J 324 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7872 (tm) REVERT: J 409 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6501 (mp10) REVERT: J 420 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6827 (tp) REVERT: J 742 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7500 (mmt-90) REVERT: J 1228 ASP cc_start: 0.6823 (m-30) cc_final: 0.6251 (m-30) outliers start: 92 outliers final: 45 residues processed: 543 average time/residue: 0.7417 time to fit residues: 487.3693 Evaluate side-chains 520 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 460 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 233 ARG Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 313 GLU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 409 GLN Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 425 SER Chi-restraints excluded: chain J residue 741 TYR Chi-restraints excluded: chain J residue 742 ARG Chi-restraints excluded: chain J residue 964 LEU Chi-restraints excluded: chain J residue 1161 VAL Chi-restraints excluded: chain J residue 1211 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 444 optimal weight: 0.7980 chunk 253 optimal weight: 4.9990 chunk 355 optimal weight: 30.0000 chunk 114 optimal weight: 5.9990 chunk 424 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 314 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 ASN A1256 ASN E 130 GLN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN B1039 ASN H 39 GLN G 89 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 ASN J 164 ASN ** J 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.148939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110150 restraints weight = 46512.015| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.93 r_work: 0.3155 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39033 Z= 0.133 Angle : 0.546 15.661 52800 Z= 0.279 Chirality : 0.044 0.247 5954 Planarity : 0.004 0.059 6780 Dihedral : 4.493 36.357 5195 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.26 % Allowed : 15.55 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.40 (0.12), residues: 4737 helix: 1.15 (0.12), residues: 1908 sheet: -0.14 (0.21), residues: 626 loop : -0.30 (0.13), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 66 TYR 0.017 0.001 TYR H 17 PHE 0.020 0.001 PHE A 918 TRP 0.016 0.001 TRP A 466 HIS 0.007 0.001 HIS J 215 Details of bonding type rmsd covalent geometry : bond 0.00312 (38999) covalent geometry : angle 0.54075 (52764) hydrogen bonds : bond 0.03781 ( 1674) hydrogen bonds : angle 4.65921 ( 4716) metal coordination : bond 0.00670 ( 34) metal coordination : angle 2.85931 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 471 time to evaluate : 1.698 Fit side-chains REVERT: A 24 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7794 (mt0) REVERT: A 96 ARG cc_start: 0.8366 (mtp-110) cc_final: 0.8066 (mtp-110) REVERT: A 382 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7589 (pt0) REVERT: A 394 LYS cc_start: 0.7862 (mtpt) cc_final: 0.7160 (mmpt) REVERT: A 806 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8758 (mtt) REVERT: A 866 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8048 (tp30) REVERT: A 890 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7811 (mp10) REVERT: A 950 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8091 (mp) REVERT: A 1093 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8064 (mt-10) REVERT: A 1425 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8061 (mmp) REVERT: A 1441 LYS cc_start: 0.7587 (mmtm) cc_final: 0.6412 (ptpt) REVERT: B 93 ASP cc_start: 0.7991 (t0) cc_final: 0.7119 (m-30) REVERT: B 302 ASN cc_start: 0.8307 (m-40) cc_final: 0.8046 (t0) REVERT: B 307 GLU cc_start: 0.8130 (tt0) cc_final: 0.7692 (mt-10) REVERT: B 336 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8174 (tm) REVERT: B 460 ARG cc_start: 0.8115 (tpp80) cc_final: 0.7858 (tpp80) REVERT: B 727 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8789 (tp) REVERT: B 1019 GLU cc_start: 0.8647 (tt0) cc_final: 0.8421 (tt0) REVERT: C 244 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7161 (mtp180) REVERT: C 354 VAL cc_start: 0.8762 (t) cc_final: 0.8369 (t) REVERT: D 1 MET cc_start: 0.5695 (ttt) cc_final: 0.4942 (tpt) REVERT: D 50 HIS cc_start: 0.8006 (m90) cc_final: 0.7510 (m90) REVERT: G 1 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.5646 (pmt) REVERT: G 28 GLU cc_start: 0.8178 (tp30) cc_final: 0.7640 (tp30) REVERT: F 103 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6487 (mp0) REVERT: F 204 GLU cc_start: 0.6951 (tp30) cc_final: 0.6322 (mt-10) REVERT: F 248 LYS cc_start: 0.6439 (mmmm) cc_final: 0.6111 (mmmm) REVERT: F 327 TRP cc_start: 0.7120 (m100) cc_final: 0.6873 (m100) REVERT: F 328 MET cc_start: 0.7171 (ttt) cc_final: 0.6534 (tmt) REVERT: J 229 ARG cc_start: 0.6799 (mtm-85) cc_final: 0.5979 (mmt180) REVERT: J 233 ARG cc_start: 0.5803 (OUTLIER) cc_final: 0.5318 (mpt-90) REVERT: J 313 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6596 (mp0) REVERT: J 324 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7848 (tm) REVERT: J 380 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6523 (mm-30) REVERT: J 409 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6459 (mp10) REVERT: J 420 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6806 (tp) REVERT: J 742 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7494 (mmt-90) REVERT: J 1061 MET cc_start: 0.8586 (ptp) cc_final: 0.8350 (ptm) REVERT: J 1130 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7084 (ttm170) REVERT: J 1228 ASP cc_start: 0.6842 (m-30) cc_final: 0.6250 (m-30) outliers start: 96 outliers final: 54 residues processed: 527 average time/residue: 0.7731 time to fit residues: 493.9791 Evaluate side-chains 526 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 456 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1190 ILE Chi-restraints excluded: chain A residue 1425 MET Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 233 ARG Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 313 GLU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 409 GLN Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain J residue 425 SER Chi-restraints excluded: chain J residue 741 TYR Chi-restraints excluded: chain J residue 742 ARG Chi-restraints excluded: chain J residue 964 LEU Chi-restraints excluded: chain J residue 990 SER Chi-restraints excluded: chain J residue 1130 ARG Chi-restraints excluded: chain J residue 1161 VAL Chi-restraints excluded: chain J residue 1211 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 187 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 298 optimal weight: 6.9990 chunk 448 optimal weight: 6.9990 chunk 301 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 312 optimal weight: 3.9990 chunk 394 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 ASN A1256 ASN E 130 GLN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN B 507 GLN H 39 GLN G 45 HIS G 89 GLN J 164 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.150921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.112168 restraints weight = 46811.893| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.86 r_work: 0.3180 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 39033 Z= 0.108 Angle : 0.528 15.930 52800 Z= 0.270 Chirality : 0.043 0.260 5954 Planarity : 0.004 0.058 6780 Dihedral : 4.342 35.632 5195 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.72 % Allowed : 16.19 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.55 (0.12), residues: 4737 helix: 1.27 (0.12), residues: 1910 sheet: -0.10 (0.21), residues: 636 loop : -0.22 (0.14), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 66 TYR 0.014 0.001 TYR J 689 PHE 0.018 0.001 PHE A 918 TRP 0.017 0.001 TRP A1154 HIS 0.006 0.001 HIS J 215 Details of bonding type rmsd covalent geometry : bond 0.00243 (38999) covalent geometry : angle 0.52396 (52764) hydrogen bonds : bond 0.03446 ( 1674) hydrogen bonds : angle 4.54697 ( 4716) metal coordination : bond 0.00529 ( 34) metal coordination : angle 2.60130 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 483 time to evaluate : 1.421 Fit side-chains REVERT: A 24 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7772 (mt0) REVERT: A 239 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8233 (mp) REVERT: A 382 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7567 (pt0) REVERT: A 394 LYS cc_start: 0.7839 (mtpt) cc_final: 0.7136 (mmpt) REVERT: A 806 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8736 (mtt) REVERT: A 890 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7806 (mp10) REVERT: A 904 ASP cc_start: 0.8343 (m-30) cc_final: 0.7903 (t0) REVERT: A 950 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8057 (mp) REVERT: A 1093 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8023 (mt-10) REVERT: A 1425 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8148 (mmp) REVERT: A 1441 LYS cc_start: 0.7544 (mmtm) cc_final: 0.6364 (ptpt) REVERT: B 93 ASP cc_start: 0.7994 (t0) cc_final: 0.7114 (m-30) REVERT: B 302 ASN cc_start: 0.8342 (m-40) cc_final: 0.8096 (t0) REVERT: B 307 GLU cc_start: 0.8076 (tt0) cc_final: 0.7659 (mt-10) REVERT: B 336 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8189 (tm) REVERT: B 369 ASP cc_start: 0.8117 (m-30) cc_final: 0.7831 (m-30) REVERT: B 371 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7948 (tt) REVERT: B 402 MET cc_start: 0.8664 (ttp) cc_final: 0.8450 (ttt) REVERT: B 460 ARG cc_start: 0.8132 (tpp80) cc_final: 0.7882 (tpp80) REVERT: B 727 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8765 (tp) REVERT: B 1019 GLU cc_start: 0.8686 (tt0) cc_final: 0.8467 (tt0) REVERT: B 1173 ASP cc_start: 0.8431 (p0) cc_final: 0.8221 (p0) REVERT: B 1199 MET cc_start: 0.7246 (mtp) cc_final: 0.7023 (ptp) REVERT: C 244 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7065 (mtp180) REVERT: C 354 VAL cc_start: 0.8656 (t) cc_final: 0.8256 (t) REVERT: D 1 MET cc_start: 0.5572 (ttt) cc_final: 0.4570 (tpt) REVERT: D 50 HIS cc_start: 0.7999 (m90) cc_final: 0.7423 (m90) REVERT: D 66 HIS cc_start: 0.6876 (m-70) cc_final: 0.6452 (m90) REVERT: H 27 GLU cc_start: 0.8402 (mp0) cc_final: 0.7813 (mt-10) REVERT: G 1 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.5571 (pmt) REVERT: G 28 GLU cc_start: 0.8118 (tp30) cc_final: 0.7642 (tp30) REVERT: F 103 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6494 (mp0) REVERT: F 204 GLU cc_start: 0.6936 (tp30) cc_final: 0.6268 (mt-10) REVERT: F 248 LYS cc_start: 0.6412 (mmmm) cc_final: 0.6071 (mmmm) REVERT: F 328 MET cc_start: 0.7151 (ttt) cc_final: 0.6552 (tmt) REVERT: J 229 ARG cc_start: 0.6830 (mtm-85) cc_final: 0.6280 (mmt180) REVERT: J 313 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: J 324 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7824 (tm) REVERT: J 380 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6483 (mm-30) REVERT: J 409 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6437 (mp10) REVERT: J 742 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7471 (mmt-90) REVERT: J 794 ASN cc_start: 0.6929 (m110) cc_final: 0.6480 (t0) REVERT: J 1228 ASP cc_start: 0.6793 (m-30) cc_final: 0.6169 (m-30) outliers start: 73 outliers final: 41 residues processed: 529 average time/residue: 0.6827 time to fit residues: 437.8650 Evaluate side-chains 507 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 452 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1425 MET Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 313 GLU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 409 GLN Chi-restraints excluded: chain J residue 741 TYR Chi-restraints excluded: chain J residue 742 ARG Chi-restraints excluded: chain J residue 964 LEU Chi-restraints excluded: chain J residue 1161 VAL Chi-restraints excluded: chain J residue 1211 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 189 optimal weight: 3.9990 chunk 328 optimal weight: 6.9990 chunk 443 optimal weight: 8.9990 chunk 388 optimal weight: 9.9990 chunk 463 optimal weight: 10.0000 chunk 451 optimal weight: 10.0000 chunk 417 optimal weight: 7.9990 chunk 286 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 ASN A1256 ASN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN H 39 GLN G 45 HIS G 89 GLN J 164 ASN J 167 ASN ** J 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 917 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.145865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106754 restraints weight = 46683.804| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.91 r_work: 0.3113 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 39033 Z= 0.256 Angle : 0.643 13.796 52800 Z= 0.328 Chirality : 0.048 0.258 5954 Planarity : 0.005 0.060 6780 Dihedral : 4.725 37.087 5195 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.24 % Favored : 95.74 % Rotamer: Outliers : 1.95 % Allowed : 16.40 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.24 (0.12), residues: 4737 helix: 1.01 (0.12), residues: 1894 sheet: -0.17 (0.20), residues: 638 loop : -0.39 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 96 TYR 0.026 0.002 TYR C 310 PHE 0.034 0.002 PHE J 495 TRP 0.016 0.002 TRP A 466 HIS 0.009 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00627 (38999) covalent geometry : angle 0.63609 (52764) hydrogen bonds : bond 0.04570 ( 1674) hydrogen bonds : angle 4.82755 ( 4716) metal coordination : bond 0.01066 ( 34) metal coordination : angle 3.64933 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 461 time to evaluate : 1.568 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7824 (mt0) REVERT: A 382 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7727 (pt0) REVERT: A 394 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7209 (mmpt) REVERT: A 690 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8827 (mmm) REVERT: A 806 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8808 (mtt) REVERT: A 890 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7807 (mp10) REVERT: A 950 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8080 (mp) REVERT: A 1093 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8064 (mt-10) REVERT: A 1441 LYS cc_start: 0.7605 (mmtm) cc_final: 0.6415 (ptpt) REVERT: E 130 GLN cc_start: 0.8834 (mt0) cc_final: 0.8633 (mt0) REVERT: B 51 MET cc_start: 0.9051 (mmp) cc_final: 0.8760 (mmp) REVERT: B 93 ASP cc_start: 0.7942 (t0) cc_final: 0.7072 (m-30) REVERT: B 302 ASN cc_start: 0.8364 (m-40) cc_final: 0.8141 (t0) REVERT: B 307 GLU cc_start: 0.8151 (tt0) cc_final: 0.7738 (mt-10) REVERT: B 330 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7883 (tm-30) REVERT: B 336 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8166 (tm) REVERT: B 369 ASP cc_start: 0.8210 (m-30) cc_final: 0.7956 (m-30) REVERT: B 402 MET cc_start: 0.8762 (ttp) cc_final: 0.8551 (ttt) REVERT: B 460 ARG cc_start: 0.8115 (tpp80) cc_final: 0.7879 (tpp80) REVERT: B 727 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8789 (tp) REVERT: B 1019 GLU cc_start: 0.8695 (tt0) cc_final: 0.8475 (tt0) REVERT: C 244 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7240 (mtp180) REVERT: C 354 VAL cc_start: 0.8820 (t) cc_final: 0.8439 (t) REVERT: D 1 MET cc_start: 0.5729 (ttt) cc_final: 0.4860 (tpt) REVERT: D 34 MET cc_start: 0.7566 (mtt) cc_final: 0.7231 (mtp) REVERT: D 50 HIS cc_start: 0.8029 (m90) cc_final: 0.7544 (m90) REVERT: H 27 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: H 50 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8362 (mt-10) REVERT: G 1 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.5703 (pmt) REVERT: F 103 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6539 (mp0) REVERT: F 145 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6824 (mtt180) REVERT: F 204 GLU cc_start: 0.6929 (tp30) cc_final: 0.6185 (mt-10) REVERT: F 248 LYS cc_start: 0.6442 (mmmm) cc_final: 0.6137 (mmmm) REVERT: F 320 ILE cc_start: 0.6691 (OUTLIER) cc_final: 0.6169 (mt) REVERT: F 328 MET cc_start: 0.7213 (ttt) cc_final: 0.6579 (tmt) REVERT: J 229 ARG cc_start: 0.6913 (mtm-85) cc_final: 0.6261 (mmt180) REVERT: J 313 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: J 324 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7821 (tm) REVERT: J 409 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.6490 (mp10) REVERT: J 742 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7425 (mmt-90) REVERT: J 1228 ASP cc_start: 0.6794 (m-30) cc_final: 0.6233 (m-30) outliers start: 83 outliers final: 49 residues processed: 513 average time/residue: 0.6742 time to fit residues: 421.9416 Evaluate side-chains 510 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 446 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1190 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1201 CYS Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 222 LEU Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 313 GLU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 409 GLN Chi-restraints excluded: chain J residue 741 TYR Chi-restraints excluded: chain J residue 742 ARG Chi-restraints excluded: chain J residue 964 LEU Chi-restraints excluded: chain J residue 990 SER Chi-restraints excluded: chain J residue 1161 VAL Chi-restraints excluded: chain J residue 1170 LEU Chi-restraints excluded: chain J residue 1211 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 77 optimal weight: 4.9990 chunk 301 optimal weight: 0.0070 chunk 296 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 340 optimal weight: 0.7980 chunk 400 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 chunk 337 optimal weight: 9.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 ASN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN B1200 ASN H 39 GLN G 89 GLN J 164 ASN J 167 ASN J 917 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.149546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.110835 restraints weight = 46828.106| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.86 r_work: 0.3175 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39033 Z= 0.123 Angle : 0.555 16.127 52800 Z= 0.284 Chirality : 0.044 0.266 5954 Planarity : 0.004 0.058 6780 Dihedral : 4.478 35.891 5195 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.76 % Allowed : 16.75 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.45 (0.12), residues: 4737 helix: 1.19 (0.12), residues: 1907 sheet: -0.11 (0.20), residues: 642 loop : -0.29 (0.14), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 66 TYR 0.032 0.001 TYR C 310 PHE 0.029 0.001 PHE J 495 TRP 0.030 0.001 TRP F 327 HIS 0.006 0.001 HIS J 215 Details of bonding type rmsd covalent geometry : bond 0.00283 (38999) covalent geometry : angle 0.55035 (52764) hydrogen bonds : bond 0.03663 ( 1674) hydrogen bonds : angle 4.63171 ( 4716) metal coordination : bond 0.00623 ( 34) metal coordination : angle 2.89962 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15056.46 seconds wall clock time: 256 minutes 45.28 seconds (15405.28 seconds total)