Starting phenix.real_space_refine on Fri Mar 6 22:48:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oba_12796/03_2026/7oba_12796.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oba_12796/03_2026/7oba_12796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oba_12796/03_2026/7oba_12796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oba_12796/03_2026/7oba_12796.map" model { file = "/net/cci-nas-00/data/ceres_data/7oba_12796/03_2026/7oba_12796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oba_12796/03_2026/7oba_12796.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 248 5.16 5 C 22728 2.51 5 N 6181 2.21 5 O 6515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35679 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 12123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1522, 12123 Classifications: {'peptide': 1522} Link IDs: {'PCIS': 3, 'PTRANS': 76, 'TRANS': 1442} Chain breaks: 7 Chain: "B" Number of atoms: 8949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1127, 8949 Classifications: {'peptide': 1127} Link IDs: {'PTRANS': 66, 'TRANS': 1060} Chain breaks: 1 Chain: "C" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2474 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 16, 'TRANS': 292} Chain: "E" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1728 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 627 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 8, 'TRANS': 150} Chain breaks: 1 Chain: "H" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1197 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain: "I" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 813 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 837 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Chain: "N" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1083 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 25, 'TRANS': 123} Chain: "O" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2849 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 19, 'TRANS': 327} Chain breaks: 6 Chain: "A" 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 64 53.856 86.770 73.937 1.00 98.07 S ATOM 483 SG CYS A 67 54.423 82.319 72.384 1.00 98.16 S ATOM 538 SG CYS A 74 57.631 83.834 73.790 1.00 89.06 S ATOM 776 SG CYS A 104 73.331 106.277 31.858 1.00107.97 S ATOM 798 SG CYS A 107 72.137 104.305 28.743 1.00112.05 S ATOM 1582 SG CYS A 205 75.313 106.092 28.835 1.00114.46 S ATOM 20568 SG CYS B1070 58.990 75.004 57.835 1.00 84.60 S ATOM 20590 SG CYS B1073 60.461 78.045 54.670 1.00 86.20 S ATOM 20788 SG CYS B1098 57.292 78.213 58.486 1.00 90.79 S ATOM 28418 SG CYS I 20 124.589 156.647 59.947 1.00 66.38 S ATOM 28438 SG CYS I 23 121.526 156.467 62.045 1.00 71.12 S ATOM 28538 SG CYS I 38 120.025 155.503 58.637 1.00 77.58 S ATOM 28563 SG CYS I 41 121.836 158.830 59.350 1.00 78.76 S ATOM 28838 SG CYS I 87 129.830 76.373 73.902 1.00 73.85 S ATOM 28862 SG CYS I 90 133.288 75.322 71.993 1.00 82.42 S ATOM 29061 SG CYS I 115 133.139 78.911 73.945 1.00 62.16 S ATOM 29082 SG CYS I 118 130.724 77.494 70.628 1.00 72.48 S ATOM 29207 SG CYS J 7 108.491 83.181 124.141 1.00 22.47 S ATOM 29231 SG CYS J 10 109.609 79.116 125.568 1.00 23.04 S ATOM 29495 SG CYS J 44 111.792 81.102 123.480 1.00 26.57 S ATOM 29501 SG CYS J 45 110.964 81.976 127.312 1.00 27.15 S ATOM 30573 SG CYS L 19 80.824 117.318 122.396 1.00 42.23 S ATOM 30592 SG CYS L 22 80.715 119.056 125.991 1.00 46.03 S ATOM 30709 SG CYS L 36 77.495 118.558 124.388 1.00 45.34 S ATOM 30735 SG CYS L 39 80.758 121.217 123.133 1.00 45.98 S Time building chain proxies: 6.96, per 1000 atoms: 0.20 Number of scatterers: 35679 At special positions: 0 Unit cell: (166.044, 187.416, 165.222, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 7 29.99 S 248 16.00 O 6515 8.00 N 6181 7.00 C 22728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 74 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 64 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 104 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 205 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1070 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1073 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 38 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 41 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 23 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 87 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 118 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 90 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 115 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 27 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8414 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 44 sheets defined 31.8% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 113 through 124 removed outlier: 3.674A pdb=" N ILE A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 removed outlier: 3.730A pdb=" N ASN A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.949A pdb=" N TYR A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.649A pdb=" N SER A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 273 removed outlier: 4.267A pdb=" N ALA A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 346 removed outlier: 3.748A pdb=" N LEU A 328 " --> pdb=" O GLN A 324 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 403 removed outlier: 3.879A pdb=" N TRP A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'A' and resid 512 through 521 removed outlier: 4.885A pdb=" N VAL A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 580 through 584 removed outlier: 3.969A pdb=" N LYS A 583 " --> pdb=" O ALA A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 633 through 642 removed outlier: 3.622A pdb=" N ALA A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.550A pdb=" N MET A 654 " --> pdb=" O ARG A 650 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 658 " --> pdb=" O MET A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 694 removed outlier: 3.665A pdb=" N VAL A 688 " --> pdb=" O GLY A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 Processing helix chain 'A' and resid 760 through 765 Processing helix chain 'A' and resid 773 through 787 removed outlier: 3.944A pdb=" N THR A 779 " --> pdb=" O GLY A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 removed outlier: 4.002A pdb=" N THR A 820 " --> pdb=" O GLU A 817 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS A 821 " --> pdb=" O GLU A 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 817 through 821' Processing helix chain 'A' and resid 824 through 829 removed outlier: 3.786A pdb=" N ALA A 829 " --> pdb=" O GLN A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 850 Processing helix chain 'A' and resid 861 through 869 removed outlier: 4.297A pdb=" N GLU A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 868 " --> pdb=" O LYS A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 881 removed outlier: 3.642A pdb=" N ILE A 876 " --> pdb=" O TYR A 872 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 877 " --> pdb=" O SER A 873 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 900 Processing helix chain 'A' and resid 907 through 914 Processing helix chain 'A' and resid 944 through 949 removed outlier: 3.698A pdb=" N GLY A 949 " --> pdb=" O ARG A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 980 removed outlier: 3.659A pdb=" N HIS A 967 " --> pdb=" O GLU A 963 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 996 Processing helix chain 'A' and resid 1018 through 1022 removed outlier: 3.793A pdb=" N ASP A1022 " --> pdb=" O TYR A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1030 removed outlier: 3.910A pdb=" N THR A1029 " --> pdb=" O ILE A1026 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A1030 " --> pdb=" O PRO A1027 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1026 through 1030' Processing helix chain 'A' and resid 1033 through 1036 Processing helix chain 'A' and resid 1037 through 1042 Processing helix chain 'A' and resid 1043 through 1048 removed outlier: 3.975A pdb=" N ILE A1047 " --> pdb=" O ASN A1043 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET A1048 " --> pdb=" O TYR A1044 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1043 through 1048' Processing helix chain 'A' and resid 1061 through 1065 removed outlier: 4.454A pdb=" N LYS A1064 " --> pdb=" O ASP A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1076 removed outlier: 3.969A pdb=" N LYS A1073 " --> pdb=" O PHE A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1097 removed outlier: 3.612A pdb=" N TYR A1092 " --> pdb=" O ALA A1088 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A1094 " --> pdb=" O LEU A1090 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A1095 " --> pdb=" O SER A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1126 removed outlier: 3.795A pdb=" N GLU A1126 " --> pdb=" O ARG A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1138 Processing helix chain 'A' and resid 1160 through 1178 removed outlier: 3.782A pdb=" N THR A1165 " --> pdb=" O GLU A1161 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A1175 " --> pdb=" O SER A1171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A1176 " --> pdb=" O GLN A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1203 removed outlier: 3.773A pdb=" N THR A1194 " --> pdb=" O ASP A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1215 removed outlier: 3.569A pdb=" N LEU A1214 " --> pdb=" O ALA A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1253 removed outlier: 3.865A pdb=" N GLU A1250 " --> pdb=" O PRO A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1284 removed outlier: 4.182A pdb=" N LYS A1276 " --> pdb=" O LYS A1272 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG A1277 " --> pdb=" O LYS A1273 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A1278 " --> pdb=" O ALA A1274 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A1279 " --> pdb=" O LEU A1275 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A1280 " --> pdb=" O LYS A1276 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A1283 " --> pdb=" O LYS A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1293 removed outlier: 3.790A pdb=" N VAL A1293 " --> pdb=" O CYS A1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1289 through 1293' Processing helix chain 'A' and resid 1323 through 1327 removed outlier: 3.569A pdb=" N TYR A1327 " --> pdb=" O HIS A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1345 removed outlier: 3.992A pdb=" N MET A1342 " --> pdb=" O ILE A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1346 through 1358 removed outlier: 3.604A pdb=" N LYS A1355 " --> pdb=" O MET A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1507 Processing helix chain 'A' and resid 1542 through 1548 Processing helix chain 'A' and resid 1584 through 1589 removed outlier: 3.913A pdb=" N LEU A1588 " --> pdb=" O ASN A1584 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1600 removed outlier: 3.888A pdb=" N LEU A1600 " --> pdb=" O LEU A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1620 through 1630 removed outlier: 4.181A pdb=" N VAL A1628 " --> pdb=" O GLU A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1637 through 1649 removed outlier: 3.773A pdb=" N LEU A1641 " --> pdb=" O ASP A1637 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A1643 " --> pdb=" O ARG A1639 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A1644 " --> pdb=" O HIS A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1675 removed outlier: 3.862A pdb=" N THR A1673 " --> pdb=" O LEU A1669 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A1675 " --> pdb=" O GLN A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1687 removed outlier: 3.917A pdb=" N ALA A1684 " --> pdb=" O PHE A1680 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1701 removed outlier: 3.879A pdb=" N LEU A1700 " --> pdb=" O SER A1697 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 49 removed outlier: 3.867A pdb=" N SER B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 46 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 removed outlier: 3.848A pdb=" N GLY B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 106 removed outlier: 3.674A pdb=" N CYS B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 158 removed outlier: 3.600A pdb=" N ILE B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.697A pdb=" N THR B 200 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 removed outlier: 3.660A pdb=" N ALA B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 268 removed outlier: 3.639A pdb=" N LEU B 268 " --> pdb=" O ILE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 292 removed outlier: 3.557A pdb=" N ASN B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 289 " --> pdb=" O MET B 285 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 308 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 338 through 358 removed outlier: 3.804A pdb=" N PHE B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 348 " --> pdb=" O TYR B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 378 through 405 removed outlier: 3.645A pdb=" N PHE B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 437 removed outlier: 4.403A pdb=" N LEU B 433 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 467 removed outlier: 3.605A pdb=" N TYR B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.697A pdb=" N ARG B 488 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 528 through 537 removed outlier: 4.649A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 576 Processing helix chain 'B' and resid 637 through 641 removed outlier: 3.755A pdb=" N ILE B 640 " --> pdb=" O MET B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 removed outlier: 3.538A pdb=" N PHE B 673 " --> pdb=" O VAL B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 689 Processing helix chain 'B' and resid 725 through 730 Processing helix chain 'B' and resid 761 through 767 Processing helix chain 'B' and resid 800 through 804 removed outlier: 3.503A pdb=" N VAL B 803 " --> pdb=" O ASP B 800 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 804 " --> pdb=" O PRO B 801 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 800 through 804' Processing helix chain 'B' and resid 898 through 902 Processing helix chain 'B' and resid 926 through 940 Processing helix chain 'B' and resid 961 through 969 Processing helix chain 'B' and resid 1038 through 1049 removed outlier: 3.511A pdb=" N ARG B1042 " --> pdb=" O GLY B1038 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP B1043 " --> pdb=" O GLU B1039 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B1044 " --> pdb=" O MET B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1060 Processing helix chain 'B' and resid 1115 through 1124 Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 69 through 83 removed outlier: 3.759A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 82 " --> pdb=" O ARG C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 removed outlier: 3.515A pdb=" N LEU C 112 " --> pdb=" O HIS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.578A pdb=" N LEU C 121 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.946A pdb=" N LEU C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 185' Processing helix chain 'C' and resid 222 through 226 removed outlier: 3.760A pdb=" N SER C 226 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.734A pdb=" N ARG C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.533A pdb=" N ASP C 281 " --> pdb=" O PRO C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'C' and resid 317 through 344 removed outlier: 3.518A pdb=" N VAL C 322 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET C 330 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY C 331 " --> pdb=" O LYS C 327 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 337 " --> pdb=" O CYS C 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 22 removed outlier: 3.920A pdb=" N ILE E 17 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS E 22 " --> pdb=" O MET E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 25 No H-bonds generated for 'chain 'E' and resid 23 through 25' Processing helix chain 'E' and resid 29 through 33 Processing helix chain 'E' and resid 38 through 43 Processing helix chain 'E' and resid 89 through 96 removed outlier: 3.622A pdb=" N ARG E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 120 removed outlier: 3.980A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 136 removed outlier: 4.152A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 136' Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 removed outlier: 3.741A pdb=" N THR E 157 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 72 removed outlier: 3.647A pdb=" N ALA F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 99 removed outlier: 3.538A pdb=" N ILE F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU F 97 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS F 98 " --> pdb=" O MET F 94 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F 99 " --> pdb=" O LYS F 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 41 removed outlier: 3.792A pdb=" N VAL G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 77 removed outlier: 3.759A pdb=" N ALA G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 53 removed outlier: 3.528A pdb=" N GLU I 51 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY I 52 " --> pdb=" O ASP I 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 27 removed outlier: 4.318A pdb=" N LEU J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 39 removed outlier: 3.518A pdb=" N LEU J 38 " --> pdb=" O LEU J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 51 removed outlier: 3.654A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 60 removed outlier: 3.556A pdb=" N MET K 60 " --> pdb=" O ARG K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 116 removed outlier: 3.650A pdb=" N PHE K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS K 109 " --> pdb=" O ASN K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 126 removed outlier: 3.994A pdb=" N GLN K 124 " --> pdb=" O ASP K 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 57 Processing helix chain 'N' and resid 52 through 57 removed outlier: 4.007A pdb=" N PHE N 56 " --> pdb=" O PRO N 53 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN N 57 " --> pdb=" O GLU N 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 114 Processing helix chain 'O' and resid 127 through 139 removed outlier: 4.051A pdb=" N ALA O 139 " --> pdb=" O ASN O 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 143 Processing helix chain 'O' and resid 144 through 154 removed outlier: 3.597A pdb=" N LEU O 148 " --> pdb=" O LEU O 144 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER O 149 " --> pdb=" O ARG O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 197 removed outlier: 3.784A pdb=" N VAL O 197 " --> pdb=" O ILE O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 198 through 204 removed outlier: 4.343A pdb=" N TRP O 202 " --> pdb=" O PRO O 198 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 211 Processing helix chain 'O' and resid 218 through 236 removed outlier: 3.578A pdb=" N LEU O 222 " --> pdb=" O SER O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 239 through 257 removed outlier: 3.517A pdb=" N ILE O 243 " --> pdb=" O LEU O 239 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN O 257 " --> pdb=" O LYS O 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 309 through 329 Processing helix chain 'O' and resid 342 through 355 Processing helix chain 'O' and resid 364 through 372 removed outlier: 4.283A pdb=" N MET O 368 " --> pdb=" O VAL O 364 " (cutoff:3.500A) Processing helix chain 'O' and resid 375 through 392 Processing helix chain 'O' and resid 396 through 413 Processing helix chain 'O' and resid 418 through 440 removed outlier: 3.727A pdb=" N VAL O 422 " --> pdb=" O PRO O 418 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN O 439 " --> pdb=" O ILE O 435 " (cutoff:3.500A) Processing helix chain 'O' and resid 454 through 470 Processing helix chain 'O' and resid 483 through 485 No H-bonds generated for 'chain 'O' and resid 483 through 485' Processing helix chain 'O' and resid 486 through 496 removed outlier: 3.606A pdb=" N MET O 496 " --> pdb=" O GLU O 492 " (cutoff:3.500A) Processing helix chain 'O' and resid 506 through 520 Processing helix chain 'O' and resid 554 through 559 removed outlier: 4.189A pdb=" N PHE O 559 " --> pdb=" O PRO O 555 " (cutoff:3.500A) Processing helix chain 'O' and resid 570 through 575 removed outlier: 3.614A pdb=" N ILE O 574 " --> pdb=" O SER O 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 19 removed outlier: 4.052A pdb=" N GLY A 14 " --> pdb=" O ASP B1133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.641A pdb=" N LYS A 31 " --> pdb=" O HIS A 80 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLU A 82 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ASP A 300 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N LEU A 85 " --> pdb=" O PHE A 298 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N PHE A 298 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 218 removed outlier: 3.599A pdb=" N LYS A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 436 through 437 removed outlier: 3.527A pdb=" N ILE B1035 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 440 through 447 removed outlier: 7.511A pdb=" N LEU A 575 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL A 444 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU A 577 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N CYS A 446 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 467 through 471 Processing sheet with id=AA7, first strand: chain 'A' and resid 647 through 648 Processing sheet with id=AA8, first strand: chain 'A' and resid 675 through 677 removed outlier: 6.506A pdb=" N VAL H 91 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE H 15 " --> pdb=" O ARG H 27 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG H 27 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU H 39 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 705 through 706 removed outlier: 6.274A pdb=" N ILE A 738 " --> pdb=" O LEU A 745 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1007 through 1008 removed outlier: 6.758A pdb=" N VAL A1007 " --> pdb=" O VAL A1015 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1577 through 1580 removed outlier: 3.725A pdb=" N MET A1264 " --> pdb=" O THR A1580 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1526 through 1527 removed outlier: 3.935A pdb=" N VAL A1527 " --> pdb=" O LEU A1317 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG A1318 " --> pdb=" O ILE A1297 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE A1297 " --> pdb=" O ARG A1318 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A1320 " --> pdb=" O GLN A1295 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1304 through 1305 Processing sheet with id=AB5, first strand: chain 'F' and resid 115 through 119 removed outlier: 3.645A pdb=" N GLU A1714 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU A1715 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A1717 " --> pdb=" O GLY G 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 67 removed outlier: 3.721A pdb=" N VAL B 122 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 77 through 82 removed outlier: 6.728A pdb=" N ASP B 117 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ALA B 80 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 115 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 82 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS B 113 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA B 116 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE B 133 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE B 118 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LYS B 131 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 170 through 172 Processing sheet with id=AB9, first strand: chain 'B' and resid 372 through 375 removed outlier: 3.639A pdb=" N LEU B 182 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N MET B 181 " --> pdb=" O HIS B 473 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 191 through 194 removed outlier: 5.198A pdb=" N TYR B 208 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN B 223 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE B 239 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 519 through 520 removed outlier: 3.560A pdb=" N LYS B 630 " --> pdb=" O ASN B 625 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC4, first strand: chain 'B' and resid 539 through 541 removed outlier: 6.887A pdb=" N VAL B 556 " --> pdb=" O VAL B 563 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TRP B 565 " --> pdb=" O TYR B 554 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TYR B 554 " --> pdb=" O TRP B 565 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LEU B 610 " --> pdb=" O CYS B 553 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU B 612 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU B 557 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 710 through 714 removed outlier: 3.629A pdb=" N LEU B 711 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N CYS B 866 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL B 854 " --> pdb=" O CYS B 866 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N CYS B 868 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE B 852 " --> pdb=" O CYS B 868 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR B 870 " --> pdb=" O ASP B 850 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 710 through 714 removed outlier: 3.629A pdb=" N LEU B 711 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N CYS B 866 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL B 854 " --> pdb=" O CYS B 866 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N CYS B 868 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE B 852 " --> pdb=" O CYS B 868 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR B 870 " --> pdb=" O ASP B 850 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE B 852 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 722 through 723 Processing sheet with id=AC8, first strand: chain 'B' and resid 976 through 977 removed outlier: 3.942A pdb=" N ALA B 884 " --> pdb=" O GLN B1000 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL B 759 " --> pdb=" O SER B 894 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 896 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ILE B 913 " --> pdb=" O ASN B 740 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE B 742 " --> pdb=" O ILE B 913 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE B 915 " --> pdb=" O ILE B 742 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA B 744 " --> pdb=" O PHE B 915 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE B 993 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 794 Processing sheet with id=AD1, first strand: chain 'B' and resid 824 through 826 removed outlier: 6.933A pdb=" N MET B 839 " --> pdb=" O TYR B 825 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1064 through 1070 removed outlier: 3.664A pdb=" N SER B1065 " --> pdb=" O VAL B1112 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 53 through 57 removed outlier: 6.805A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 63 " --> pdb=" O PHE C 308 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C 306 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N ARG C 301 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE C 239 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ARG C 303 " --> pdb=" O PRO C 237 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N HIS C 305 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU C 235 " --> pdb=" O HIS C 305 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE C 307 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR C 233 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER C 309 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 231 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLU C 311 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 173 through 175 removed outlier: 3.724A pdb=" N PHE C 140 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP C 209 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL L 53 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.568A pdb=" N THR C 147 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 262 through 267 removed outlier: 3.780A pdb=" N LYS C 270 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.558A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.836A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE E 194 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 52 through 54 Processing sheet with id=AE1, first strand: chain 'G' and resid 57 through 59 Processing sheet with id=AE2, first strand: chain 'G' and resid 135 through 138 removed outlier: 7.310A pdb=" N GLY G 144 " --> pdb=" O ASN G 136 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS G 193 " --> pdb=" O ASP G 185 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP G 185 " --> pdb=" O CYS G 193 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG G 195 " --> pdb=" O ARG G 183 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG G 183 " --> pdb=" O ARG G 195 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 35 through 37 Processing sheet with id=AE4, first strand: chain 'I' and resid 82 through 83 Processing sheet with id=AE5, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AE6, first strand: chain 'M' and resid 11 through 13 removed outlier: 5.984A pdb=" N GLN M 12 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ASP M 103 " --> pdb=" O GLN M 12 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL M 89 " --> pdb=" O TYR M 102 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS M 87 " --> pdb=" O ALA M 104 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 24 through 25 removed outlier: 6.236A pdb=" N ALA M 23 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE M 107 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU M 25 " --> pdb=" O PHE M 107 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N MET M 109 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLN M 27 " --> pdb=" O MET M 109 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL M 26 " --> pdb=" O THR N 93 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR N 93 " --> pdb=" O VAL M 26 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 66 through 67 removed outlier: 3.831A pdb=" N GLN N 67 " --> pdb=" O VAL N 82 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL N 82 " --> pdb=" O GLN N 67 " (cutoff:3.500A) 1045 hydrogen bonds defined for protein. 2907 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: 7.33 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9822 1.33 - 1.45: 7273 1.45 - 1.58: 18971 1.58 - 1.70: 1 1.70 - 1.82: 380 Bond restraints: 36447 Sorted by residual: bond pdb=" C PRO N 22 " pdb=" N PRO N 23 " ideal model delta sigma weight residual 1.333 1.391 -0.058 7.80e-03 1.64e+04 5.59e+01 bond pdb=" CA PRO N 138 " pdb=" C PRO N 138 " ideal model delta sigma weight residual 1.517 1.541 -0.024 6.70e-03 2.23e+04 1.30e+01 bond pdb=" CB VAL B 566 " pdb=" CG2 VAL B 566 " ideal model delta sigma weight residual 1.521 1.409 0.112 3.30e-02 9.18e+02 1.15e+01 bond pdb=" C ILE A1026 " pdb=" N PRO A1027 " ideal model delta sigma weight residual 1.335 1.379 -0.044 1.30e-02 5.92e+03 1.14e+01 bond pdb=" C ASP O 575 " pdb=" N PRO O 576 " ideal model delta sigma weight residual 1.335 1.377 -0.042 1.30e-02 5.92e+03 1.05e+01 ... (remaining 36442 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 47820 2.88 - 5.76: 1244 5.76 - 8.64: 165 8.64 - 11.52: 42 11.52 - 14.40: 8 Bond angle restraints: 49279 Sorted by residual: angle pdb=" N THR A 464 " pdb=" CA THR A 464 " pdb=" C THR A 464 " ideal model delta sigma weight residual 114.31 101.99 12.32 1.29e+00 6.01e-01 9.13e+01 angle pdb=" N LEU A 935 " pdb=" CA LEU A 935 " pdb=" C LEU A 935 " ideal model delta sigma weight residual 108.22 101.63 6.59 9.00e-01 1.23e+00 5.36e+01 angle pdb=" N VAL A1254 " pdb=" CA VAL A1254 " pdb=" C VAL A1254 " ideal model delta sigma weight residual 112.96 107.45 5.51 1.00e+00 1.00e+00 3.04e+01 angle pdb=" C LYS B 69 " pdb=" N ASP B 70 " pdb=" CA ASP B 70 " ideal model delta sigma weight residual 121.54 131.62 -10.08 1.91e+00 2.74e-01 2.78e+01 angle pdb=" C LEU B 558 " pdb=" N ASP B 559 " pdb=" CA ASP B 559 " ideal model delta sigma weight residual 121.54 131.61 -10.07 1.91e+00 2.74e-01 2.78e+01 ... (remaining 49274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 20567 15.63 - 31.26: 1284 31.26 - 46.88: 286 46.88 - 62.51: 23 62.51 - 78.14: 27 Dihedral angle restraints: 22187 sinusoidal: 9166 harmonic: 13021 Sorted by residual: dihedral pdb=" CA SER O 138 " pdb=" C SER O 138 " pdb=" N ALA O 139 " pdb=" CA ALA O 139 " ideal model delta harmonic sigma weight residual 180.00 135.19 44.81 0 5.00e+00 4.00e-02 8.03e+01 dihedral pdb=" CA HIS A 491 " pdb=" C HIS A 491 " pdb=" N PRO A 492 " pdb=" CA PRO A 492 " ideal model delta harmonic sigma weight residual 180.00 136.55 43.45 0 5.00e+00 4.00e-02 7.55e+01 dihedral pdb=" CA GLU I 77 " pdb=" C GLU I 77 " pdb=" N CYS I 78 " pdb=" CA CYS I 78 " ideal model delta harmonic sigma weight residual 180.00 -143.78 -36.22 0 5.00e+00 4.00e-02 5.25e+01 ... (remaining 22184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3663 0.060 - 0.120: 1416 0.120 - 0.181: 298 0.181 - 0.241: 54 0.241 - 0.301: 16 Chirality restraints: 5447 Sorted by residual: chirality pdb=" CB ILE A1338 " pdb=" CA ILE A1338 " pdb=" CG1 ILE A1338 " pdb=" CG2 ILE A1338 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CG LEU A1040 " pdb=" CB LEU A1040 " pdb=" CD1 LEU A1040 " pdb=" CD2 LEU A1040 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB ILE G 112 " pdb=" CA ILE G 112 " pdb=" CG1 ILE G 112 " pdb=" CG2 ILE G 112 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 5444 not shown) Planarity restraints: 6375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 387 " 0.035 2.00e-02 2.50e+03 7.13e-02 5.08e+01 pdb=" C LEU A 387 " -0.123 2.00e-02 2.50e+03 pdb=" O LEU A 387 " 0.048 2.00e-02 2.50e+03 pdb=" N TYR A 388 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY N 154 " -0.030 2.00e-02 2.50e+03 5.81e-02 3.38e+01 pdb=" C GLY N 154 " 0.101 2.00e-02 2.50e+03 pdb=" O GLY N 154 " -0.037 2.00e-02 2.50e+03 pdb=" N ASN N 155 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 501 " 0.030 2.00e-02 2.50e+03 5.81e-02 3.38e+01 pdb=" C ASP A 501 " -0.101 2.00e-02 2.50e+03 pdb=" O ASP A 501 " 0.037 2.00e-02 2.50e+03 pdb=" N GLY A 502 " 0.033 2.00e-02 2.50e+03 ... (remaining 6372 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 7408 2.78 - 3.31: 31292 3.31 - 3.84: 57728 3.84 - 4.37: 68468 4.37 - 4.90: 118830 Nonbonded interactions: 283726 Sorted by model distance: nonbonded pdb=" OE1 GLU A 997 " pdb=" OG SER A1697 " model vdw 2.250 3.040 nonbonded pdb=" O ALA A 483 " pdb=" OG SER A 495 " model vdw 2.261 3.040 nonbonded pdb=" OE1 GLU A1021 " pdb=" OG SER E 197 " model vdw 2.271 3.040 nonbonded pdb=" OG SER I 15 " pdb=" O ASN M 30 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP H 8 " pdb=" OG SER H 34 " model vdw 2.275 3.040 ... (remaining 283721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.780 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.460 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 : 0.012 0.541 36473 Z= 0.484 Angle : 1.210 60.307 49306 Z= 0.609 Chirality : 0.066 0.301 5447 Planarity : 0.009 0.102 6375 Dihedral : 11.314 78.140 13773 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.00 % Favored : 91.96 % Rotamer: Outliers : 0.48 % Allowed : 3.86 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.57 (0.10), residues: 4415 helix: -3.52 (0.09), residues: 1387 sheet: -2.62 (0.18), residues: 654 loop : -2.86 (0.10), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 972 TYR 0.067 0.004 TYR B 999 PHE 0.052 0.004 PHE B 883 TRP 0.062 0.004 TRP A 846 HIS 0.026 0.004 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.01082 (36447) covalent geometry : angle 1.13766 (49279) hydrogen bonds : bond 0.20884 ( 1029) hydrogen bonds : angle 8.63177 ( 2907) metal coordination : bond 0.22482 ( 26) metal coordination : angle 17.63492 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 738 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 954 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7173 (ptt90) REVERT: B 1091 MET cc_start: 0.5335 (mtp) cc_final: 0.4614 (ttm) REVERT: C 345 MET cc_start: 0.7180 (mpt) cc_final: 0.6833 (mmt) REVERT: F 52 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7335 (pp) REVERT: G 75 LEU cc_start: 0.9162 (mt) cc_final: 0.8925 (mp) REVERT: O 223 GLU cc_start: 0.0109 (tt0) cc_final: -0.0747 (tm-30) REVERT: O 251 LEU cc_start: 0.7691 (mt) cc_final: 0.7366 (tt) outliers start: 19 outliers final: 2 residues processed: 756 average time/residue: 0.2385 time to fit residues: 284.1061 Evaluate side-chains 391 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 387 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 108 HIS A 133 GLN A 180 HIS A 183 ASN A 199 HIS A 264 HIS A 381 GLN A 476 ASN A 521 GLN A 595 ASN A 700 HIS A 704 ASN A 995 HIS A1036 GLN ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 HIS ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1109 ASN A1118 GLN A1526 GLN ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1579 ASN A1584 ASN A1606 HIS A1610 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 263 GLN B 313 ASN B 365 ASN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN B 679 HIS ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 GLN B 740 ASN B 787 GLN B 846 ASN ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1060 ASN C 160 ASN C 172 HIS ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 142 HIS E 168 ASN G 53 HIS ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN G 148 HIS G 152 ASN G 165 GLN H 44 ASN I 92 HIS I 117 ASN J 52 HIS K 45 HIS K 108 GLN O 227 HIS O 478 ASN O 490 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.087821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.063944 restraints weight = 127016.633| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 4.01 r_work: 0.3204 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 36473 Z= 0.220 Angle : 0.757 17.038 49306 Z= 0.383 Chirality : 0.047 0.176 5447 Planarity : 0.006 0.079 6375 Dihedral : 6.255 46.527 4885 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.78 % Allowed : 10.19 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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 are not related in a simple way. whole: -3.41 (0.11), residues: 4415 helix: -2.20 (0.12), residues: 1456 sheet: -2.25 (0.19), residues: 624 loop : -2.29 (0.11), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 146 TYR 0.026 0.002 TYR A1044 PHE 0.023 0.002 PHE A1319 TRP 0.028 0.002 TRP A 846 HIS 0.011 0.002 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00494 (36447) covalent geometry : angle 0.74120 (49279) hydrogen bonds : bond 0.04481 ( 1029) hydrogen bonds : angle 5.94237 ( 2907) metal coordination : bond 0.00958 ( 26) metal coordination : angle 6.58625 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 416 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 HIS cc_start: 0.8587 (m-70) cc_final: 0.8328 (m-70) REVERT: A 200 MET cc_start: 0.8454 (tpp) cc_final: 0.8077 (ttm) REVERT: A 406 MET cc_start: 0.8752 (mtm) cc_final: 0.8357 (ptp) REVERT: A 496 MET cc_start: 0.6256 (mmm) cc_final: 0.5767 (mmm) REVERT: A 550 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8309 (mm) REVERT: A 571 GLU cc_start: 0.8040 (pt0) cc_final: 0.7714 (pp20) REVERT: A 910 MET cc_start: 0.9026 (mtp) cc_final: 0.8692 (mtm) REVERT: A 954 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7094 (ptt90) REVERT: A 1026 ILE cc_start: 0.8430 (mm) cc_final: 0.8203 (mm) REVERT: A 1292 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: A 1540 MET cc_start: 0.9133 (mmm) cc_final: 0.8925 (mmm) REVERT: B 639 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8632 (pt0) REVERT: B 753 MET cc_start: 0.9089 (mtm) cc_final: 0.8790 (mtt) REVERT: B 965 MET cc_start: 0.8569 (mmm) cc_final: 0.8281 (mmm) REVERT: C 345 MET cc_start: 0.7595 (mpt) cc_final: 0.7142 (mmt) REVERT: E 115 LYS cc_start: 0.9075 (mtmt) cc_final: 0.8822 (pttp) REVERT: F 52 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7657 (pp) REVERT: G 78 GLU cc_start: 0.8856 (pt0) cc_final: 0.8569 (pt0) REVERT: I 18 ASP cc_start: 0.9232 (t0) cc_final: 0.8991 (t0) REVERT: I 29 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8426 (mt) REVERT: I 107 GLU cc_start: 0.8341 (pm20) cc_final: 0.8000 (pm20) REVERT: J 26 GLN cc_start: 0.9323 (tt0) cc_final: 0.8672 (tm-30) REVERT: M 11 TRP cc_start: 0.8420 (t-100) cc_final: 0.8040 (t-100) REVERT: M 32 LYS cc_start: 0.8180 (mtmm) cc_final: 0.7786 (pttt) REVERT: M 34 GLN cc_start: 0.8772 (tt0) cc_final: 0.8560 (tt0) REVERT: N 56 PHE cc_start: 0.8934 (m-10) cc_final: 0.8668 (m-10) REVERT: O 251 LEU cc_start: 0.6548 (mt) cc_final: 0.6273 (tt) REVERT: O 509 VAL cc_start: 0.7474 (t) cc_final: 0.7260 (p) outliers start: 70 outliers final: 31 residues processed: 469 average time/residue: 0.2088 time to fit residues: 161.4152 Evaluate side-chains 394 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 357 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1292 GLU Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 639 GLN Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain M residue 103 ASP Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 407 ILE Chi-restraints excluded: chain O residue 475 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 333 optimal weight: 50.0000 chunk 108 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 277 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 31 optimal weight: 0.0870 chunk 229 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 358 optimal weight: 20.0000 chunk 380 optimal weight: 0.9980 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 HIS ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 HIS ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN C 305 HIS E 129 GLN E 168 ASN G 53 HIS G 113 HIS G 115 ASN I 79 GLN K 109 HIS ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN O 227 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.087924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.064191 restraints weight = 126543.291| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.97 r_work: 0.3218 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 36473 Z= 0.154 Angle : 0.669 15.797 49306 Z= 0.336 Chirality : 0.045 0.188 5447 Planarity : 0.005 0.073 6375 Dihedral : 5.709 44.803 4885 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.24 % Allowed : 11.16 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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 are not related in a simple way. whole: -2.72 (0.12), residues: 4415 helix: -1.51 (0.13), residues: 1433 sheet: -1.91 (0.19), residues: 634 loop : -1.95 (0.12), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 81 TYR 0.028 0.001 TYR G 45 PHE 0.018 0.001 PHE E 44 TRP 0.022 0.001 TRP C 40 HIS 0.012 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00345 (36447) covalent geometry : angle 0.65882 (49279) hydrogen bonds : bond 0.03703 ( 1029) hydrogen bonds : angle 5.45188 ( 2907) metal coordination : bond 0.00859 ( 26) metal coordination : angle 5.07326 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 387 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8481 (tpp) cc_final: 0.8158 (ttm) REVERT: A 406 MET cc_start: 0.8707 (mtm) cc_final: 0.8405 (ptp) REVERT: A 478 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8231 (pm20) REVERT: A 496 MET cc_start: 0.6277 (mmm) cc_final: 0.6005 (mmm) REVERT: A 571 GLU cc_start: 0.8099 (pt0) cc_final: 0.7738 (pp20) REVERT: A 881 MET cc_start: 0.8793 (tpp) cc_final: 0.8532 (tpp) REVERT: A 954 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7536 (ptt90) REVERT: A 1026 ILE cc_start: 0.8464 (mm) cc_final: 0.8169 (mm) REVERT: A 1253 MET cc_start: 0.8830 (mmt) cc_final: 0.8412 (mmt) REVERT: A 1292 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: B 639 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8677 (pt0) REVERT: B 753 MET cc_start: 0.9060 (mtm) cc_final: 0.8849 (mtm) REVERT: C 98 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.8938 (p) REVERT: C 345 MET cc_start: 0.7597 (mpt) cc_final: 0.6985 (mmt) REVERT: F 52 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7607 (pp) REVERT: G 78 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8416 (pt0) REVERT: G 115 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7848 (p0) REVERT: I 18 ASP cc_start: 0.9262 (t0) cc_final: 0.8946 (t0) REVERT: I 107 GLU cc_start: 0.8418 (pm20) cc_final: 0.8118 (pm20) REVERT: J 26 GLN cc_start: 0.9261 (tt0) cc_final: 0.8623 (tm-30) REVERT: K 66 GLU cc_start: 0.8207 (tt0) cc_final: 0.8000 (tt0) REVERT: M 10 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7799 (mmm160) REVERT: M 32 LYS cc_start: 0.8042 (mtmm) cc_final: 0.7655 (pttt) REVERT: M 64 THR cc_start: 0.7516 (OUTLIER) cc_final: 0.7159 (p) REVERT: M 102 TYR cc_start: 0.8498 (m-80) cc_final: 0.8281 (m-80) REVERT: N 112 GLN cc_start: 0.7660 (tp40) cc_final: 0.7326 (tm-30) outliers start: 88 outliers final: 42 residues processed: 451 average time/residue: 0.2059 time to fit residues: 154.7790 Evaluate side-chains 409 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 357 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1292 GLU Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 639 GLN Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 78 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 238 THR Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 407 ILE Chi-restraints excluded: chain O residue 475 LEU Chi-restraints excluded: chain O residue 567 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 294 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 352 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 424 optimal weight: 2.9990 chunk 402 optimal weight: 1.9990 chunk 277 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 HIS A1030 GLN ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1690 HIS A1717 GLN B 188 ASN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN E 168 ASN G 53 HIS M 12 GLN ** N 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 227 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.087187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.063479 restraints weight = 126385.176| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.96 r_work: 0.3199 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 36473 Z= 0.170 Angle : 0.655 13.326 49306 Z= 0.327 Chirality : 0.045 0.217 5447 Planarity : 0.005 0.073 6375 Dihedral : 5.429 43.894 4885 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.49 % Allowed : 11.82 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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 are not related in a simple way. whole: -2.33 (0.12), residues: 4415 helix: -1.07 (0.14), residues: 1437 sheet: -1.69 (0.19), residues: 653 loop : -1.79 (0.12), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 148 TYR 0.030 0.001 TYR G 45 PHE 0.018 0.001 PHE G 120 TRP 0.014 0.001 TRP A 846 HIS 0.012 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00385 (36447) covalent geometry : angle 0.64544 (49279) hydrogen bonds : bond 0.03489 ( 1029) hydrogen bonds : angle 5.21731 ( 2907) metal coordination : bond 0.00963 ( 26) metal coordination : angle 4.74363 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 370 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8454 (tpp) cc_final: 0.8229 (ttm) REVERT: A 406 MET cc_start: 0.8691 (mtm) cc_final: 0.8471 (ptp) REVERT: A 520 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7739 (ttmm) REVERT: A 550 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8468 (mm) REVERT: A 571 GLU cc_start: 0.8134 (pt0) cc_final: 0.7757 (pp20) REVERT: A 954 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7347 (ptt90) REVERT: A 1026 ILE cc_start: 0.8531 (mm) cc_final: 0.8178 (mm) REVERT: A 1226 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7233 (mtp) REVERT: A 1253 MET cc_start: 0.8812 (mmt) cc_final: 0.8398 (mmt) REVERT: A 1292 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: B 639 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8746 (pt0) REVERT: C 98 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8853 (p) REVERT: C 345 MET cc_start: 0.7594 (mpt) cc_final: 0.6925 (mmt) REVERT: E 27 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8169 (mm) REVERT: F 52 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7650 (pp) REVERT: I 18 ASP cc_start: 0.9246 (t0) cc_final: 0.8907 (t0) REVERT: I 29 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8375 (mm) REVERT: I 51 GLU cc_start: 0.7810 (mp0) cc_final: 0.7543 (mp0) REVERT: I 78 CYS cc_start: 0.8259 (t) cc_final: 0.7862 (t) REVERT: I 107 GLU cc_start: 0.8486 (pm20) cc_final: 0.8180 (pm20) REVERT: I 113 TYR cc_start: 0.8778 (m-80) cc_final: 0.8475 (m-80) REVERT: I 124 GLU cc_start: 0.6748 (mp0) cc_final: 0.6183 (mp0) REVERT: J 26 GLN cc_start: 0.9251 (tt0) cc_final: 0.8639 (tm-30) REVERT: M 34 GLN cc_start: 0.8881 (tt0) cc_final: 0.8663 (tt0) REVERT: M 98 GLN cc_start: 0.9088 (mt0) cc_final: 0.8796 (mm110) REVERT: M 102 TYR cc_start: 0.8577 (m-80) cc_final: 0.8292 (m-80) REVERT: N 46 GLN cc_start: 0.8474 (tt0) cc_final: 0.8103 (tp40) REVERT: N 78 HIS cc_start: 0.7025 (p-80) cc_final: 0.5997 (t70) REVERT: N 112 GLN cc_start: 0.7696 (tp40) cc_final: 0.7348 (tm-30) outliers start: 98 outliers final: 50 residues processed: 439 average time/residue: 0.2053 time to fit residues: 150.9730 Evaluate side-chains 416 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 356 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain A residue 1292 GLU Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 639 GLN Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 238 THR Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 407 ILE Chi-restraints excluded: chain O residue 475 LEU Chi-restraints excluded: chain O residue 567 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 64 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 238 optimal weight: 9.9990 chunk 299 optimal weight: 9.9990 chunk 273 optimal weight: 20.0000 chunk 308 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 225 optimal weight: 0.4980 chunk 297 optimal weight: 6.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 ASN B 887 HIS B1023 ASN ** C 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN G 53 HIS ** N 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 227 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.087875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.064516 restraints weight = 126414.204| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.89 r_work: 0.3228 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36473 Z= 0.120 Angle : 0.609 13.607 49306 Z= 0.304 Chirality : 0.043 0.196 5447 Planarity : 0.004 0.072 6375 Dihedral : 5.127 44.986 4885 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.11 % Allowed : 13.16 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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 are not related in a simple way. whole: -1.96 (0.12), residues: 4415 helix: -0.77 (0.14), residues: 1432 sheet: -1.42 (0.20), residues: 647 loop : -1.57 (0.13), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 86 TYR 0.023 0.001 TYR O 235 PHE 0.014 0.001 PHE O 369 TRP 0.021 0.001 TRP C 40 HIS 0.012 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00271 (36447) covalent geometry : angle 0.60193 (49279) hydrogen bonds : bond 0.03180 ( 1029) hydrogen bonds : angle 4.99337 ( 2907) metal coordination : bond 0.00671 ( 26) metal coordination : angle 3.90557 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 385 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8458 (tpp) cc_final: 0.8191 (ttm) REVERT: A 550 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8370 (mm) REVERT: A 571 GLU cc_start: 0.8081 (pt0) cc_final: 0.7671 (pp20) REVERT: A 910 MET cc_start: 0.9291 (mtt) cc_final: 0.8676 (mtm) REVERT: A 954 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7580 (ptt90) REVERT: A 1026 ILE cc_start: 0.8472 (mm) cc_final: 0.8098 (mm) REVERT: A 1226 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.7131 (mtp) REVERT: A 1292 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: A 1540 MET cc_start: 0.9277 (mmm) cc_final: 0.9033 (tpp) REVERT: B 1057 ARG cc_start: 0.9105 (mmm160) cc_final: 0.8897 (mmp-170) REVERT: C 98 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8929 (p) REVERT: C 345 MET cc_start: 0.7561 (mpt) cc_final: 0.6964 (mmt) REVERT: E 27 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8131 (mm) REVERT: E 110 MET cc_start: 0.8749 (tpp) cc_final: 0.7983 (tpp) REVERT: G 93 TYR cc_start: 0.8441 (p90) cc_final: 0.7974 (p90) REVERT: G 132 MET cc_start: 0.1556 (mtt) cc_final: 0.1347 (mtp) REVERT: H 123 MET cc_start: 0.9109 (ttt) cc_final: 0.8841 (ttp) REVERT: I 18 ASP cc_start: 0.9253 (t0) cc_final: 0.8906 (t0) REVERT: I 29 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8445 (mt) REVERT: I 48 ARG cc_start: 0.8806 (tpp-160) cc_final: 0.8309 (tpp-160) REVERT: I 51 GLU cc_start: 0.7906 (mp0) cc_final: 0.7547 (mp0) REVERT: I 78 CYS cc_start: 0.8076 (t) cc_final: 0.7640 (t) REVERT: I 107 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8152 (pm20) REVERT: J 26 GLN cc_start: 0.9241 (tt0) cc_final: 0.8788 (tm-30) REVERT: K 47 GLU cc_start: 0.8803 (tp30) cc_final: 0.8524 (tp30) REVERT: M 10 ARG cc_start: 0.8099 (mmm160) cc_final: 0.7793 (mmm160) REVERT: M 32 LYS cc_start: 0.8157 (mtmm) cc_final: 0.7474 (pttp) REVERT: M 34 GLN cc_start: 0.8914 (tt0) cc_final: 0.8584 (tt0) REVERT: M 64 THR cc_start: 0.7476 (OUTLIER) cc_final: 0.7031 (p) REVERT: M 102 TYR cc_start: 0.8574 (m-80) cc_final: 0.8277 (m-80) REVERT: N 46 GLN cc_start: 0.8540 (tt0) cc_final: 0.8152 (tp40) REVERT: N 78 HIS cc_start: 0.6992 (p-80) cc_final: 0.6011 (t70) REVERT: N 112 GLN cc_start: 0.7611 (tp40) cc_final: 0.7274 (tm-30) REVERT: O 195 ARG cc_start: 0.8796 (tpm170) cc_final: 0.8330 (tmm160) REVERT: O 416 PHE cc_start: 0.8289 (m-80) cc_final: 0.8040 (m-80) outliers start: 83 outliers final: 43 residues processed: 442 average time/residue: 0.2038 time to fit residues: 151.4138 Evaluate side-chains 412 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 360 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain A residue 1292 GLU Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 140 GLN Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 469 PHE Chi-restraints excluded: chain O residue 475 LEU Chi-restraints excluded: chain O residue 567 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 5 optimal weight: 30.0000 chunk 300 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 425 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1717 GLN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 168 ASN G 53 HIS K 53 ASN ** N 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 227 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.086055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.062370 restraints weight = 127104.002| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.92 r_work: 0.3180 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 36473 Z= 0.200 Angle : 0.653 12.037 49306 Z= 0.325 Chirality : 0.045 0.203 5447 Planarity : 0.004 0.067 6375 Dihedral : 5.070 44.698 4883 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.31 % Allowed : 13.34 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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 are not related in a simple way. whole: -1.73 (0.13), residues: 4415 helix: -0.53 (0.14), residues: 1429 sheet: -1.37 (0.20), residues: 628 loop : -1.45 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1103 TYR 0.028 0.002 TYR G 45 PHE 0.013 0.001 PHE O 559 TRP 0.014 0.001 TRP C 40 HIS 0.012 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00456 (36447) covalent geometry : angle 0.64419 (49279) hydrogen bonds : bond 0.03382 ( 1029) hydrogen bonds : angle 5.02694 ( 2907) metal coordination : bond 0.01136 ( 26) metal coordination : angle 4.53564 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 356 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.6559 (mmm) cc_final: 0.6245 (mmm) REVERT: A 550 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8490 (mm) REVERT: A 663 ASP cc_start: 0.8236 (p0) cc_final: 0.8018 (t0) REVERT: A 910 MET cc_start: 0.9266 (mtt) cc_final: 0.8658 (mtm) REVERT: A 954 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7157 (ptt90) REVERT: A 1026 ILE cc_start: 0.8576 (mm) cc_final: 0.8294 (mm) REVERT: A 1226 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7216 (mtp) REVERT: A 1253 MET cc_start: 0.8878 (mmt) cc_final: 0.8437 (mmt) REVERT: A 1292 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: A 1540 MET cc_start: 0.9260 (mmm) cc_final: 0.9020 (tpp) REVERT: B 1057 ARG cc_start: 0.9110 (mmm160) cc_final: 0.8909 (mmp-170) REVERT: B 1131 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8758 (tttm) REVERT: C 98 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8821 (p) REVERT: C 345 MET cc_start: 0.7622 (mpt) cc_final: 0.7150 (mmt) REVERT: E 27 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8240 (mm) REVERT: E 44 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8582 (m-80) REVERT: E 110 MET cc_start: 0.8819 (tpp) cc_final: 0.8175 (tpp) REVERT: G 40 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6832 (tt) REVERT: G 93 TYR cc_start: 0.8409 (p90) cc_final: 0.7868 (p90) REVERT: G 115 ASN cc_start: 0.8055 (p0) cc_final: 0.7768 (p0) REVERT: I 18 ASP cc_start: 0.9257 (t0) cc_final: 0.8854 (t0) REVERT: I 29 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8475 (mt) REVERT: I 48 ARG cc_start: 0.8834 (tpp-160) cc_final: 0.8221 (tpp-160) REVERT: I 51 GLU cc_start: 0.8018 (mp0) cc_final: 0.7604 (mp0) REVERT: I 78 CYS cc_start: 0.8154 (t) cc_final: 0.7713 (t) REVERT: I 107 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8392 (pp20) REVERT: J 26 GLN cc_start: 0.9340 (tt0) cc_final: 0.8632 (tm-30) REVERT: J 28 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8610 (mp0) REVERT: K 47 GLU cc_start: 0.8791 (tp30) cc_final: 0.8492 (tp30) REVERT: M 10 ARG cc_start: 0.8174 (mmm160) cc_final: 0.7819 (mmm160) REVERT: M 34 GLN cc_start: 0.8855 (tt0) cc_final: 0.8623 (tt0) REVERT: M 64 THR cc_start: 0.7547 (OUTLIER) cc_final: 0.7115 (p) REVERT: M 102 TYR cc_start: 0.8655 (m-80) cc_final: 0.8405 (m-80) REVERT: N 46 GLN cc_start: 0.8584 (tt0) cc_final: 0.8245 (tp40) REVERT: N 112 GLN cc_start: 0.7595 (tp40) cc_final: 0.7351 (tm-30) REVERT: O 416 PHE cc_start: 0.8367 (m-80) cc_final: 0.8154 (m-80) outliers start: 91 outliers final: 60 residues processed: 422 average time/residue: 0.2153 time to fit residues: 150.5182 Evaluate side-chains 411 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 340 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain A residue 1292 GLU Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 889 GLN Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 140 GLN Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 372 CYS Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 475 LEU Chi-restraints excluded: chain O residue 567 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 64 optimal weight: 8.9990 chunk 431 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 328 optimal weight: 8.9990 chunk 264 optimal weight: 9.9990 chunk 102 optimal weight: 30.0000 chunk 171 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 282 optimal weight: 0.9990 chunk 226 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 HIS ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.085677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.062023 restraints weight = 128754.904| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.97 r_work: 0.3165 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 36473 Z= 0.197 Angle : 0.656 12.361 49306 Z= 0.327 Chirality : 0.045 0.194 5447 Planarity : 0.004 0.068 6375 Dihedral : 5.053 46.099 4883 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.52 % Allowed : 13.62 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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 are not related in a simple way. whole: -1.60 (0.13), residues: 4415 helix: -0.42 (0.14), residues: 1433 sheet: -1.32 (0.20), residues: 637 loop : -1.36 (0.13), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 482 TYR 0.022 0.002 TYR O 235 PHE 0.013 0.001 PHE O 559 TRP 0.011 0.001 TRP A 846 HIS 0.013 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00449 (36447) covalent geometry : angle 0.64727 (49279) hydrogen bonds : bond 0.03341 ( 1029) hydrogen bonds : angle 5.00295 ( 2907) metal coordination : bond 0.01138 ( 26) metal coordination : angle 4.62339 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 348 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.6757 (p90) REVERT: A 496 MET cc_start: 0.6352 (mmm) cc_final: 0.6086 (mmm) REVERT: A 550 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8405 (mm) REVERT: A 881 MET cc_start: 0.8819 (tpp) cc_final: 0.8509 (tpp) REVERT: A 910 MET cc_start: 0.9156 (mtt) cc_final: 0.8626 (mtm) REVERT: A 954 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7133 (ptt90) REVERT: A 1026 ILE cc_start: 0.8634 (mm) cc_final: 0.8349 (mm) REVERT: A 1253 MET cc_start: 0.8874 (mmt) cc_final: 0.8454 (mmt) REVERT: A 1292 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: A 1540 MET cc_start: 0.9290 (mmm) cc_final: 0.9024 (tpp) REVERT: B 1057 ARG cc_start: 0.9122 (mmm160) cc_final: 0.8921 (mmp-170) REVERT: B 1131 LYS cc_start: 0.9058 (mmmm) cc_final: 0.8738 (tttm) REVERT: C 98 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8812 (p) REVERT: C 345 MET cc_start: 0.7653 (mpt) cc_final: 0.7297 (mmt) REVERT: E 18 MET cc_start: 0.8810 (ttm) cc_final: 0.8584 (ppp) REVERT: E 44 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: E 110 MET cc_start: 0.8808 (tpp) cc_final: 0.8259 (tpp) REVERT: F 75 MET cc_start: 0.8171 (mtp) cc_final: 0.7954 (mtp) REVERT: G 40 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6724 (tt) REVERT: G 45 TYR cc_start: 0.8074 (p90) cc_final: 0.7874 (p90) REVERT: G 93 TYR cc_start: 0.8404 (p90) cc_final: 0.7908 (p90) REVERT: G 115 ASN cc_start: 0.8019 (p0) cc_final: 0.7725 (p0) REVERT: I 18 ASP cc_start: 0.9254 (t0) cc_final: 0.8808 (t0) REVERT: I 29 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8483 (mt) REVERT: I 78 CYS cc_start: 0.8098 (t) cc_final: 0.7743 (t) REVERT: J 26 GLN cc_start: 0.9346 (tt0) cc_final: 0.8667 (tm-30) REVERT: J 28 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8610 (mp0) REVERT: K 47 GLU cc_start: 0.8825 (tp30) cc_final: 0.8496 (tp30) REVERT: M 10 ARG cc_start: 0.8203 (mmm160) cc_final: 0.7230 (mmm160) REVERT: M 13 TYR cc_start: 0.9113 (t80) cc_final: 0.8889 (t80) REVERT: M 32 LYS cc_start: 0.8290 (mtmm) cc_final: 0.7606 (pttp) REVERT: M 34 GLN cc_start: 0.8913 (tt0) cc_final: 0.8609 (tt0) REVERT: M 64 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7091 (p) REVERT: M 98 GLN cc_start: 0.9123 (mt0) cc_final: 0.8874 (mm110) REVERT: M 102 TYR cc_start: 0.8604 (m-80) cc_final: 0.8322 (m-80) REVERT: N 46 GLN cc_start: 0.8589 (tt0) cc_final: 0.8195 (tp40) REVERT: N 112 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: O 416 PHE cc_start: 0.8365 (m-80) cc_final: 0.8127 (m-80) outliers start: 99 outliers final: 62 residues processed: 421 average time/residue: 0.2072 time to fit residues: 145.3017 Evaluate side-chains 402 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 330 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1068 HIS Chi-restraints excluded: chain A residue 1292 GLU Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 889 GLN Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 112 GLN Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 372 CYS Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 475 LEU Chi-restraints excluded: chain O residue 479 LEU Chi-restraints excluded: chain O residue 567 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 130 optimal weight: 20.0000 chunk 325 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 157 optimal weight: 20.0000 chunk 343 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN G 53 HIS ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 227 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.085318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.061696 restraints weight = 128030.616| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.89 r_work: 0.3166 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 36473 Z= 0.199 Angle : 0.663 12.228 49306 Z= 0.329 Chirality : 0.045 0.229 5447 Planarity : 0.004 0.067 6375 Dihedral : 5.041 46.784 4883 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.41 % Allowed : 14.03 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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 are not related in a simple way. whole: -1.50 (0.13), residues: 4415 helix: -0.33 (0.14), residues: 1434 sheet: -1.29 (0.20), residues: 640 loop : -1.29 (0.13), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1042 TYR 0.023 0.002 TYR O 235 PHE 0.022 0.001 PHE H 150 TRP 0.009 0.001 TRP M 11 HIS 0.012 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00455 (36447) covalent geometry : angle 0.65442 (49279) hydrogen bonds : bond 0.03365 ( 1029) hydrogen bonds : angle 5.01346 ( 2907) metal coordination : bond 0.01150 ( 26) metal coordination : angle 4.59650 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 342 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.6846 (p90) REVERT: A 200 MET cc_start: 0.8489 (ttm) cc_final: 0.7616 (ttt) REVERT: A 406 MET cc_start: 0.8910 (ptp) cc_final: 0.8388 (ptp) REVERT: A 496 MET cc_start: 0.6430 (mmm) cc_final: 0.6040 (mmm) REVERT: A 550 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8470 (mm) REVERT: A 881 MET cc_start: 0.8831 (tpp) cc_final: 0.8536 (tpp) REVERT: A 910 MET cc_start: 0.9162 (mtt) cc_final: 0.8608 (mtm) REVERT: A 954 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7114 (ptt90) REVERT: A 1026 ILE cc_start: 0.8634 (mm) cc_final: 0.8342 (mm) REVERT: A 1123 MET cc_start: 0.8636 (mtp) cc_final: 0.8434 (mtm) REVERT: A 1253 MET cc_start: 0.8880 (mmt) cc_final: 0.8439 (mmt) REVERT: A 1292 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: A 1540 MET cc_start: 0.9271 (mmm) cc_final: 0.9065 (tpp) REVERT: B 235 MET cc_start: 0.9196 (mmm) cc_final: 0.8938 (mmm) REVERT: B 600 MET cc_start: 0.8674 (mtt) cc_final: 0.8381 (mtt) REVERT: B 1131 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8745 (tttm) REVERT: C 345 MET cc_start: 0.7718 (mpt) cc_final: 0.7427 (mmt) REVERT: E 27 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8291 (mm) REVERT: E 44 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8552 (m-80) REVERT: E 110 MET cc_start: 0.8755 (tpp) cc_final: 0.8266 (tpp) REVERT: F 75 MET cc_start: 0.8247 (mtp) cc_final: 0.7870 (mtp) REVERT: G 40 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6716 (tp) REVERT: G 93 TYR cc_start: 0.8442 (p90) cc_final: 0.7928 (p90) REVERT: G 115 ASN cc_start: 0.8020 (p0) cc_final: 0.7721 (p0) REVERT: I 18 ASP cc_start: 0.9224 (t0) cc_final: 0.8779 (t0) REVERT: I 29 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8492 (mt) REVERT: I 78 CYS cc_start: 0.8267 (t) cc_final: 0.7913 (t) REVERT: J 26 GLN cc_start: 0.9312 (tt0) cc_final: 0.8641 (tm-30) REVERT: J 28 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8688 (mp0) REVERT: K 47 GLU cc_start: 0.8820 (tp30) cc_final: 0.8485 (tp30) REVERT: M 10 ARG cc_start: 0.8216 (mmm160) cc_final: 0.7232 (mmm160) REVERT: M 32 LYS cc_start: 0.8354 (mtmm) cc_final: 0.7642 (pttp) REVERT: M 34 GLN cc_start: 0.8880 (tt0) cc_final: 0.8576 (tt0) REVERT: M 64 THR cc_start: 0.7623 (OUTLIER) cc_final: 0.7144 (p) REVERT: M 98 GLN cc_start: 0.9091 (mt0) cc_final: 0.8846 (mm110) REVERT: M 99 MET cc_start: 0.8510 (tpp) cc_final: 0.8282 (tpp) REVERT: M 102 TYR cc_start: 0.8605 (m-80) cc_final: 0.8358 (m-80) REVERT: N 78 HIS cc_start: 0.6873 (p-80) cc_final: 0.5947 (t70) REVERT: O 416 PHE cc_start: 0.8408 (m-80) cc_final: 0.8134 (m-80) outliers start: 95 outliers final: 71 residues processed: 417 average time/residue: 0.2054 time to fit residues: 143.3984 Evaluate side-chains 407 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 327 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1068 HIS Chi-restraints excluded: chain A residue 1292 GLU Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 889 GLN Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 112 GLN Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 372 CYS Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 469 PHE Chi-restraints excluded: chain O residue 475 LEU Chi-restraints excluded: chain O residue 479 LEU Chi-restraints excluded: chain O residue 567 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 113 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 chunk 224 optimal weight: 5.9990 chunk 242 optimal weight: 0.7980 chunk 363 optimal weight: 9.9990 chunk 181 optimal weight: 0.5980 chunk 308 optimal weight: 9.9990 chunk 63 optimal weight: 0.3980 chunk 370 optimal weight: 4.9990 chunk 262 optimal weight: 0.0070 chunk 166 optimal weight: 3.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 ASN E 43 GLN E 168 ASN I 14 GLN ** N 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 227 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.087613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.064261 restraints weight = 125999.039| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.95 r_work: 0.3231 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 36473 Z= 0.108 Angle : 0.619 12.988 49306 Z= 0.307 Chirality : 0.044 0.193 5447 Planarity : 0.004 0.067 6375 Dihedral : 4.790 48.115 4883 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.93 % Allowed : 14.79 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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 are not related in a simple way. whole: -1.25 (0.13), residues: 4415 helix: -0.16 (0.14), residues: 1437 sheet: -1.04 (0.20), residues: 629 loop : -1.16 (0.13), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 482 TYR 0.033 0.001 TYR G 45 PHE 0.021 0.001 PHE H 150 TRP 0.018 0.001 TRP A 682 HIS 0.012 0.001 HIS O 227 Details of bonding type rmsd covalent geometry : bond 0.00242 (36447) covalent geometry : angle 0.61401 (49279) hydrogen bonds : bond 0.03039 ( 1029) hydrogen bonds : angle 4.81087 ( 2907) metal coordination : bond 0.00437 ( 26) metal coordination : angle 3.25234 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 355 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.6547 (p90) REVERT: A 200 MET cc_start: 0.8361 (ttm) cc_final: 0.7482 (ttm) REVERT: A 406 MET cc_start: 0.8803 (ptp) cc_final: 0.8338 (ptp) REVERT: A 496 MET cc_start: 0.6033 (mmm) cc_final: 0.5797 (mmm) REVERT: A 881 MET cc_start: 0.8796 (tpp) cc_final: 0.8571 (tpp) REVERT: A 910 MET cc_start: 0.9075 (mtt) cc_final: 0.8537 (mtm) REVERT: A 954 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7501 (ptt90) REVERT: A 1026 ILE cc_start: 0.8546 (mm) cc_final: 0.8303 (mm) REVERT: A 1123 MET cc_start: 0.8628 (mtp) cc_final: 0.8396 (mtm) REVERT: A 1253 MET cc_start: 0.8812 (mmt) cc_final: 0.8379 (mmt) REVERT: A 1292 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: A 1540 MET cc_start: 0.9227 (mmm) cc_final: 0.9021 (tpp) REVERT: B 129 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8917 (mp) REVERT: B 235 MET cc_start: 0.9155 (mmm) cc_final: 0.8874 (mmm) REVERT: B 1131 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8715 (tttm) REVERT: C 345 MET cc_start: 0.7572 (mpt) cc_final: 0.7216 (mmt) REVERT: E 44 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8287 (m-80) REVERT: E 94 MET cc_start: 0.8488 (ttt) cc_final: 0.8111 (ttt) REVERT: E 110 MET cc_start: 0.8824 (tpp) cc_final: 0.8308 (tpp) REVERT: F 75 MET cc_start: 0.8207 (mtp) cc_final: 0.7808 (mtp) REVERT: G 40 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6605 (tp) REVERT: G 45 TYR cc_start: 0.8014 (p90) cc_final: 0.7798 (p90) REVERT: G 93 TYR cc_start: 0.8460 (p90) cc_final: 0.8023 (p90) REVERT: G 115 ASN cc_start: 0.8079 (p0) cc_final: 0.7786 (p0) REVERT: I 18 ASP cc_start: 0.9263 (t0) cc_final: 0.8844 (t0) REVERT: I 29 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8324 (mt) REVERT: I 49 ASP cc_start: 0.9278 (m-30) cc_final: 0.8866 (p0) REVERT: I 78 CYS cc_start: 0.8186 (t) cc_final: 0.7878 (t) REVERT: J 26 GLN cc_start: 0.9317 (tt0) cc_final: 0.8654 (tm-30) REVERT: J 28 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8606 (mp0) REVERT: K 47 GLU cc_start: 0.8880 (tp30) cc_final: 0.8562 (tp30) REVERT: L 30 SER cc_start: 0.9164 (p) cc_final: 0.8938 (t) REVERT: L 31 ARG cc_start: 0.8658 (mpp80) cc_final: 0.8304 (mpp80) REVERT: M 10 ARG cc_start: 0.8222 (mmm160) cc_final: 0.7327 (mmm160) REVERT: M 32 LYS cc_start: 0.8281 (mtmm) cc_final: 0.7635 (pttp) REVERT: M 64 THR cc_start: 0.7519 (OUTLIER) cc_final: 0.7064 (p) REVERT: M 98 GLN cc_start: 0.9119 (mt0) cc_final: 0.8861 (mm110) REVERT: M 102 TYR cc_start: 0.8498 (m-80) cc_final: 0.8253 (m-80) REVERT: N 46 GLN cc_start: 0.8511 (tt0) cc_final: 0.8162 (tp40) REVERT: N 78 HIS cc_start: 0.6891 (p-80) cc_final: 0.5918 (t70) REVERT: O 195 ARG cc_start: 0.8698 (tpm170) cc_final: 0.8185 (ttp80) REVERT: O 416 PHE cc_start: 0.8265 (m-80) cc_final: 0.8037 (m-80) outliers start: 76 outliers final: 51 residues processed: 410 average time/residue: 0.2088 time to fit residues: 141.7358 Evaluate side-chains 397 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 338 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1292 GLU Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 112 GLN Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 372 CYS Chi-restraints excluded: chain O residue 376 LEU Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 469 PHE Chi-restraints excluded: chain O residue 475 LEU Chi-restraints excluded: chain O residue 567 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 355 optimal weight: 20.0000 chunk 372 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 426 optimal weight: 2.9990 chunk 421 optimal weight: 20.0000 chunk 373 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 HIS ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** N 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 227 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.085186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.061712 restraints weight = 128399.957| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.90 r_work: 0.3158 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 36473 Z= 0.215 Angle : 0.690 16.745 49306 Z= 0.340 Chirality : 0.046 0.184 5447 Planarity : 0.004 0.071 6375 Dihedral : 4.913 47.264 4883 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.73 % Allowed : 15.15 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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 are not related in a simple way. whole: -1.25 (0.13), residues: 4415 helix: -0.12 (0.14), residues: 1443 sheet: -1.12 (0.20), residues: 650 loop : -1.15 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B1103 TYR 0.028 0.002 TYR G 45 PHE 0.020 0.001 PHE H 150 TRP 0.013 0.001 TRP O 202 HIS 0.012 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00497 (36447) covalent geometry : angle 0.68050 (49279) hydrogen bonds : bond 0.03350 ( 1029) hydrogen bonds : angle 4.94006 ( 2907) metal coordination : bond 0.01284 ( 26) metal coordination : angle 4.86174 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 335 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.6719 (p90) REVERT: A 200 MET cc_start: 0.8470 (ttm) cc_final: 0.7494 (ttt) REVERT: A 406 MET cc_start: 0.8784 (ptp) cc_final: 0.8313 (ptp) REVERT: A 432 MET cc_start: 0.8550 (mtp) cc_final: 0.8250 (mtp) REVERT: A 496 MET cc_start: 0.6217 (mmm) cc_final: 0.5843 (mmm) REVERT: A 881 MET cc_start: 0.8824 (tpp) cc_final: 0.8563 (tpp) REVERT: A 910 MET cc_start: 0.9135 (mtt) cc_final: 0.8598 (mtm) REVERT: A 954 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7056 (ptt90) REVERT: A 1026 ILE cc_start: 0.8638 (mm) cc_final: 0.8412 (mm) REVERT: A 1123 MET cc_start: 0.8658 (mtp) cc_final: 0.8365 (mtm) REVERT: A 1253 MET cc_start: 0.8826 (mmt) cc_final: 0.8493 (mmt) REVERT: A 1540 MET cc_start: 0.9269 (mmm) cc_final: 0.8998 (tpp) REVERT: A 1672 MET cc_start: 0.7900 (mtm) cc_final: 0.7657 (ptp) REVERT: B 235 MET cc_start: 0.9200 (mmm) cc_final: 0.8941 (mmm) REVERT: B 924 MET cc_start: 0.8288 (mtm) cc_final: 0.7630 (mtm) REVERT: B 1131 LYS cc_start: 0.9080 (mmmm) cc_final: 0.8733 (tttm) REVERT: C 345 MET cc_start: 0.7637 (mpt) cc_final: 0.7359 (mmt) REVERT: E 94 MET cc_start: 0.8477 (ttt) cc_final: 0.8074 (ttt) REVERT: E 110 MET cc_start: 0.8786 (tpp) cc_final: 0.8300 (tpp) REVERT: F 75 MET cc_start: 0.8312 (mtp) cc_final: 0.7804 (mtp) REVERT: F 90 LEU cc_start: 0.8825 (mm) cc_final: 0.7864 (mm) REVERT: F 94 MET cc_start: 0.8850 (mtp) cc_final: 0.8571 (mpp) REVERT: G 40 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6698 (tp) REVERT: G 115 ASN cc_start: 0.8103 (p0) cc_final: 0.7809 (p0) REVERT: H 123 MET cc_start: 0.9005 (tmm) cc_final: 0.8757 (ttp) REVERT: I 18 ASP cc_start: 0.9230 (t0) cc_final: 0.8757 (t0) REVERT: I 29 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8391 (mt) REVERT: I 49 ASP cc_start: 0.9294 (m-30) cc_final: 0.8892 (p0) REVERT: I 78 CYS cc_start: 0.8255 (t) cc_final: 0.7946 (t) REVERT: J 26 GLN cc_start: 0.9281 (tt0) cc_final: 0.8630 (tm-30) REVERT: J 28 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8649 (mp0) REVERT: K 47 GLU cc_start: 0.8890 (tp30) cc_final: 0.8577 (tp30) REVERT: L 30 SER cc_start: 0.9123 (p) cc_final: 0.8902 (t) REVERT: L 31 ARG cc_start: 0.8653 (mpp80) cc_final: 0.8319 (mpp80) REVERT: M 10 ARG cc_start: 0.8243 (mmm160) cc_final: 0.7324 (mmm160) REVERT: M 32 LYS cc_start: 0.8381 (mtmm) cc_final: 0.7863 (pttp) REVERT: M 64 THR cc_start: 0.7534 (OUTLIER) cc_final: 0.7037 (p) REVERT: M 98 GLN cc_start: 0.9096 (mt0) cc_final: 0.8836 (mm110) REVERT: M 102 TYR cc_start: 0.8551 (m-80) cc_final: 0.8337 (m-80) REVERT: N 78 HIS cc_start: 0.6906 (p-80) cc_final: 0.5928 (t70) REVERT: O 416 PHE cc_start: 0.8328 (m-80) cc_final: 0.8112 (m-80) outliers start: 68 outliers final: 56 residues processed: 386 average time/residue: 0.2028 time to fit residues: 129.9598 Evaluate side-chains 388 residues out of total 3935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 327 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 112 GLN Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 372 CYS Chi-restraints excluded: chain O residue 376 LEU Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 475 LEU Chi-restraints excluded: chain O residue 567 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 335 optimal weight: 8.9990 chunk 277 optimal weight: 5.9990 chunk 313 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 102 optimal weight: 0.6980 chunk 395 optimal weight: 20.0000 chunk 240 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 227 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.085254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.062027 restraints weight = 127894.529| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.79 r_work: 0.3174 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 36473 Z= 0.190 Angle : 0.667 11.546 49306 Z= 0.331 Chirality : 0.045 0.361 5447 Planarity : 0.004 0.067 6375 Dihedral : 4.941 49.263 4883 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.68 % Allowed : 15.25 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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 are not related in a simple way. whole: -1.22 (0.13), residues: 4415 helix: -0.08 (0.14), residues: 1444 sheet: -1.15 (0.20), residues: 646 loop : -1.13 (0.13), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1103 TYR 0.023 0.001 TYR O 235 PHE 0.021 0.001 PHE H 150 TRP 0.010 0.001 TRP B1088 HIS 0.012 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00439 (36447) covalent geometry : angle 0.65949 (49279) hydrogen bonds : bond 0.03307 ( 1029) hydrogen bonds : angle 4.93207 ( 2907) metal coordination : bond 0.01042 ( 26) metal coordination : angle 4.21051 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12426.09 seconds wall clock time: 212 minutes 3.83 seconds (12723.83 seconds total)