Starting phenix.real_space_refine on Fri Jan 16 16:43:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f5p_28867/01_2026/8f5p_28867.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f5p_28867/01_2026/8f5p_28867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f5p_28867/01_2026/8f5p_28867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f5p_28867/01_2026/8f5p_28867.map" model { file = "/net/cci-nas-00/data/ceres_data/8f5p_28867/01_2026/8f5p_28867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f5p_28867/01_2026/8f5p_28867.cif" } resolution = 3.4 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= 0.007 sd= 0.778 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 4 6.06 5 S 249 5.16 5 C 24891 2.51 5 N 6880 2.21 5 O 7413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39437 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "B" Number of atoms: 8917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1128, 8917 Classifications: {'peptide': 1128} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1089} Chain breaks: 3 Chain: "C" Number of atoms: 9337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9337 Classifications: {'peptide': 1176} Link IDs: {'PTRANS': 44, 'TRANS': 1131} Chain breaks: 2 Chain: "D" Number of atoms: 4826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4826 Classifications: {'peptide': 612} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 589} Chain breaks: 7 Chain: "E" Number of atoms: 8269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8269 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 4, 'PTRANS': 38, 'TRANS': 1014} Chain breaks: 8 Chain: "F" Number of atoms: 7499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 7499 Classifications: {'peptide': 970} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 931} Chain breaks: 1 Chain: "B" 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: "C" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9009 SG CYS B1174 130.964 114.749 246.888 1.00137.21 S ATOM 9029 SG CYS B1177 132.607 114.730 250.289 1.00140.08 S ATOM 9121 SG CYS B1188 129.063 115.945 249.830 1.00125.04 S ATOM 9144 SG CYS B1191 131.939 118.099 248.645 1.00132.66 S ATOM 9313 SG CYS B1214 114.226 101.634 231.283 1.00105.95 S ATOM 9332 SG CYS B1217 113.165 104.087 234.017 1.00 94.87 S ATOM 9457 SG CYS B1232 113.042 100.649 234.791 1.00105.01 S ATOM 9478 SG CYS B1235 110.557 101.947 232.136 1.00 96.99 S ATOM 17440 SG CYS C1044 74.249 115.867 50.661 1.00221.01 S ATOM 17468 SG CYS C1047 77.966 116.275 49.657 1.00224.80 S ATOM 17572 SG CYS C1061 76.238 112.788 49.770 1.00218.72 S ATOM 17593 SG CYS C1064 76.941 114.669 52.909 1.00230.25 S ATOM 18451 SG CYS C1232 56.356 115.095 69.723 1.00149.33 S ATOM 18469 SG CYS C1235 59.419 113.986 68.134 1.00151.36 S ATOM 18620 SG CYS C1254 55.942 112.168 67.453 1.00132.34 S ATOM 18641 SG CYS C1257 58.023 111.688 70.663 1.00130.86 S Time building chain proxies: 8.29, per 1000 atoms: 0.21 Number of scatterers: 39437 At special positions: 0 Unit cell: (146.08, 150.23, 317.89, 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 4 29.99 S 249 16.00 O 7413 8.00 N 6880 7.00 C 24891 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B3000 " pdb="ZN ZN B3000 " - pdb=" SG CYS B1188 " pdb="ZN ZN B3000 " - pdb=" SG CYS B1174 " pdb="ZN ZN B3000 " - pdb=" SG CYS B1177 " pdb="ZN ZN B3000 " - pdb=" SG CYS B1191 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1217 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1232 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1214 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1235 " pdb=" ZN C3000 " pdb="ZN ZN C3000 " - pdb=" SG CYS C1064 " pdb="ZN ZN C3000 " - pdb=" SG CYS C1044 " pdb="ZN ZN C3000 " - pdb=" SG CYS C1061 " pdb="ZN ZN C3000 " - pdb=" SG CYS C1047 " pdb=" ZN C3001 " pdb="ZN ZN C3001 " - pdb=" SG CYS C1232 " pdb="ZN ZN C3001 " - pdb=" SG CYS C1235 " pdb="ZN ZN C3001 " - pdb=" SG CYS C1257 " pdb="ZN ZN C3001 " - pdb=" SG CYS C1254 " Number of angles added : 24 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9512 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 70 sheets defined 40.2% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.690A pdb=" N ASP A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 171 removed outlier: 3.810A pdb=" N MET A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 215 removed outlier: 3.872A pdb=" N GLN A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 15 Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 207 through 210 Processing helix chain 'B' and resid 447 through 455 Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 647 through 659 Processing helix chain 'B' and resid 661 through 673 Processing helix chain 'B' and resid 674 through 688 Processing helix chain 'B' and resid 690 through 701 removed outlier: 4.268A pdb=" N ALA B 694 " --> pdb=" O ASP B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 715 Processing helix chain 'B' and resid 718 through 730 Processing helix chain 'B' and resid 732 through 742 Processing helix chain 'B' and resid 745 through 757 removed outlier: 3.865A pdb=" N ALA B 749 " --> pdb=" O ARG B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 Processing helix chain 'B' and resid 775 through 790 Processing helix chain 'B' and resid 792 through 804 Processing helix chain 'B' and resid 805 through 817 removed outlier: 3.834A pdb=" N ARG B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 830 removed outlier: 3.699A pdb=" N LEU B 822 " --> pdb=" O ASP B 818 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N SER B 827 " --> pdb=" O THR B 823 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N MET B 828 " --> pdb=" O GLN B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 847 Processing helix chain 'B' and resid 848 through 859 Processing helix chain 'B' and resid 862 through 872 Processing helix chain 'B' and resid 874 through 882 removed outlier: 3.674A pdb=" N ALA B 882 " --> pdb=" O ALA B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 904 removed outlier: 3.670A pdb=" N LYS B 896 " --> pdb=" O GLN B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 917 removed outlier: 3.518A pdb=" N ILE B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 936 removed outlier: 3.741A pdb=" N ALA B 923 " --> pdb=" O LYS B 919 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU B 936 " --> pdb=" O LYS B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 959 removed outlier: 3.822A pdb=" N ALA B 942 " --> pdb=" O ASP B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 990 removed outlier: 4.193A pdb=" N ALA B 990 " --> pdb=" O LEU B 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 987 through 990' Processing helix chain 'B' and resid 991 through 1009 removed outlier: 3.681A pdb=" N TYR B 997 " --> pdb=" O GLY B 993 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN B1004 " --> pdb=" O LEU B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1022 Processing helix chain 'B' and resid 1023 through 1026 Processing helix chain 'B' and resid 1030 through 1045 Processing helix chain 'B' and resid 1047 through 1067 removed outlier: 3.848A pdb=" N CYS B1051 " --> pdb=" O ASN B1047 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG B1057 " --> pdb=" O LYS B1053 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B1066 " --> pdb=" O GLU B1062 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B1067 " --> pdb=" O ARG B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1149 through 1160 removed outlier: 3.836A pdb=" N ASP B1153 " --> pdb=" O ARG B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1209 No H-bonds generated for 'chain 'B' and resid 1207 through 1209' Processing helix chain 'B' and resid 1223 through 1227 Processing helix chain 'C' and resid 561 through 572 removed outlier: 4.148A pdb=" N ALA C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS C 568 " --> pdb=" O HIS C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 584 removed outlier: 3.745A pdb=" N LEU C 584 " --> pdb=" O GLU C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 601 Processing helix chain 'C' and resid 603 through 611 removed outlier: 3.677A pdb=" N ALA C 607 " --> pdb=" O ARG C 603 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 631 removed outlier: 3.586A pdb=" N VAL C 620 " --> pdb=" O ASP C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 689 removed outlier: 3.741A pdb=" N GLY C 682 " --> pdb=" O SER C 678 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER C 683 " --> pdb=" O VAL C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 701 removed outlier: 3.586A pdb=" N THR C 701 " --> pdb=" O GLN C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 714 Processing helix chain 'C' and resid 716 through 724 removed outlier: 3.671A pdb=" N ALA C 720 " --> pdb=" O MET C 716 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS C 722 " --> pdb=" O ASP C 718 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE C 723 " --> pdb=" O ASN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 744 removed outlier: 4.185A pdb=" N LYS C 731 " --> pdb=" O GLU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 758 Processing helix chain 'C' and resid 759 through 771 removed outlier: 4.368A pdb=" N GLY C 765 " --> pdb=" O ALA C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 783 Processing helix chain 'C' and resid 784 through 786 No H-bonds generated for 'chain 'C' and resid 784 through 786' Processing helix chain 'C' and resid 787 through 801 removed outlier: 3.839A pdb=" N ILE C 791 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU C 793 " --> pdb=" O THR C 789 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE C 797 " --> pdb=" O GLU C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 815 Processing helix chain 'C' and resid 816 through 828 removed outlier: 3.762A pdb=" N LEU C 820 " --> pdb=" O ASP C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 840 Processing helix chain 'C' and resid 841 through 843 No H-bonds generated for 'chain 'C' and resid 841 through 843' Processing helix chain 'C' and resid 844 through 858 removed outlier: 3.517A pdb=" N VAL C 849 " --> pdb=" O ARG C 845 " (cutoff:3.500A) Proline residue: C 850 - end of helix Processing helix chain 'C' and resid 860 through 871 removed outlier: 4.089A pdb=" N GLU C 866 " --> pdb=" O ASP C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 891 Processing helix chain 'C' and resid 893 through 908 Processing helix chain 'C' and resid 918 through 951 removed outlier: 4.453A pdb=" N GLY C 944 " --> pdb=" O TYR C 940 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL C 945 " --> pdb=" O ALA C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 972 removed outlier: 4.230A pdb=" N ALA C 972 " --> pdb=" O PHE C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 996 removed outlier: 3.647A pdb=" N ILE C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1010 Processing helix chain 'C' and resid 1018 through 1029 Processing helix chain 'C' and resid 1091 through 1101 removed outlier: 4.240A pdb=" N GLU C1095 " --> pdb=" O ASP C1091 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG C1096 " --> pdb=" O GLU C1092 " (cutoff:3.500A) Processing helix chain 'C' and resid 1168 through 1174 Processing helix chain 'C' and resid 1199 through 1201 No H-bonds generated for 'chain 'C' and resid 1199 through 1201' Processing helix chain 'C' and resid 1241 through 1248 Processing helix chain 'C' and resid 1249 through 1251 No H-bonds generated for 'chain 'C' and resid 1249 through 1251' Processing helix chain 'C' and resid 1264 through 1282 removed outlier: 3.560A pdb=" N ILE C1272 " --> pdb=" O SER C1268 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C1273 " --> pdb=" O MET C1269 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C1282 " --> pdb=" O THR C1278 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 881 removed outlier: 3.773A pdb=" N ALA D 881 " --> pdb=" O ALA D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 898 Processing helix chain 'D' and resid 901 through 915 removed outlier: 3.697A pdb=" N ARG D 905 " --> pdb=" O LEU D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 917 through 927 Processing helix chain 'D' and resid 954 through 972 removed outlier: 3.504A pdb=" N ALA D 958 " --> pdb=" O ALA D 954 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1009 removed outlier: 4.192A pdb=" N ALA D 998 " --> pdb=" O ASN D 994 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA D 999 " --> pdb=" O HIS D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1021 removed outlier: 4.254A pdb=" N ARG D1019 " --> pdb=" O GLU D1015 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR D1021 " --> pdb=" O GLN D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1023 through 1048 removed outlier: 3.529A pdb=" N THR D1028 " --> pdb=" O PRO D1024 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLN D1030 " --> pdb=" O VAL D1026 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ARG D1031 " --> pdb=" O ILE D1027 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL D1032 " --> pdb=" O THR D1028 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL D1033 " --> pdb=" O GLU D1029 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N MET D1034 " --> pdb=" O GLN D1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 1063 through 1094 removed outlier: 3.650A pdb=" N GLU D1085 " --> pdb=" O THR D1081 " (cutoff:3.500A) Processing helix chain 'D' and resid 1097 through 1111 Processing helix chain 'D' and resid 1115 through 1121 Processing helix chain 'D' and resid 1123 through 1128 Processing helix chain 'D' and resid 1133 through 1148 removed outlier: 3.570A pdb=" N ALA D1137 " --> pdb=" O ASN D1133 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D1140 " --> pdb=" O ASP D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1165 removed outlier: 3.508A pdb=" N PHE D1158 " --> pdb=" O ALA D1154 " (cutoff:3.500A) Processing helix chain 'D' and resid 1168 through 1183 Processing helix chain 'D' and resid 1184 through 1187 Processing helix chain 'D' and resid 1188 through 1198 Processing helix chain 'D' and resid 1206 through 1220 Processing helix chain 'D' and resid 1222 through 1234 Processing helix chain 'D' and resid 1241 through 1255 Processing helix chain 'D' and resid 1305 through 1319 Processing helix chain 'D' and resid 1325 through 1339 removed outlier: 3.752A pdb=" N ALA D1333 " --> pdb=" O ARG D1329 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR D1339 " --> pdb=" O CYS D1335 " (cutoff:3.500A) Processing helix chain 'D' and resid 1341 through 1361 Processing helix chain 'D' and resid 1401 through 1418 Processing helix chain 'D' and resid 1429 through 1435 Processing helix chain 'D' and resid 1439 through 1454 Processing helix chain 'D' and resid 1455 through 1468 removed outlier: 3.580A pdb=" N ALA D1459 " --> pdb=" O GLN D1455 " (cutoff:3.500A) Processing helix chain 'D' and resid 1520 through 1535 removed outlier: 3.561A pdb=" N GLN D1535 " --> pdb=" O TYR D1531 " (cutoff:3.500A) Processing helix chain 'D' and resid 1539 through 1553 Processing helix chain 'D' and resid 1556 through 1570 Processing helix chain 'D' and resid 1572 through 1588 Processing helix chain 'D' and resid 1591 through 1606 Processing helix chain 'D' and resid 1607 through 1622 Processing helix chain 'D' and resid 1628 through 1639 removed outlier: 5.355A pdb=" N ASP D1634 " --> pdb=" O ALA D1630 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ALA D1635 " --> pdb=" O ASP D1631 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 98 Processing helix chain 'E' and resid 105 through 119 removed outlier: 4.016A pdb=" N ALA E 119 " --> pdb=" O ILE E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 410 through 412 No H-bonds generated for 'chain 'E' and resid 410 through 412' Processing helix chain 'E' and resid 564 through 568 Processing helix chain 'E' and resid 686 through 689 Processing helix chain 'E' and resid 708 through 713 Processing helix chain 'E' and resid 772 through 775 Processing helix chain 'E' and resid 776 through 783 Processing helix chain 'E' and resid 867 through 882 Processing helix chain 'E' and resid 884 through 894 removed outlier: 4.028A pdb=" N SER E 894 " --> pdb=" O ARG E 890 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 912 removed outlier: 3.882A pdb=" N TRP E 901 " --> pdb=" O ASN E 897 " (cutoff:3.500A) Processing helix chain 'E' and resid 914 through 924 removed outlier: 3.614A pdb=" N VAL E 919 " --> pdb=" O ASP E 915 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET E 924 " --> pdb=" O CYS E 920 " (cutoff:3.500A) Processing helix chain 'E' and resid 926 through 940 Processing helix chain 'E' and resid 943 through 955 removed outlier: 4.127A pdb=" N GLN E 947 " --> pdb=" O ASP E 943 " (cutoff:3.500A) Processing helix chain 'E' and resid 957 through 968 Processing helix chain 'E' and resid 970 through 981 Processing helix chain 'E' and resid 983 through 994 Processing helix chain 'E' and resid 998 through 1014 removed outlier: 3.692A pdb=" N VAL E1002 " --> pdb=" O ARG E 998 " (cutoff:3.500A) Processing helix chain 'E' and resid 1015 through 1026 removed outlier: 4.076A pdb=" N MET E1021 " --> pdb=" O ASP E1017 " (cutoff:3.500A) Processing helix chain 'E' and resid 1032 through 1040 removed outlier: 3.831A pdb=" N THR E1040 " --> pdb=" O ILE E1036 " (cutoff:3.500A) Processing helix chain 'E' and resid 1042 through 1051 removed outlier: 3.517A pdb=" N LEU E1046 " --> pdb=" O ARG E1042 " (cutoff:3.500A) Processing helix chain 'E' and resid 1079 through 1083 Processing helix chain 'E' and resid 1086 through 1100 Processing helix chain 'E' and resid 1102 through 1114 Processing helix chain 'E' and resid 1115 through 1126 Processing helix chain 'E' and resid 1130 through 1156 removed outlier: 3.506A pdb=" N ALA E1134 " --> pdb=" O LYS E1130 " (cutoff:3.500A) Processing helix chain 'E' and resid 1176 through 1186 removed outlier: 3.848A pdb=" N VAL E1180 " --> pdb=" O SER E1176 " (cutoff:3.500A) Processing helix chain 'E' and resid 1189 through 1201 Processing helix chain 'E' and resid 1202 through 1211 Processing helix chain 'E' and resid 1228 through 1240 removed outlier: 3.905A pdb=" N GLU E1240 " --> pdb=" O ALA E1236 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 228 removed outlier: 3.643A pdb=" N GLY F 228 " --> pdb=" O SER F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 removed outlier: 3.642A pdb=" N ARG F 316 " --> pdb=" O GLU F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 663 through 673 Processing helix chain 'F' and resid 675 through 680 Processing helix chain 'F' and resid 685 through 699 Processing helix chain 'F' and resid 701 through 710 removed outlier: 3.572A pdb=" N ARG F 707 " --> pdb=" O GLU F 703 " (cutoff:3.500A) Processing helix chain 'F' and resid 714 through 723 removed outlier: 3.641A pdb=" N LYS F 723 " --> pdb=" O LEU F 719 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 742 Processing helix chain 'F' and resid 743 through 754 Processing helix chain 'F' and resid 757 through 767 removed outlier: 3.880A pdb=" N LEU F 761 " --> pdb=" O PRO F 757 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG F 764 " --> pdb=" O ALA F 760 " (cutoff:3.500A) Processing helix chain 'F' and resid 769 through 778 Processing helix chain 'F' and resid 781 through 783 No H-bonds generated for 'chain 'F' and resid 781 through 783' Processing helix chain 'F' and resid 784 through 799 Processing helix chain 'F' and resid 802 through 812 removed outlier: 3.908A pdb=" N GLU F 807 " --> pdb=" O ALA F 803 " (cutoff:3.500A) Processing helix chain 'F' and resid 822 through 851 Processing helix chain 'F' and resid 852 through 863 removed outlier: 3.858A pdb=" N ALA F 856 " --> pdb=" O ASN F 852 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS F 858 " --> pdb=" O ALA F 854 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR F 859 " --> pdb=" O ASP F 855 " (cutoff:3.500A) Processing helix chain 'F' and resid 865 through 874 removed outlier: 3.771A pdb=" N LYS F 874 " --> pdb=" O LYS F 870 " (cutoff:3.500A) Processing helix chain 'F' and resid 875 through 877 No H-bonds generated for 'chain 'F' and resid 875 through 877' Processing helix chain 'F' and resid 881 through 892 removed outlier: 3.503A pdb=" N ALA F 885 " --> pdb=" O LYS F 881 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU F 890 " --> pdb=" O ALA F 886 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS F 891 " --> pdb=" O GLN F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 895 through 905 Processing helix chain 'F' and resid 908 through 916 removed outlier: 3.526A pdb=" N ALA F 912 " --> pdb=" O ASN F 908 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG F 914 " --> pdb=" O LYS F 910 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU F 915 " --> pdb=" O ALA F 911 " (cutoff:3.500A) Processing helix chain 'F' and resid 917 through 919 No H-bonds generated for 'chain 'F' and resid 917 through 919' Processing helix chain 'F' and resid 921 through 933 removed outlier: 3.527A pdb=" N ILE F 925 " --> pdb=" O SER F 921 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE F 927 " --> pdb=" O ASN F 923 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG F 930 " --> pdb=" O GLY F 926 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY F 931 " --> pdb=" O ILE F 927 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS F 932 " --> pdb=" O TYR F 928 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU F 933 " --> pdb=" O ALA F 929 " (cutoff:3.500A) Processing helix chain 'F' and resid 934 through 936 No H-bonds generated for 'chain 'F' and resid 934 through 936' Processing helix chain 'F' and resid 937 through 948 removed outlier: 3.527A pdb=" N ALA F 946 " --> pdb=" O GLU F 942 " (cutoff:3.500A) Processing helix chain 'F' and resid 950 through 961 removed outlier: 4.562A pdb=" N ARG F 956 " --> pdb=" O ASP F 952 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE F 959 " --> pdb=" O VAL F 955 " (cutoff:3.500A) Processing helix chain 'F' and resid 964 through 976 Processing helix chain 'F' and resid 977 through 991 Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 10 removed outlier: 6.313A pdb=" N PHE B 320 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG B 8 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL B 318 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 22 removed outlier: 3.891A pdb=" N SER B 19 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU B 38 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER B 57 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 74 removed outlier: 3.750A pdb=" N MET B 103 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL B 93 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLU B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N HIS B 95 " --> pdb=" O TRP B 99 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TRP B 99 " --> pdb=" O HIS B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114 removed outlier: 3.678A pdb=" N ASP B 114 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA B 132 " --> pdb=" O TYR B 128 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP B 144 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 155 removed outlier: 6.810A pdb=" N GLY B 167 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL B 155 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU B 165 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP B 177 " --> pdb=" O HIS B 183 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N HIS B 183 " --> pdb=" O ASP B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 200 through 205 removed outlier: 4.258A pdb=" N LYS B 227 " --> pdb=" O TYR B 223 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU B 228 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 250 through 253 removed outlier: 3.575A pdb=" N PHE B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER B 282 " --> pdb=" O HIS B 287 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS B 287 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 332 Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 374 removed outlier: 6.640A pdb=" N ILE B 381 " --> pdb=" O GLN B 369 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N MET B 371 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 379 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA B 373 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG B 391 " --> pdb=" O PHE B 407 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE B 407 " --> pdb=" O ARG B 391 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE B 393 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR B 405 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 395 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 414 through 417 Processing sheet with id=AB2, first strand: chain 'B' and resid 487 through 492 removed outlier: 4.331A pdb=" N THR B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN B 510 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU B 516 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 526 through 531 removed outlier: 6.588A pdb=" N ILE B 541 " --> pdb=" O GLN B 527 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N MET B 529 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA B 539 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL B 531 " --> pdb=" O GLN B 537 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN B 537 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ILE B 546 " --> pdb=" O HIS B 542 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 575 through 580 Processing sheet with id=AB5, first strand: chain 'B' and resid 613 through 618 removed outlier: 6.679A pdb=" N ARG B 623 " --> pdb=" O CYS B 615 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE B 617 " --> pdb=" O LYS B 621 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS B 621 " --> pdb=" O PHE B 617 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1172 through 1173 Processing sheet with id=AB7, first strand: chain 'B' and resid 1196 through 1197 removed outlier: 4.087A pdb=" N ASN B1196 " --> pdb=" O ILE B1205 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1211 through 1213 Processing sheet with id=AB9, first strand: chain 'C' and resid 2 through 10 removed outlier: 5.379A pdb=" N THR C 3 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR C 294 " --> pdb=" O THR C 3 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N VAL C 5 " --> pdb=" O ASP C 292 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ASP C 292 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP C 7 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.730A pdb=" N HIS C 53 " --> pdb=" O VAL C 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 62 through 67 removed outlier: 3.511A pdb=" N PHE C 74 " --> pdb=" O TRP C 86 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 76 " --> pdb=" O ILE C 84 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE C 84 " --> pdb=" O SER C 76 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY C 78 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL C 83 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS C 95 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL C 85 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 102 through 107 removed outlier: 6.519A pdb=" N VAL C 117 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU C 105 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA C 115 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 114 " --> pdb=" O TRP C 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP C 125 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 143 through 146 removed outlier: 3.685A pdb=" N ILE C 155 " --> pdb=" O MET C 163 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET C 163 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 181 through 186 removed outlier: 4.565A pdb=" N ALA C 183 " --> pdb=" O GLY C 200 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 226 through 232 removed outlier: 6.831A pdb=" N SER C 241 " --> pdb=" O CYS C 227 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL C 229 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 239 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TYR C 231 " --> pdb=" O TYR C 237 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR C 237 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY C 242 " --> pdb=" O LYS C 246 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C 247 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 258 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR C 251 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG C 256 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 299 through 302 Processing sheet with id=AC8, first strand: chain 'C' and resid 336 through 340 removed outlier: 3.680A pdb=" N LYS C 336 " --> pdb=" O GLN C 347 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 352 " --> pdb=" O GLN C 372 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLN C 372 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL C 354 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 381 through 384 removed outlier: 6.583A pdb=" N ILE C 397 " --> pdb=" O GLU C 409 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU C 409 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N MET C 399 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 416 through 423 removed outlier: 6.586A pdb=" N GLY C 434 " --> pdb=" O GLN C 417 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET C 419 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 432 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL C 421 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE C 430 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS C 442 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU C 452 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 462 through 465 removed outlier: 6.693A pdb=" N LEU C 481 " --> pdb=" O SER C 495 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER C 495 " --> pdb=" O LEU C 481 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL C 483 " --> pdb=" O LEU C 493 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 499 through 504 Processing sheet with id=AD4, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.588A pdb=" N PHE C 548 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE C 542 " --> pdb=" O HIS C 546 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N HIS C 546 " --> pdb=" O PHE C 542 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1043 through 1044 Processing sheet with id=AD6, first strand: chain 'C' and resid 1188 through 1190 removed outlier: 4.483A pdb=" N PHE C1188 " --> pdb=" O GLU C1082 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C1190 " --> pdb=" O VAL C1084 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1229 through 1231 Processing sheet with id=AD8, first strand: chain 'E' and resid 2 through 7 Processing sheet with id=AD9, first strand: chain 'E' and resid 14 through 22 removed outlier: 10.889A pdb=" N GLU E 17 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 11.857A pdb=" N VAL E 34 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU E 19 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 32 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN E 43 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL E 48 " --> pdb=" O ASN E 43 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 67 through 70 Processing sheet with id=AE2, first strand: chain 'E' and resid 137 through 142 removed outlier: 4.339A pdb=" N HIS E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 137 through 142 removed outlier: 4.339A pdb=" N HIS E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 190 through 193 Processing sheet with id=AE5, first strand: chain 'E' and resid 254 through 260 removed outlier: 4.182A pdb=" N MET E 274 " --> pdb=" O THR E 270 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU E 290 " --> pdb=" O VAL E 277 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA E 279 " --> pdb=" O SER E 288 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER E 288 " --> pdb=" O ALA E 279 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 314 through 319 removed outlier: 5.755A pdb=" N MET E 315 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLY E 326 " --> pdb=" O MET E 315 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TRP E 317 " --> pdb=" O ALA E 324 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ALA E 324 " --> pdb=" O TRP E 317 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 354 through 356 removed outlier: 7.206A pdb=" N GLY E 369 " --> pdb=" O SER E 355 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 354 through 356 removed outlier: 7.206A pdb=" N GLY E 369 " --> pdb=" O SER E 355 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE E 374 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN E 379 " --> pdb=" O ALA E 416 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ALA E 416 " --> pdb=" O GLN E 379 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 456 through 458 Processing sheet with id=AF1, first strand: chain 'E' and resid 492 through 496 Processing sheet with id=AF2, first strand: chain 'E' and resid 533 through 535 removed outlier: 3.667A pdb=" N ARG E 547 " --> pdb=" O LYS E 544 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 570 through 576 removed outlier: 6.703A pdb=" N VAL E 583 " --> pdb=" O VAL E 571 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET E 573 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL E 581 " --> pdb=" O MET E 573 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE E 575 " --> pdb=" O TYR E 579 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR E 579 " --> pdb=" O ILE E 575 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR E 588 " --> pdb=" O SER E 584 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 570 through 576 removed outlier: 6.703A pdb=" N VAL E 583 " --> pdb=" O VAL E 571 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET E 573 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL E 581 " --> pdb=" O MET E 573 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE E 575 " --> pdb=" O TYR E 579 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR E 579 " --> pdb=" O ILE E 575 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR E 588 " --> pdb=" O SER E 584 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 589 " --> pdb=" O ARG E 606 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 640 through 647 removed outlier: 6.511A pdb=" N MET E 657 " --> pdb=" O SER E 643 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA E 645 " --> pdb=" O ALA E 655 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA E 655 " --> pdb=" O ALA E 645 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL E 647 " --> pdb=" O ARG E 653 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ARG E 653 " --> pdb=" O VAL E 647 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL E 654 " --> pdb=" O TRP E 671 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TRP E 671 " --> pdb=" O VAL E 654 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU E 656 " --> pdb=" O ARG E 669 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ARG E 669 " --> pdb=" O LEU E 656 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N SER E 658 " --> pdb=" O ASP E 667 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP E 667 " --> pdb=" O SER E 658 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 691 through 697 removed outlier: 6.120A pdb=" N TYR E 720 " --> pdb=" O PRO E 692 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER E 694 " --> pdb=" O GLU E 718 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE E 802 " --> pdb=" O LEU E 810 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU E 810 " --> pdb=" O PHE E 802 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR E 804 " --> pdb=" O LEU E 808 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU E 808 " --> pdb=" O THR E 804 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 820 through 827 removed outlier: 5.544A pdb=" N LEU E 823 " --> pdb=" O ALA E 834 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA E 834 " --> pdb=" O LEU E 823 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY E 825 " --> pdb=" O LEU E 832 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 832 " --> pdb=" O GLY E 825 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 820 through 827 removed outlier: 5.544A pdb=" N LEU E 823 " --> pdb=" O ALA E 834 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA E 834 " --> pdb=" O LEU E 823 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY E 825 " --> pdb=" O LEU E 832 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 832 " --> pdb=" O GLY E 825 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.678A pdb=" N ILE F 30 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 78 through 83 Processing sheet with id=AG2, first strand: chain 'F' and resid 122 through 124 removed outlier: 4.220A pdb=" N LEU F 122 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL F 131 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG F 129 " --> pdb=" O ASN F 124 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 141 through 146 removed outlier: 7.008A pdb=" N ILE F 157 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY F 144 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU F 155 " --> pdb=" O GLY F 144 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 164 through 166 removed outlier: 7.989A pdb=" N ILE F 165 " --> pdb=" O LEU F 173 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 202 through 203 removed outlier: 4.233A pdb=" N VAL F 202 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU F 209 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE F 210 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA F 219 " --> pdb=" O ILE F 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'F' and resid 233 through 235 removed outlier: 3.732A pdb=" N THR F 234 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU F 242 " --> pdb=" O THR F 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'F' and resid 250 through 256 removed outlier: 7.485A pdb=" N VAL F 250 " --> pdb=" O SER F 265 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N SER F 265 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N LEU F 252 " --> pdb=" O ARG F 263 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG F 263 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP F 254 " --> pdb=" O ARG F 261 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 275 through 278 removed outlier: 3.850A pdb=" N MET F 275 " --> pdb=" O VAL F 288 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL F 288 " --> pdb=" O MET F 275 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN F 277 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA F 286 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL F 285 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 319 through 324 removed outlier: 4.117A pdb=" N ASP F 320 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N GLY F 334 " --> pdb=" O ASP F 320 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU F 322 " --> pdb=" O PHE F 332 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N PHE F 332 " --> pdb=" O LEU F 322 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TRP F 324 " --> pdb=" O GLN F 330 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N GLN F 330 " --> pdb=" O TRP F 324 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU F 331 " --> pdb=" O PHE F 343 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE F 343 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL F 333 " --> pdb=" O THR F 341 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 341 " --> pdb=" O VAL F 333 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'F' and resid 352 through 354 removed outlier: 3.711A pdb=" N CYS F 379 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN F 371 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL F 377 " --> pdb=" O ASN F 371 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 389 through 392 removed outlier: 6.413A pdb=" N VAL F 405 " --> pdb=" O THR F 441 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR F 441 " --> pdb=" O VAL F 405 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR F 407 " --> pdb=" O LEU F 439 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 451 through 453 Processing sheet with id=AH4, first strand: chain 'F' and resid 491 through 496 removed outlier: 7.259A pdb=" N ALA F 504 " --> pdb=" O VAL F 492 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE F 494 " --> pdb=" O LEU F 502 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU F 502 " --> pdb=" O ILE F 494 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU F 496 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE F 500 " --> pdb=" O LEU F 496 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG F 508 " --> pdb=" O THR F 505 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 521 " --> pdb=" O VAL F 511 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA F 513 " --> pdb=" O GLN F 519 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN F 519 " --> pdb=" O ALA F 513 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 540 through 544 Processing sheet with id=AH6, first strand: chain 'F' and resid 572 through 575 Processing sheet with id=AH7, first strand: chain 'F' and resid 628 through 633 removed outlier: 6.286A pdb=" N GLN F 640 " --> pdb=" O PRO F 629 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR F 631 " --> pdb=" O VAL F 638 " (cutoff:3.500A) 1851 hydrogen bonds defined for protein. 5292 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: 11.88 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13183 1.34 - 1.46: 8709 1.46 - 1.58: 17924 1.58 - 1.70: 0 1.70 - 1.82: 382 Bond restraints: 40198 Sorted by residual: bond pdb=" CG LEU D 972 " pdb=" CD2 LEU D 972 " ideal model delta sigma weight residual 1.521 1.559 -0.038 3.30e-02 9.18e+02 1.35e+00 bond pdb=" CA VAL D1437 " pdb=" CB VAL D1437 " ideal model delta sigma weight residual 1.540 1.525 0.016 1.36e-02 5.41e+03 1.32e+00 bond pdb=" CG1 ILE B 826 " pdb=" CD1 ILE B 826 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.18e+00 bond pdb=" CG LEU D1550 " pdb=" CD1 LEU D1550 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" CG ARG B 212 " pdb=" CD ARG B 212 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.34e-01 ... (remaining 40193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 53825 1.82 - 3.64: 595 3.64 - 5.46: 60 5.46 - 7.28: 17 7.28 - 9.10: 2 Bond angle restraints: 54499 Sorted by residual: angle pdb=" N ILE D1201 " pdb=" CA ILE D1201 " pdb=" C ILE D1201 " ideal model delta sigma weight residual 113.20 109.82 3.38 9.60e-01 1.09e+00 1.24e+01 angle pdb=" N ASN E 524 " pdb=" CA ASN E 524 " pdb=" C ASN E 524 " ideal model delta sigma weight residual 108.14 112.92 -4.78 1.52e+00 4.33e-01 9.87e+00 angle pdb=" N VAL C 39 " pdb=" CA VAL C 39 " pdb=" C VAL C 39 " ideal model delta sigma weight residual 112.29 109.67 2.62 9.40e-01 1.13e+00 7.78e+00 angle pdb=" C PRO D1054 " pdb=" N PHE D1055 " pdb=" CA PHE D1055 " ideal model delta sigma weight residual 122.46 126.38 -3.92 1.41e+00 5.03e-01 7.73e+00 angle pdb=" CA GLU B 905 " pdb=" CB GLU B 905 " pdb=" CG GLU B 905 " ideal model delta sigma weight residual 114.10 119.49 -5.39 2.00e+00 2.50e-01 7.27e+00 ... (remaining 54494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.22: 22435 18.22 - 36.44: 1475 36.44 - 54.66: 318 54.66 - 72.88: 62 72.88 - 91.10: 15 Dihedral angle restraints: 24305 sinusoidal: 9626 harmonic: 14679 Sorted by residual: dihedral pdb=" CA ALA D1051 " pdb=" C ALA D1051 " pdb=" N PRO D1052 " pdb=" CA PRO D1052 " ideal model delta harmonic sigma weight residual -180.00 -153.18 -26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ALA E 496 " pdb=" C ALA E 496 " pdb=" N PHE E 497 " pdb=" CA PHE E 497 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA TYR B 509 " pdb=" C TYR B 509 " pdb=" N GLN B 510 " pdb=" CA GLN B 510 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 24302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3807 0.032 - 0.064: 1610 0.064 - 0.095: 454 0.095 - 0.127: 285 0.127 - 0.159: 22 Chirality restraints: 6178 Sorted by residual: chirality pdb=" CA ILE C 397 " pdb=" N ILE C 397 " pdb=" C ILE C 397 " pdb=" CB ILE C 397 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CB ILE E 850 " pdb=" CA ILE E 850 " pdb=" CG1 ILE E 850 " pdb=" CG2 ILE E 850 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA ILE B 541 " pdb=" N ILE B 541 " pdb=" C ILE B 541 " pdb=" CB ILE B 541 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 6175 not shown) Planarity restraints: 7034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 118 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO B 119 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 861 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO B 862 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 862 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 862 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 884 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C GLU B 884 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU B 884 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS B 885 " 0.010 2.00e-02 2.50e+03 ... (remaining 7031 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3088 2.74 - 3.28: 39305 3.28 - 3.82: 66483 3.82 - 4.36: 78177 4.36 - 4.90: 133457 Nonbonded interactions: 320510 Sorted by model distance: nonbonded pdb=" O ARG D1044 " pdb=" OG SER D1048 " model vdw 2.202 3.040 nonbonded pdb=" O VAL E 194 " pdb=" OG SER E 225 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR C 516 " pdb=" OD1 ASP C 518 " model vdw 2.223 3.040 nonbonded pdb=" OG SER A 181 " pdb=" O ALA D1237 " model vdw 2.228 3.040 nonbonded pdb=" O HIS D1016 " pdb=" OG1 THR D1020 " model vdw 2.228 3.040 ... (remaining 320505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 21.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 44.100 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40214 Z= 0.127 Angle : 0.522 10.159 54523 Z= 0.275 Chirality : 0.042 0.159 6178 Planarity : 0.004 0.047 7034 Dihedral : 12.992 91.100 14793 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.41 % Rotamer: Outliers : 1.95 % Allowed : 9.57 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.12), residues: 4964 helix: 0.73 (0.12), residues: 1815 sheet: -0.19 (0.16), residues: 1102 loop : -0.73 (0.14), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 961 TYR 0.013 0.001 TYR F 503 PHE 0.019 0.001 PHE D1055 TRP 0.013 0.001 TRP B 576 HIS 0.005 0.001 HIS B 672 Details of bonding type rmsd covalent geometry : bond 0.00275 (40198) covalent geometry : angle 0.51511 (54499) hydrogen bonds : bond 0.13127 ( 1833) hydrogen bonds : angle 5.82203 ( 5292) metal coordination : bond 0.00925 ( 16) metal coordination : angle 4.02113 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 411 time to evaluate : 1.445 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: B 182 GLU cc_start: 0.6529 (tp30) cc_final: 0.6216 (mm-30) REVERT: B 630 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7612 (tt) REVERT: B 638 ARG cc_start: 0.7337 (mtm110) cc_final: 0.7099 (mtm110) REVERT: B 680 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7612 (tt) REVERT: B 739 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8092 (mp) REVERT: B 1060 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7654 (tm-30) REVERT: B 1186 GLN cc_start: 0.7402 (pp30) cc_final: 0.7032 (pp30) REVERT: C 157 MET cc_start: 0.3559 (tpt) cc_final: 0.3185 (tpt) REVERT: C 365 MET cc_start: 0.4837 (ptt) cc_final: 0.4591 (ptt) REVERT: C 497 ASP cc_start: 0.8024 (m-30) cc_final: 0.7554 (m-30) REVERT: C 797 PHE cc_start: 0.8790 (m-80) cc_final: 0.8346 (m-80) REVERT: C 846 GLU cc_start: 0.7503 (tt0) cc_final: 0.6853 (tt0) REVERT: C 881 MET cc_start: 0.7517 (ttp) cc_final: 0.7194 (ttp) REVERT: C 1019 MET cc_start: 0.8236 (mpp) cc_final: 0.7959 (pmm) REVERT: C 1020 GLU cc_start: 0.8792 (mp0) cc_final: 0.8298 (mp0) REVERT: C 1023 ASP cc_start: 0.8751 (m-30) cc_final: 0.8532 (m-30) REVERT: C 1025 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7514 (mt-10) REVERT: E 366 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6824 (mpp) outliers start: 83 outliers final: 39 residues processed: 481 average time/residue: 0.2251 time to fit residues: 183.9096 Evaluate side-chains 391 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 348 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 693 ASP Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1072 PHE Chi-restraints excluded: chain C residue 1272 ILE Chi-restraints excluded: chain D residue 972 LEU Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1522 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 511 TYR Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 1224 MET Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 643 ASN Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 695 LYS Chi-restraints excluded: chain F residue 863 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 432 optimal weight: 0.0000 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 494 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 GLN B 876 ASN C 318 HIS ** D1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1223 ASN D1350 HIS D1570 ASN ** D1622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS E 380 HIS F 519 GLN F 561 ASN F 674 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.169024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.130075 restraints weight = 89349.249| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 4.11 r_work: 0.3763 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 40214 Z= 0.150 Angle : 0.538 9.587 54523 Z= 0.279 Chirality : 0.042 0.176 6178 Planarity : 0.004 0.108 7034 Dihedral : 5.332 59.746 5550 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 2.63 % Allowed : 12.04 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.12), residues: 4964 helix: 0.92 (0.12), residues: 1858 sheet: -0.13 (0.16), residues: 1105 loop : -0.71 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 904 TYR 0.016 0.001 TYR F 798 PHE 0.025 0.001 PHE D1055 TRP 0.011 0.001 TRP B 576 HIS 0.005 0.001 HIS B 672 Details of bonding type rmsd covalent geometry : bond 0.00332 (40198) covalent geometry : angle 0.52919 (54499) hydrogen bonds : bond 0.03796 ( 1833) hydrogen bonds : angle 4.82829 ( 5292) metal coordination : bond 0.01077 ( 16) metal coordination : angle 4.55244 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 389 time to evaluate : 1.498 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: B 9 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8083 (mp) REVERT: B 182 GLU cc_start: 0.7106 (tp30) cc_final: 0.6705 (mm-30) REVERT: B 630 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7813 (tt) REVERT: B 638 ARG cc_start: 0.7858 (mtm110) cc_final: 0.7576 (mtm110) REVERT: B 680 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7775 (tt) REVERT: B 739 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7923 (mp) REVERT: B 1057 ARG cc_start: 0.8072 (mmm-85) cc_final: 0.7610 (mmm-85) REVERT: B 1060 GLN cc_start: 0.8314 (tm-30) cc_final: 0.8002 (tm-30) REVERT: B 1186 GLN cc_start: 0.8224 (pp30) cc_final: 0.7703 (pp30) REVERT: C 91 GLU cc_start: 0.7143 (mp0) cc_final: 0.6907 (mp0) REVERT: C 624 LYS cc_start: 0.8783 (ptpp) cc_final: 0.8255 (tptp) REVERT: C 908 TYR cc_start: 0.6152 (OUTLIER) cc_final: 0.5199 (t80) REVERT: C 1020 GLU cc_start: 0.8811 (mp0) cc_final: 0.8591 (mp0) REVERT: C 1023 ASP cc_start: 0.8699 (m-30) cc_final: 0.8482 (m-30) REVERT: C 1025 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7418 (mt-10) REVERT: C 1269 MET cc_start: 0.7615 (tpt) cc_final: 0.7331 (tpt) REVERT: E 274 MET cc_start: 0.8663 (mmm) cc_final: 0.8311 (mmm) REVERT: E 291 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7567 (ttp80) REVERT: E 680 MET cc_start: 0.6780 (tpt) cc_final: 0.6550 (tpt) REVERT: E 924 MET cc_start: 0.7625 (mtm) cc_final: 0.7341 (mtm) REVERT: E 1232 MET cc_start: 0.9431 (mtm) cc_final: 0.9224 (mpp) REVERT: F 396 MET cc_start: 0.4627 (tpp) cc_final: 0.4357 (tpp) outliers start: 112 outliers final: 71 residues processed: 480 average time/residue: 0.2314 time to fit residues: 187.7858 Evaluate side-chains 438 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 361 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1158 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 1072 PHE Chi-restraints excluded: chain C residue 1272 ILE Chi-restraints excluded: chain D residue 972 LEU Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1157 MET Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1428 THR Chi-restraints excluded: chain D residue 1463 LEU Chi-restraints excluded: chain D residue 1522 ILE Chi-restraints excluded: chain D residue 1541 ASP Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1584 TRP Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 511 TYR Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 691 ILE Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 1224 MET Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 643 ASN Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 653 THR Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 839 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 298 optimal weight: 0.0870 chunk 208 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 481 optimal weight: 9.9990 chunk 402 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 396 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 291 optimal weight: 0.8980 chunk 342 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 GLN ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 HIS E 844 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.169601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.129645 restraints weight = 89915.388| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.80 r_work: 0.3763 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 40214 Z= 0.129 Angle : 0.511 9.547 54523 Z= 0.264 Chirality : 0.041 0.191 6178 Planarity : 0.004 0.082 7034 Dihedral : 4.869 55.613 5526 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.47 % Rotamer: Outliers : 3.25 % Allowed : 12.80 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.12), residues: 4964 helix: 1.07 (0.12), residues: 1861 sheet: -0.06 (0.16), residues: 1100 loop : -0.68 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 904 TYR 0.034 0.001 TYR D 965 PHE 0.020 0.001 PHE C 797 TRP 0.013 0.001 TRP B 576 HIS 0.005 0.001 HIS B 672 Details of bonding type rmsd covalent geometry : bond 0.00286 (40198) covalent geometry : angle 0.50243 (54499) hydrogen bonds : bond 0.03508 ( 1833) hydrogen bonds : angle 4.62250 ( 5292) metal coordination : bond 0.00919 ( 16) metal coordination : angle 4.48999 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 384 time to evaluate : 1.529 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: B 9 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8065 (mp) REVERT: B 41 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8234 (mt) REVERT: B 182 GLU cc_start: 0.7026 (tp30) cc_final: 0.6657 (mm-30) REVERT: B 530 SER cc_start: 0.8578 (t) cc_final: 0.8258 (m) REVERT: B 630 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7799 (tt) REVERT: B 739 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7998 (mp) REVERT: B 758 ASP cc_start: 0.6664 (t0) cc_final: 0.5839 (p0) REVERT: B 1057 ARG cc_start: 0.8222 (mmm-85) cc_final: 0.7672 (mmm-85) REVERT: B 1060 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8044 (tm-30) REVERT: B 1186 GLN cc_start: 0.8290 (pp30) cc_final: 0.7812 (pp30) REVERT: C 91 GLU cc_start: 0.7291 (mp0) cc_final: 0.7029 (mp0) REVERT: C 624 LYS cc_start: 0.8756 (ptpp) cc_final: 0.8269 (tptp) REVERT: C 908 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.5443 (t80) REVERT: C 1020 GLU cc_start: 0.8810 (mp0) cc_final: 0.8595 (mp0) REVERT: C 1023 ASP cc_start: 0.8780 (m-30) cc_final: 0.8543 (m-30) REVERT: C 1025 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7405 (mt-10) REVERT: C 1269 MET cc_start: 0.7543 (tpt) cc_final: 0.7187 (tpt) REVERT: D 1410 MET cc_start: 0.7856 (mmm) cc_final: 0.7442 (ttm) REVERT: D 1439 HIS cc_start: 0.7147 (OUTLIER) cc_final: 0.6669 (t-90) REVERT: E 313 MET cc_start: 0.7302 (mtp) cc_final: 0.7094 (ttp) REVERT: E 512 MET cc_start: 0.7466 (mmm) cc_final: 0.7043 (mmm) REVERT: E 680 MET cc_start: 0.6818 (tpt) cc_final: 0.6593 (tpt) REVERT: E 924 MET cc_start: 0.7776 (mtm) cc_final: 0.7458 (mtm) REVERT: E 1232 MET cc_start: 0.9469 (mtm) cc_final: 0.9209 (mpp) REVERT: F 60 MET cc_start: -0.4459 (ttt) cc_final: -0.4911 (ttm) REVERT: F 396 MET cc_start: 0.5101 (tpp) cc_final: 0.4845 (tpp) outliers start: 138 outliers final: 98 residues processed: 493 average time/residue: 0.2290 time to fit residues: 191.1228 Evaluate side-chains 456 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 352 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1158 ILE Chi-restraints excluded: chain B residue 1199 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 712 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 919 ASP Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1066 HIS Chi-restraints excluded: chain C residue 1072 PHE Chi-restraints excluded: chain C residue 1272 ILE Chi-restraints excluded: chain D residue 993 ASP Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1157 MET Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1405 GLN Chi-restraints excluded: chain D residue 1439 HIS Chi-restraints excluded: chain D residue 1463 LEU Chi-restraints excluded: chain D residue 1522 ILE Chi-restraints excluded: chain D residue 1541 ASP Chi-restraints excluded: chain D residue 1584 TRP Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 511 TYR Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 691 ILE Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 1221 ASN Chi-restraints excluded: chain E residue 1224 MET Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 643 ASN Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 653 THR Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 830 GLN Chi-restraints excluded: chain F residue 839 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 357 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 438 optimal weight: 8.9990 chunk 311 optimal weight: 10.0000 chunk 431 optimal weight: 20.0000 chunk 396 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 366 optimal weight: 0.0170 chunk 314 optimal weight: 10.0000 chunk 490 optimal weight: 8.9990 chunk 404 optimal weight: 6.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN B 249 HIS B 722 GLN B1231 ASN ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 ASN ** C 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1150 GLN F 349 ASN F 373 GLN F 519 GLN F 756 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.161477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.125290 restraints weight = 80091.966| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 3.49 r_work: 0.3643 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.169 40214 Z= 0.388 Angle : 0.749 14.626 54523 Z= 0.388 Chirality : 0.049 0.265 6178 Planarity : 0.006 0.058 7034 Dihedral : 5.559 56.715 5524 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.64 % Rotamer: Outliers : 4.49 % Allowed : 14.21 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.12), residues: 4964 helix: 0.26 (0.12), residues: 1839 sheet: -0.56 (0.16), residues: 1133 loop : -0.83 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 869 TYR 0.026 0.002 TYR B 729 PHE 0.026 0.002 PHE B1159 TRP 0.021 0.002 TRP D 913 HIS 0.011 0.002 HIS C 562 Details of bonding type rmsd covalent geometry : bond 0.00851 (40198) covalent geometry : angle 0.73877 (54499) hydrogen bonds : bond 0.04813 ( 1833) hydrogen bonds : angle 5.39243 ( 5292) metal coordination : bond 0.02272 ( 16) metal coordination : angle 5.98866 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 359 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8047 (mp) REVERT: B 41 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8037 (mt) REVERT: B 184 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7528 (mm) REVERT: B 553 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.5669 (mp0) REVERT: B 629 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7562 (mt-10) REVERT: B 630 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8011 (tt) REVERT: B 739 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8104 (mp) REVERT: B 752 LEU cc_start: 0.3991 (OUTLIER) cc_final: 0.3371 (tp) REVERT: B 821 MET cc_start: 0.8737 (mpp) cc_final: 0.8520 (mpp) REVERT: B 1060 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8022 (tm-30) REVERT: B 1186 GLN cc_start: 0.8412 (pp30) cc_final: 0.8057 (pp30) REVERT: C 103 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7915 (mp10) REVERT: C 485 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6308 (tm-30) REVERT: C 496 GLU cc_start: 0.7773 (tp30) cc_final: 0.7299 (tm-30) REVERT: C 624 LYS cc_start: 0.8836 (ptpp) cc_final: 0.8303 (tptp) REVERT: C 766 MET cc_start: 0.7248 (tpp) cc_final: 0.6964 (tpp) REVERT: C 846 GLU cc_start: 0.7693 (tt0) cc_final: 0.7059 (tt0) REVERT: C 881 MET cc_start: 0.7291 (ttp) cc_final: 0.6970 (ttp) REVERT: C 1018 MET cc_start: 0.7270 (tpp) cc_final: 0.6883 (tpp) REVERT: C 1025 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7494 (mt-10) REVERT: D 1242 CYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8729 (p) REVERT: D 1520 ASP cc_start: 0.8538 (p0) cc_final: 0.8258 (p0) REVERT: D 1569 ARG cc_start: 0.8065 (tpt90) cc_final: 0.7802 (tpt90) REVERT: E 291 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7451 (ttp80) REVERT: E 366 MET cc_start: 0.7124 (mpt) cc_final: 0.6838 (mpt) REVERT: E 576 MET cc_start: 0.4010 (ppp) cc_final: 0.3692 (ppp) REVERT: E 680 MET cc_start: 0.6939 (tpt) cc_final: 0.6651 (tpt) REVERT: F 613 ASP cc_start: 0.8255 (m-30) cc_final: 0.7881 (t70) REVERT: F 770 TRP cc_start: 0.6381 (m100) cc_final: 0.5662 (m100) outliers start: 191 outliers final: 125 residues processed: 516 average time/residue: 0.2289 time to fit residues: 200.4114 Evaluate side-chains 475 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 340 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 533 CYS Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 1013 LYS Chi-restraints excluded: chain B residue 1020 MET Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1199 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 712 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 832 ASN Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1066 HIS Chi-restraints excluded: chain C residue 1272 ILE Chi-restraints excluded: chain D residue 993 ASP Chi-restraints excluded: chain D residue 1014 LEU Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1153 ASP Chi-restraints excluded: chain D residue 1157 MET Chi-restraints excluded: chain D residue 1242 CYS Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1330 ILE Chi-restraints excluded: chain D residue 1405 GLN Chi-restraints excluded: chain D residue 1463 LEU Chi-restraints excluded: chain D residue 1511 ILE Chi-restraints excluded: chain D residue 1522 ILE Chi-restraints excluded: chain D residue 1541 ASP Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1566 ILE Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 511 TYR Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 573 MET Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 691 ILE Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 805 HIS Chi-restraints excluded: chain E residue 833 LEU Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 1221 ASN Chi-restraints excluded: chain E residue 1224 MET Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 643 ASN Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 653 THR Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 739 MET Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 830 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 391 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 173 optimal weight: 0.6980 chunk 420 optimal weight: 40.0000 chunk 63 optimal weight: 1.9990 chunk 400 optimal weight: 20.0000 chunk 271 optimal weight: 2.9990 chunk 438 optimal weight: 0.3980 chunk 192 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 230 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS B1231 ASN ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.167895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.129392 restraints weight = 84489.974| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 3.69 r_work: 0.3721 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 40214 Z= 0.128 Angle : 0.552 14.230 54523 Z= 0.281 Chirality : 0.042 0.256 6178 Planarity : 0.004 0.057 7034 Dihedral : 5.045 58.140 5518 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 3.25 % Allowed : 16.00 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.12), residues: 4964 helix: 0.94 (0.12), residues: 1854 sheet: -0.33 (0.16), residues: 1095 loop : -0.72 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1057 TYR 0.013 0.001 TYR C 26 PHE 0.045 0.001 PHE D1055 TRP 0.019 0.001 TRP B 576 HIS 0.004 0.001 HIS B 672 Details of bonding type rmsd covalent geometry : bond 0.00284 (40198) covalent geometry : angle 0.54219 (54499) hydrogen bonds : bond 0.03545 ( 1833) hydrogen bonds : angle 4.73543 ( 5292) metal coordination : bond 0.00859 ( 16) metal coordination : angle 4.99664 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 374 time to evaluate : 1.562 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: A 197 MET cc_start: 0.6309 (tpp) cc_final: 0.5989 (tpp) REVERT: B 9 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.7987 (mp) REVERT: B 28 TRP cc_start: 0.8488 (m100) cc_final: 0.8277 (m100) REVERT: B 41 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8086 (mt) REVERT: B 88 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7348 (ttp-170) REVERT: B 182 GLU cc_start: 0.7123 (tp30) cc_final: 0.6793 (tp30) REVERT: B 636 ARG cc_start: 0.8652 (mmm160) cc_final: 0.8448 (mmm160) REVERT: B 739 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8089 (mp) REVERT: B 1060 GLN cc_start: 0.8349 (tm-30) cc_final: 0.8064 (tm-30) REVERT: B 1186 GLN cc_start: 0.8458 (pp30) cc_final: 0.8037 (pp30) REVERT: C 103 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: C 485 GLU cc_start: 0.6856 (tm-30) cc_final: 0.6322 (tm-30) REVERT: C 496 GLU cc_start: 0.7747 (tp30) cc_final: 0.7409 (tm-30) REVERT: C 621 GLU cc_start: 0.8298 (pt0) cc_final: 0.8069 (pt0) REVERT: C 624 LYS cc_start: 0.8763 (ptpp) cc_final: 0.8283 (tptp) REVERT: C 846 GLU cc_start: 0.7589 (tt0) cc_final: 0.6981 (tt0) REVERT: C 881 MET cc_start: 0.7293 (ttp) cc_final: 0.6947 (ttp) REVERT: C 1018 MET cc_start: 0.7507 (tpp) cc_final: 0.7071 (tpp) REVERT: C 1023 ASP cc_start: 0.8841 (m-30) cc_final: 0.8601 (m-30) REVERT: C 1025 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7598 (mt-10) REVERT: C 1186 GLN cc_start: 0.6875 (tm-30) cc_final: 0.6593 (tm-30) REVERT: D 1160 ASP cc_start: 0.8673 (p0) cc_final: 0.8300 (p0) REVERT: D 1242 CYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8680 (p) REVERT: D 1410 MET cc_start: 0.7945 (mmm) cc_final: 0.7599 (ttm) REVERT: E 274 MET cc_start: 0.8690 (mmm) cc_final: 0.8227 (mmm) REVERT: E 291 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7355 (ttp80) REVERT: E 512 MET cc_start: 0.7780 (mmm) cc_final: 0.7329 (mmm) REVERT: E 576 MET cc_start: 0.4635 (ppp) cc_final: 0.4308 (ppp) REVERT: E 680 MET cc_start: 0.6996 (tpt) cc_final: 0.6736 (tpt) REVERT: E 924 MET cc_start: 0.7815 (mtm) cc_final: 0.7464 (mtm) REVERT: E 1232 MET cc_start: 0.9474 (mtt) cc_final: 0.9226 (mpp) REVERT: F 613 ASP cc_start: 0.8046 (m-30) cc_final: 0.7704 (t70) REVERT: F 770 TRP cc_start: 0.6589 (m100) cc_final: 0.6011 (m100) outliers start: 138 outliers final: 101 residues processed: 482 average time/residue: 0.2243 time to fit residues: 182.9025 Evaluate side-chains 460 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 352 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 1199 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1231 ASN Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 712 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 1066 HIS Chi-restraints excluded: chain C residue 1072 PHE Chi-restraints excluded: chain C residue 1272 ILE Chi-restraints excluded: chain D residue 993 ASP Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1157 MET Chi-restraints excluded: chain D residue 1242 CYS Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1405 GLN Chi-restraints excluded: chain D residue 1407 LEU Chi-restraints excluded: chain D residue 1463 LEU Chi-restraints excluded: chain D residue 1522 ILE Chi-restraints excluded: chain D residue 1541 ASP Chi-restraints excluded: chain D residue 1584 TRP Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 511 TYR Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 691 ILE Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 810 LEU Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 1221 ASN Chi-restraints excluded: chain E residue 1224 MET Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 653 THR Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 739 MET Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 830 GLN Chi-restraints excluded: chain F residue 839 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 361 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 479 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 490 optimal weight: 7.9990 chunk 295 optimal weight: 0.5980 chunk 182 optimal weight: 4.9990 chunk 287 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 298 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN B 249 HIS B1231 ASN ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 ASN ** D1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.167990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.130420 restraints weight = 77032.164| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 4.00 r_work: 0.3734 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 40214 Z= 0.135 Angle : 0.550 13.749 54523 Z= 0.278 Chirality : 0.042 0.263 6178 Planarity : 0.004 0.126 7034 Dihedral : 4.884 59.953 5513 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 3.53 % Allowed : 16.80 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.12), residues: 4964 helix: 1.03 (0.12), residues: 1861 sheet: -0.30 (0.16), residues: 1103 loop : -0.66 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG B 904 TYR 0.012 0.001 TYR F 503 PHE 0.019 0.001 PHE C 797 TRP 0.021 0.001 TRP D1262 HIS 0.004 0.001 HIS B 672 Details of bonding type rmsd covalent geometry : bond 0.00304 (40198) covalent geometry : angle 0.53964 (54499) hydrogen bonds : bond 0.03452 ( 1833) hydrogen bonds : angle 4.65462 ( 5292) metal coordination : bond 0.00935 ( 16) metal coordination : angle 4.97889 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 364 time to evaluate : 1.623 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: A 197 MET cc_start: 0.6216 (tpp) cc_final: 0.5896 (tpp) REVERT: B 9 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8070 (mp) REVERT: B 41 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8101 (mt) REVERT: B 88 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7378 (ttp-170) REVERT: B 182 GLU cc_start: 0.7049 (tp30) cc_final: 0.6694 (tp30) REVERT: B 635 GLU cc_start: 0.8245 (mp0) cc_final: 0.7989 (pm20) REVERT: B 739 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8126 (mp) REVERT: B 804 ARG cc_start: 0.8008 (mtt180) cc_final: 0.7684 (ptp-110) REVERT: B 1057 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.7955 (mmm-85) REVERT: B 1060 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 1186 GLN cc_start: 0.8476 (pp30) cc_final: 0.8081 (pp30) REVERT: C 103 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: C 621 GLU cc_start: 0.8155 (pt0) cc_final: 0.7955 (pt0) REVERT: C 624 LYS cc_start: 0.8737 (ptpp) cc_final: 0.8215 (tptp) REVERT: C 846 GLU cc_start: 0.7563 (tt0) cc_final: 0.6974 (tt0) REVERT: C 881 MET cc_start: 0.7291 (ttp) cc_final: 0.6966 (ttp) REVERT: C 1025 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7598 (mt-10) REVERT: C 1186 GLN cc_start: 0.6928 (tm-30) cc_final: 0.6643 (tm-30) REVERT: D 993 ASP cc_start: 0.5370 (OUTLIER) cc_final: 0.4705 (m-30) REVERT: D 1242 CYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8662 (p) REVERT: D 1410 MET cc_start: 0.8051 (mmm) cc_final: 0.7682 (ttm) REVERT: D 1569 ARG cc_start: 0.7982 (tpt90) cc_final: 0.7762 (tpt90) REVERT: E 274 MET cc_start: 0.8595 (mmm) cc_final: 0.8127 (mmm) REVERT: E 291 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7337 (ttp80) REVERT: E 366 MET cc_start: 0.7156 (mpt) cc_final: 0.6779 (mpt) REVERT: E 512 MET cc_start: 0.7676 (mmm) cc_final: 0.7235 (mmm) REVERT: E 576 MET cc_start: 0.4820 (ppp) cc_final: 0.4476 (ppp) REVERT: E 680 MET cc_start: 0.7002 (tpt) cc_final: 0.6709 (tpt) REVERT: E 924 MET cc_start: 0.7731 (mtm) cc_final: 0.7372 (mtm) REVERT: F 770 TRP cc_start: 0.6583 (m100) cc_final: 0.6021 (m100) outliers start: 150 outliers final: 117 residues processed: 484 average time/residue: 0.2325 time to fit residues: 189.2477 Evaluate side-chains 479 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 354 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 533 CYS Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 1199 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1231 ASN Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 712 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1066 HIS Chi-restraints excluded: chain C residue 1072 PHE Chi-restraints excluded: chain C residue 1272 ILE Chi-restraints excluded: chain D residue 993 ASP Chi-restraints excluded: chain D residue 1061 ASP Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1157 MET Chi-restraints excluded: chain D residue 1242 CYS Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1405 GLN Chi-restraints excluded: chain D residue 1463 LEU Chi-restraints excluded: chain D residue 1522 ILE Chi-restraints excluded: chain D residue 1541 ASP Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1584 TRP Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain D residue 1624 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 511 TYR Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 691 ILE Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 802 PHE Chi-restraints excluded: chain E residue 805 HIS Chi-restraints excluded: chain E residue 810 LEU Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 1221 ASN Chi-restraints excluded: chain E residue 1224 MET Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 653 THR Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 739 MET Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 830 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 407 optimal weight: 30.0000 chunk 462 optimal weight: 0.9980 chunk 377 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 341 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 432 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B1231 ASN ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 ASN ** C 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.166974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.129909 restraints weight = 77595.874| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 3.81 r_work: 0.3729 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 40214 Z= 0.161 Angle : 0.566 13.297 54523 Z= 0.286 Chirality : 0.043 0.247 6178 Planarity : 0.004 0.118 7034 Dihedral : 4.886 58.425 5513 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 3.60 % Allowed : 16.70 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.12), residues: 4964 helix: 1.00 (0.12), residues: 1863 sheet: -0.30 (0.16), residues: 1098 loop : -0.69 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 904 TYR 0.013 0.001 TYR F 503 PHE 0.019 0.001 PHE C 797 TRP 0.013 0.001 TRP B 576 HIS 0.004 0.001 HIS B 672 Details of bonding type rmsd covalent geometry : bond 0.00361 (40198) covalent geometry : angle 0.55599 (54499) hydrogen bonds : bond 0.03494 ( 1833) hydrogen bonds : angle 4.68263 ( 5292) metal coordination : bond 0.01037 ( 16) metal coordination : angle 5.07351 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 361 time to evaluate : 1.519 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: A 197 MET cc_start: 0.6299 (tpp) cc_final: 0.6013 (tpp) REVERT: B 9 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8041 (mp) REVERT: B 41 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8100 (mt) REVERT: B 88 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7252 (ttp-170) REVERT: B 182 GLU cc_start: 0.6968 (tp30) cc_final: 0.6615 (tp30) REVERT: B 635 GLU cc_start: 0.8236 (mp0) cc_final: 0.7996 (pm20) REVERT: B 739 LEU cc_start: 0.8442 (mt) cc_final: 0.8180 (mp) REVERT: B 758 ASP cc_start: 0.6819 (t0) cc_final: 0.5897 (p0) REVERT: B 804 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7720 (ptp-110) REVERT: B 1060 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8086 (tm-30) REVERT: B 1186 GLN cc_start: 0.8487 (pp30) cc_final: 0.8103 (pp30) REVERT: C 103 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8087 (mp10) REVERT: C 292 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7463 (p0) REVERT: C 442 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8210 (mtpt) REVERT: C 846 GLU cc_start: 0.7559 (tt0) cc_final: 0.6941 (tt0) REVERT: C 881 MET cc_start: 0.7365 (ttp) cc_final: 0.7043 (ttp) REVERT: C 1025 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7610 (mt-10) REVERT: C 1186 GLN cc_start: 0.6981 (tm-30) cc_final: 0.6697 (tm-30) REVERT: D 1242 CYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8682 (p) REVERT: D 1410 MET cc_start: 0.8049 (mmm) cc_final: 0.7704 (ttm) REVERT: D 1569 ARG cc_start: 0.7976 (tpt90) cc_final: 0.7734 (tpt90) REVERT: E 274 MET cc_start: 0.8574 (mmm) cc_final: 0.8230 (mmm) REVERT: E 291 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7249 (ttp80) REVERT: E 366 MET cc_start: 0.7153 (mpt) cc_final: 0.6804 (mpt) REVERT: E 576 MET cc_start: 0.4957 (ppp) cc_final: 0.4599 (ppp) REVERT: E 680 MET cc_start: 0.6971 (tpt) cc_final: 0.6665 (tpt) REVERT: F 770 TRP cc_start: 0.6635 (m100) cc_final: 0.6096 (m100) REVERT: F 804 LYS cc_start: 0.8873 (ptmt) cc_final: 0.8459 (ptmm) outliers start: 153 outliers final: 124 residues processed: 480 average time/residue: 0.2295 time to fit residues: 185.9172 Evaluate side-chains 487 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 355 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 533 CYS Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 1158 ILE Chi-restraints excluded: chain B residue 1199 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1231 ASN Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 712 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1066 HIS Chi-restraints excluded: chain C residue 1072 PHE Chi-restraints excluded: chain C residue 1272 ILE Chi-restraints excluded: chain D residue 993 ASP Chi-restraints excluded: chain D residue 1061 ASP Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1153 ASP Chi-restraints excluded: chain D residue 1157 MET Chi-restraints excluded: chain D residue 1242 CYS Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1405 GLN Chi-restraints excluded: chain D residue 1463 LEU Chi-restraints excluded: chain D residue 1522 ILE Chi-restraints excluded: chain D residue 1541 ASP Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1584 TRP Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain D residue 1624 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 511 TYR Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 691 ILE Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 802 PHE Chi-restraints excluded: chain E residue 805 HIS Chi-restraints excluded: chain E residue 810 LEU Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 958 THR Chi-restraints excluded: chain E residue 1221 ASN Chi-restraints excluded: chain E residue 1224 MET Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 653 THR Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 739 MET Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 830 GLN Chi-restraints excluded: chain F residue 839 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 125 optimal weight: 9.9990 chunk 464 optimal weight: 7.9990 chunk 320 optimal weight: 10.0000 chunk 384 optimal weight: 0.9980 chunk 345 optimal weight: 1.9990 chunk 326 optimal weight: 7.9990 chunk 431 optimal weight: 20.0000 chunk 233 optimal weight: 2.9990 chunk 381 optimal weight: 2.9990 chunk 274 optimal weight: 0.7980 chunk 234 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 249 HIS ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1316 GLN ** D1439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.164294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.128121 restraints weight = 78461.196| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 4.10 r_work: 0.3688 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 40214 Z= 0.248 Angle : 0.645 12.741 54523 Z= 0.328 Chirality : 0.045 0.250 6178 Planarity : 0.005 0.120 7034 Dihedral : 5.057 58.419 5511 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.75 % Favored : 95.19 % Rotamer: Outliers : 3.74 % Allowed : 16.89 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.12), residues: 4964 helix: 0.73 (0.12), residues: 1852 sheet: -0.43 (0.16), residues: 1108 loop : -0.76 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 904 TYR 0.022 0.002 TYR D1174 PHE 0.032 0.002 PHE D1055 TRP 0.015 0.002 TRP D 913 HIS 0.006 0.001 HIS C 562 Details of bonding type rmsd covalent geometry : bond 0.00552 (40198) covalent geometry : angle 0.63460 (54499) hydrogen bonds : bond 0.03914 ( 1833) hydrogen bonds : angle 4.94520 ( 5292) metal coordination : bond 0.01523 ( 16) metal coordination : angle 5.50719 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 360 time to evaluate : 1.592 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: A 197 MET cc_start: 0.6571 (tpp) cc_final: 0.6298 (tpp) REVERT: B 9 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.7968 (mp) REVERT: B 41 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8081 (mt) REVERT: B 182 GLU cc_start: 0.7121 (tp30) cc_final: 0.6901 (tp30) REVERT: B 184 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7453 (mm) REVERT: B 739 LEU cc_start: 0.8348 (mt) cc_final: 0.8076 (mp) REVERT: B 752 LEU cc_start: 0.4163 (OUTLIER) cc_final: 0.3662 (tp) REVERT: B 1060 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8055 (tm-30) REVERT: B 1186 GLN cc_start: 0.8416 (pp30) cc_final: 0.8062 (pp30) REVERT: C 103 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: C 292 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7552 (p0) REVERT: C 485 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6450 (tm-30) REVERT: C 603 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.5111 (ttp80) REVERT: C 881 MET cc_start: 0.7207 (ttp) cc_final: 0.6860 (ttp) REVERT: C 1010 GLN cc_start: 0.8939 (mt0) cc_final: 0.8347 (tp40) REVERT: C 1018 MET cc_start: 0.7435 (tpp) cc_final: 0.7022 (tpp) REVERT: C 1025 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7598 (mt-10) REVERT: C 1186 GLN cc_start: 0.6805 (tm-30) cc_final: 0.6514 (tm-30) REVERT: D 1242 CYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8713 (p) REVERT: E 274 MET cc_start: 0.8658 (mmm) cc_final: 0.8291 (mmm) REVERT: E 291 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7539 (ttp80) REVERT: E 366 MET cc_start: 0.7201 (mpt) cc_final: 0.6878 (mpt) REVERT: E 576 MET cc_start: 0.4729 (ppp) cc_final: 0.4374 (ppp) REVERT: E 680 MET cc_start: 0.6940 (tpt) cc_final: 0.6658 (tpt) REVERT: E 924 MET cc_start: 0.7826 (mtm) cc_final: 0.7459 (mtm) REVERT: F 613 ASP cc_start: 0.8244 (m-30) cc_final: 0.7831 (t70) REVERT: F 770 TRP cc_start: 0.6432 (m100) cc_final: 0.5819 (m100) REVERT: F 804 LYS cc_start: 0.8756 (ptmt) cc_final: 0.8462 (ptmm) outliers start: 159 outliers final: 133 residues processed: 489 average time/residue: 0.2343 time to fit residues: 193.9835 Evaluate side-chains 493 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 351 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 533 CYS Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 1158 ILE Chi-restraints excluded: chain B residue 1199 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 603 ARG Chi-restraints excluded: chain C residue 712 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1066 HIS Chi-restraints excluded: chain C residue 1072 PHE Chi-restraints excluded: chain C residue 1272 ILE Chi-restraints excluded: chain D residue 993 ASP Chi-restraints excluded: chain D residue 1061 ASP Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1153 ASP Chi-restraints excluded: chain D residue 1157 MET Chi-restraints excluded: chain D residue 1242 CYS Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1339 THR Chi-restraints excluded: chain D residue 1351 LEU Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1405 GLN Chi-restraints excluded: chain D residue 1463 LEU Chi-restraints excluded: chain D residue 1522 ILE Chi-restraints excluded: chain D residue 1541 ASP Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain D residue 1624 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 511 TYR Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 691 ILE Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 802 PHE Chi-restraints excluded: chain E residue 805 HIS Chi-restraints excluded: chain E residue 833 LEU Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 958 THR Chi-restraints excluded: chain E residue 1221 ASN Chi-restraints excluded: chain E residue 1224 MET Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 653 THR Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 739 MET Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 830 GLN Chi-restraints excluded: chain F residue 839 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 229 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 399 optimal weight: 6.9990 chunk 230 optimal weight: 1.9990 chunk 340 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 160 optimal weight: 0.0570 chunk 98 optimal weight: 0.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS B 548 ASN ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1223 ASN ** D1439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 GLN F 349 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.167122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.131791 restraints weight = 77554.479| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 4.11 r_work: 0.3706 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 40214 Z= 0.144 Angle : 0.589 13.465 54523 Z= 0.295 Chirality : 0.043 0.242 6178 Planarity : 0.004 0.074 7034 Dihedral : 4.889 57.001 5511 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 3.48 % Allowed : 17.05 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.12), residues: 4964 helix: 0.97 (0.12), residues: 1862 sheet: -0.35 (0.16), residues: 1105 loop : -0.72 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 904 TYR 0.013 0.001 TYR F 503 PHE 0.023 0.001 PHE C 797 TRP 0.019 0.001 TRP B 576 HIS 0.004 0.001 HIS D1439 Details of bonding type rmsd covalent geometry : bond 0.00326 (40198) covalent geometry : angle 0.57967 (54499) hydrogen bonds : bond 0.03483 ( 1833) hydrogen bonds : angle 4.70667 ( 5292) metal coordination : bond 0.00920 ( 16) metal coordination : angle 5.02576 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 366 time to evaluate : 1.477 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: A 197 MET cc_start: 0.6589 (tpp) cc_final: 0.6291 (tpp) REVERT: B 9 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8032 (mp) REVERT: B 41 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8147 (mt) REVERT: B 88 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7325 (ttp-170) REVERT: B 182 GLU cc_start: 0.7071 (tp30) cc_final: 0.6766 (tp30) REVERT: B 739 LEU cc_start: 0.8330 (mt) cc_final: 0.8061 (mp) REVERT: B 758 ASP cc_start: 0.6764 (t0) cc_final: 0.5852 (p0) REVERT: B 804 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7933 (ptp-110) REVERT: B 1060 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8072 (tm-30) REVERT: B 1186 GLN cc_start: 0.8455 (pp30) cc_final: 0.8075 (pp30) REVERT: C 103 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8063 (mp10) REVERT: C 292 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7536 (p0) REVERT: C 485 GLU cc_start: 0.6892 (tm-30) cc_final: 0.6318 (tm-30) REVERT: C 846 GLU cc_start: 0.7555 (tt0) cc_final: 0.6963 (tt0) REVERT: C 881 MET cc_start: 0.7205 (ttp) cc_final: 0.6833 (ttp) REVERT: C 1006 PHE cc_start: 0.7799 (m-80) cc_final: 0.7566 (m-80) REVERT: C 1010 GLN cc_start: 0.8910 (mt0) cc_final: 0.8303 (tp40) REVERT: C 1018 MET cc_start: 0.7435 (tpp) cc_final: 0.7015 (tpp) REVERT: C 1025 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7757 (mt-10) REVERT: C 1186 GLN cc_start: 0.6794 (tm-30) cc_final: 0.6513 (tm-30) REVERT: D 1242 CYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8683 (p) REVERT: E 291 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7476 (ttp80) REVERT: E 313 MET cc_start: 0.6411 (ttp) cc_final: 0.5982 (ttt) REVERT: E 366 MET cc_start: 0.7186 (mpt) cc_final: 0.6775 (mpp) REVERT: E 512 MET cc_start: 0.7692 (mmm) cc_final: 0.7237 (mmm) REVERT: E 576 MET cc_start: 0.4859 (ppp) cc_final: 0.4512 (ppp) REVERT: E 680 MET cc_start: 0.6943 (tpt) cc_final: 0.6665 (tpt) REVERT: E 924 MET cc_start: 0.7848 (mtm) cc_final: 0.7498 (mtm) REVERT: F 145 MET cc_start: -0.2889 (mmm) cc_final: -0.5563 (ttt) REVERT: F 770 TRP cc_start: 0.6524 (m100) cc_final: 0.5956 (m100) REVERT: F 804 LYS cc_start: 0.8788 (ptmt) cc_final: 0.8416 (ptmm) outliers start: 148 outliers final: 125 residues processed: 483 average time/residue: 0.2297 time to fit residues: 187.9952 Evaluate side-chains 489 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 357 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 533 CYS Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 1158 ILE Chi-restraints excluded: chain B residue 1199 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 603 ARG Chi-restraints excluded: chain C residue 712 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1066 HIS Chi-restraints excluded: chain C residue 1072 PHE Chi-restraints excluded: chain C residue 1272 ILE Chi-restraints excluded: chain D residue 993 ASP Chi-restraints excluded: chain D residue 1061 ASP Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1157 MET Chi-restraints excluded: chain D residue 1242 CYS Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1405 GLN Chi-restraints excluded: chain D residue 1463 LEU Chi-restraints excluded: chain D residue 1522 ILE Chi-restraints excluded: chain D residue 1541 ASP Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1584 TRP Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain D residue 1624 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 511 TYR Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 691 ILE Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 802 PHE Chi-restraints excluded: chain E residue 805 HIS Chi-restraints excluded: chain E residue 810 LEU Chi-restraints excluded: chain E residue 833 LEU Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 958 THR Chi-restraints excluded: chain E residue 1221 ASN Chi-restraints excluded: chain E residue 1224 MET Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 653 THR Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 739 MET Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 830 GLN Chi-restraints excluded: chain F residue 839 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 302 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 446 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 448 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 198 optimal weight: 0.4980 chunk 455 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN ** D1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.164691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.127622 restraints weight = 78024.852| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 4.10 r_work: 0.3714 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 40214 Z= 0.221 Angle : 0.639 12.891 54523 Z= 0.323 Chirality : 0.044 0.245 6178 Planarity : 0.004 0.058 7034 Dihedral : 5.014 57.662 5511 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.75 % Favored : 95.19 % Rotamer: Outliers : 3.36 % Allowed : 17.38 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.12), residues: 4964 helix: 0.80 (0.12), residues: 1859 sheet: -0.42 (0.16), residues: 1108 loop : -0.77 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 873 TYR 0.017 0.002 TYR D1174 PHE 0.031 0.002 PHE D1055 TRP 0.012 0.001 TRP D 913 HIS 0.006 0.001 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00496 (40198) covalent geometry : angle 0.62981 (54499) hydrogen bonds : bond 0.03796 ( 1833) hydrogen bonds : angle 4.87093 ( 5292) metal coordination : bond 0.01318 ( 16) metal coordination : angle 5.27426 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9928 Ramachandran restraints generated. 4964 Oldfield, 0 Emsley, 4964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 350 time to evaluate : 1.570 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: B 9 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8032 (mp) REVERT: B 41 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8135 (mt) REVERT: B 182 GLU cc_start: 0.7000 (tp30) cc_final: 0.6766 (tp30) REVERT: B 184 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7433 (mm) REVERT: B 450 MET cc_start: 0.8295 (ttm) cc_final: 0.7862 (ttm) REVERT: B 739 LEU cc_start: 0.8368 (mt) cc_final: 0.8091 (mp) REVERT: B 752 LEU cc_start: 0.4181 (OUTLIER) cc_final: 0.3694 (tp) REVERT: B 758 ASP cc_start: 0.6744 (t0) cc_final: 0.5819 (p0) REVERT: B 804 ARG cc_start: 0.7860 (mtt180) cc_final: 0.7503 (mtm-85) REVERT: B 1060 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7980 (tm-30) REVERT: B 1186 GLN cc_start: 0.8370 (pp30) cc_final: 0.8006 (pp30) REVERT: C 103 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: C 292 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7497 (p0) REVERT: C 485 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6454 (tm-30) REVERT: C 603 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.5198 (ttp80) REVERT: C 881 MET cc_start: 0.7113 (ttp) cc_final: 0.6786 (ttp) REVERT: C 1006 PHE cc_start: 0.7817 (m-80) cc_final: 0.7585 (m-80) REVERT: C 1010 GLN cc_start: 0.8858 (mt0) cc_final: 0.8270 (tp40) REVERT: C 1018 MET cc_start: 0.7472 (tpp) cc_final: 0.7199 (tpp) REVERT: C 1025 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7726 (mt-10) REVERT: C 1186 GLN cc_start: 0.6782 (tm-30) cc_final: 0.6497 (tm-30) REVERT: D 1242 CYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8702 (p) REVERT: E 274 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8246 (mmm) REVERT: E 291 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7516 (ttp80) REVERT: E 313 MET cc_start: 0.6495 (ttp) cc_final: 0.6028 (ttt) REVERT: E 366 MET cc_start: 0.7188 (mpt) cc_final: 0.6865 (mpt) REVERT: E 576 MET cc_start: 0.4737 (ppp) cc_final: 0.4391 (ppp) REVERT: E 680 MET cc_start: 0.6889 (tpt) cc_final: 0.6617 (tpt) REVERT: E 924 MET cc_start: 0.7886 (mtm) cc_final: 0.7532 (mtm) REVERT: F 145 MET cc_start: -0.3142 (mmm) cc_final: -0.5470 (ttt) REVERT: F 613 ASP cc_start: 0.8210 (m-30) cc_final: 0.7761 (t70) REVERT: F 770 TRP cc_start: 0.6401 (m100) cc_final: 0.5821 (m100) REVERT: F 804 LYS cc_start: 0.8759 (ptmt) cc_final: 0.8459 (ptmm) outliers start: 143 outliers final: 129 residues processed: 463 average time/residue: 0.2341 time to fit residues: 183.5696 Evaluate side-chains 486 residues out of total 4251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 347 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 533 CYS Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 1158 ILE Chi-restraints excluded: chain B residue 1199 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 202 TRP Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 290 CYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 603 ARG Chi-restraints excluded: chain C residue 712 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1066 HIS Chi-restraints excluded: chain C residue 1072 PHE Chi-restraints excluded: chain C residue 1272 ILE Chi-restraints excluded: chain D residue 993 ASP Chi-restraints excluded: chain D residue 1061 ASP Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1153 ASP Chi-restraints excluded: chain D residue 1157 MET Chi-restraints excluded: chain D residue 1242 CYS Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1404 LEU Chi-restraints excluded: chain D residue 1405 GLN Chi-restraints excluded: chain D residue 1463 LEU Chi-restraints excluded: chain D residue 1522 ILE Chi-restraints excluded: chain D residue 1541 ASP Chi-restraints excluded: chain D residue 1565 LEU Chi-restraints excluded: chain D residue 1584 TRP Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain D residue 1624 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 511 TYR Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 679 LYS Chi-restraints excluded: chain E residue 691 ILE Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 802 PHE Chi-restraints excluded: chain E residue 805 HIS Chi-restraints excluded: chain E residue 810 LEU Chi-restraints excluded: chain E residue 833 LEU Chi-restraints excluded: chain E residue 909 VAL Chi-restraints excluded: chain E residue 958 THR Chi-restraints excluded: chain E residue 1221 ASN Chi-restraints excluded: chain E residue 1224 MET Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 653 THR Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 739 MET Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 830 GLN Chi-restraints excluded: chain F residue 839 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 493 optimal weight: 30.0000 chunk 226 optimal weight: 7.9990 chunk 301 optimal weight: 4.9990 chunk 438 optimal weight: 9.9990 chunk 320 optimal weight: 0.9980 chunk 264 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 448 optimal weight: 3.9990 chunk 439 optimal weight: 9.9990 chunk 429 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN ** D1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.164952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.127572 restraints weight = 78265.728| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 4.73 r_work: 0.3686 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 40214 Z= 0.210 Angle : 0.635 12.994 54523 Z= 0.322 Chirality : 0.044 0.243 6178 Planarity : 0.004 0.057 7034 Dihedral : 5.048 58.815 5511 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.37 % Rotamer: Outliers : 3.51 % Allowed : 17.24 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.12), residues: 4964 helix: 0.76 (0.12), residues: 1856 sheet: -0.45 (0.16), residues: 1117 loop : -0.80 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 873 TYR 0.015 0.001 TYR F 503 PHE 0.023 0.002 PHE C 797 TRP 0.014 0.001 TRP B 576 HIS 0.005 0.001 HIS C 613 Details of bonding type rmsd covalent geometry : bond 0.00470 (40198) covalent geometry : angle 0.62578 (54499) hydrogen bonds : bond 0.03785 ( 1833) hydrogen bonds : angle 4.87892 ( 5292) metal coordination : bond 0.01246 ( 16) metal coordination : angle 5.24832 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15079.37 seconds wall clock time: 257 minutes 25.25 seconds (15445.25 seconds total)