Starting phenix.real_space_refine on Mon Aug 25 06:05:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hmf_34898/08_2025/8hmf_34898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hmf_34898/08_2025/8hmf_34898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hmf_34898/08_2025/8hmf_34898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hmf_34898/08_2025/8hmf_34898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hmf_34898/08_2025/8hmf_34898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hmf_34898/08_2025/8hmf_34898.map" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 114 5.16 5 C 16074 2.51 5 N 4287 2.21 5 O 4853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25330 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4388 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 19, 'TRANS': 513} Chain: "D" Number of atoms: 11344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 11344 Classifications: {'peptide': 1407} Link IDs: {'PTRANS': 35, 'TRANS': 1371} Chain: "E" Number of atoms: 9596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9596 Classifications: {'peptide': 1195} Link IDs: {'PTRANS': 32, 'TRANS': 1162} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2688 SG CYS A1044 128.158 77.430 91.042 1.00187.49 S ATOM 2713 SG CYS A1047 130.733 79.659 90.925 1.00170.68 S ATOM 2815 SG CYS A1060 126.551 80.582 92.334 1.00191.23 S ATOM 4047 SG CYS A1210 112.276 82.955 69.216 1.00136.73 S ATOM 4071 SG CYS A1213 111.149 84.168 72.535 1.00136.56 S ATOM 4233 SG CYS A1232 109.142 80.974 70.802 1.00139.38 S Time building chain proxies: 6.05, per 1000 atoms: 0.24 Number of scatterers: 25330 At special positions: 0 Unit cell: (163.9, 210.1, 184.8, 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 2 29.99 S 114 16.00 O 4853 8.00 N 4287 7.00 C 16074 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: 2.70 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1044 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1047 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1060 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A1213 " pdb="ZN ZN A2002 " - pdb=" SG CYS A1232 " pdb="ZN ZN A2002 " - pdb=" SG CYS A1210 " 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5980 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 36 sheets defined 47.1% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 719 through 740 removed outlier: 3.664A pdb=" N GLN A 739 " --> pdb=" O TRP A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 754 through 766 Processing helix chain 'A' and resid 768 through 778 Processing helix chain 'A' and resid 783 through 797 Processing helix chain 'A' and resid 799 through 811 Processing helix chain 'A' and resid 812 through 823 Processing helix chain 'A' and resid 826 through 836 Processing helix chain 'A' and resid 840 through 854 Proline residue: A 846 - end of helix Processing helix chain 'A' and resid 856 through 868 Processing helix chain 'A' and resid 870 through 887 Processing helix chain 'A' and resid 889 through 909 Processing helix chain 'A' and resid 915 through 947 removed outlier: 3.588A pdb=" N ILE A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 947 " --> pdb=" O SER A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 973 Processing helix chain 'A' and resid 983 through 996 Processing helix chain 'A' and resid 998 through 1012 Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1018 through 1031 removed outlier: 4.163A pdb=" N SER A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1104 removed outlier: 3.598A pdb=" N GLU A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1123 Processing helix chain 'A' and resid 1144 through 1161 Processing helix chain 'A' and resid 1169 through 1175 removed outlier: 3.859A pdb=" N VAL A1173 " --> pdb=" O ASP A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1229 removed outlier: 4.537A pdb=" N PHE A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 282 Processing helix chain 'D' and resid 617 through 630 removed outlier: 3.693A pdb=" N GLN D 621 " --> pdb=" O ASN D 617 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN D 630 " --> pdb=" O ALA D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 649 removed outlier: 4.110A pdb=" N LYS D 649 " --> pdb=" O ASP D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 739 removed outlier: 3.914A pdb=" N ALA D 729 " --> pdb=" O GLN D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 751 removed outlier: 4.197A pdb=" N GLN D 751 " --> pdb=" O LYS D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 754 through 769 Processing helix chain 'D' and resid 771 through 782 Processing helix chain 'D' and resid 783 through 794 Processing helix chain 'D' and resid 798 through 810 removed outlier: 3.877A pdb=" N GLN D 802 " --> pdb=" O GLU D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 823 Processing helix chain 'D' and resid 826 through 837 Processing helix chain 'D' and resid 838 through 850 Processing helix chain 'D' and resid 853 through 868 Processing helix chain 'D' and resid 870 through 881 Processing helix chain 'D' and resid 886 through 896 Processing helix chain 'D' and resid 898 through 909 Processing helix chain 'D' and resid 910 through 924 Processing helix chain 'D' and resid 926 through 938 Processing helix chain 'D' and resid 939 through 950 removed outlier: 3.579A pdb=" N MET D 943 " --> pdb=" O ASP D 939 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D 950 " --> pdb=" O LEU D 946 " (cutoff:3.500A) Processing helix chain 'D' and resid 952 through 964 removed outlier: 3.603A pdb=" N ALA D 956 " --> pdb=" O ASP D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 980 removed outlier: 3.777A pdb=" N MET D 978 " --> pdb=" O LYS D 974 " (cutoff:3.500A) Processing helix chain 'D' and resid 981 through 992 Processing helix chain 'D' and resid 994 through 1006 removed outlier: 3.593A pdb=" N ALA D 998 " --> pdb=" O HIS D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1008 through 1016 removed outlier: 3.859A pdb=" N MET D1012 " --> pdb=" O ASP D1008 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1033 Processing helix chain 'D' and resid 1035 through 1046 removed outlier: 4.153A pdb=" N ALA D1039 " --> pdb=" O PHE D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1049 through 1060 Processing helix chain 'D' and resid 1062 through 1082 removed outlier: 4.152A pdb=" N LYS D1082 " --> pdb=" O GLN D1078 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1099 Processing helix chain 'D' and resid 1100 through 1111 Proline residue: D1106 - end of helix Processing helix chain 'D' and resid 1113 through 1124 Processing helix chain 'D' and resid 1129 through 1137 Processing helix chain 'D' and resid 1144 through 1166 Processing helix chain 'D' and resid 1167 through 1179 Processing helix chain 'D' and resid 1180 through 1192 Processing helix chain 'D' and resid 1194 through 1205 Processing helix chain 'D' and resid 1206 through 1220 Processing helix chain 'D' and resid 1225 through 1240 removed outlier: 3.572A pdb=" N MET D1229 " --> pdb=" O ASN D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1241 through 1260 Processing helix chain 'D' and resid 1262 through 1279 Processing helix chain 'D' and resid 1284 through 1308 Processing helix chain 'D' and resid 1312 through 1326 Processing helix chain 'D' and resid 1328 through 1332 Processing helix chain 'D' and resid 1334 through 1350 removed outlier: 3.634A pdb=" N ILE D1338 " --> pdb=" O ARG D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1351 through 1365 removed outlier: 3.647A pdb=" N LYS D1365 " --> pdb=" O LYS D1361 " (cutoff:3.500A) Processing helix chain 'D' and resid 1368 through 1373 removed outlier: 4.617A pdb=" N TYR D1372 " --> pdb=" O ILE D1368 " (cutoff:3.500A) Processing helix chain 'D' and resid 1374 through 1386 Processing helix chain 'D' and resid 1388 through 1405 removed outlier: 3.568A pdb=" N LYS D1392 " --> pdb=" O SER D1388 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 102 Processing helix chain 'E' and resid 264 through 269 removed outlier: 4.568A pdb=" N ARG E 269 " --> pdb=" O LEU E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 325 Processing helix chain 'E' and resid 659 through 665 Processing helix chain 'E' and resid 672 through 686 Processing helix chain 'E' and resid 687 through 698 removed outlier: 3.619A pdb=" N LEU E 698 " --> pdb=" O ALA E 694 " (cutoff:3.500A) Processing helix chain 'E' and resid 700 through 714 Processing helix chain 'E' and resid 716 through 728 Processing helix chain 'E' and resid 730 through 742 removed outlier: 3.845A pdb=" N THR E 735 " --> pdb=" O SER E 731 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE E 742 " --> pdb=" O SER E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 744 through 757 Processing helix chain 'E' and resid 759 through 769 Processing helix chain 'E' and resid 771 through 783 removed outlier: 4.010A pdb=" N ALA E 775 " --> pdb=" O GLN E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 784 through 796 Processing helix chain 'E' and resid 799 through 814 removed outlier: 3.993A pdb=" N ILE E 803 " --> pdb=" O GLU E 799 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 834 removed outlier: 3.973A pdb=" N ALA E 820 " --> pdb=" O ASN E 816 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG E 821 " --> pdb=" O ASN E 817 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS E 822 " --> pdb=" O GLN E 818 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG E 834 " --> pdb=" O ASN E 830 " (cutoff:3.500A) Processing helix chain 'E' and resid 837 through 859 removed outlier: 3.597A pdb=" N ILE E 841 " --> pdb=" O ASP E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 872 removed outlier: 3.611A pdb=" N LEU E 872 " --> pdb=" O ILE E 868 " (cutoff:3.500A) Processing helix chain 'E' and resid 874 through 889 removed outlier: 3.609A pdb=" N LYS E 889 " --> pdb=" O CYS E 885 " (cutoff:3.500A) Processing helix chain 'E' and resid 891 through 901 Processing helix chain 'E' and resid 904 through 914 Processing helix chain 'E' and resid 916 through 927 Proline residue: E 922 - end of helix Processing helix chain 'E' and resid 929 through 944 Processing helix chain 'E' and resid 945 through 956 Processing helix chain 'E' and resid 959 through 969 removed outlier: 3.550A pdb=" N VAL E 963 " --> pdb=" O TRP E 959 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG E 964 " --> pdb=" O GLU E 960 " (cutoff:3.500A) Processing helix chain 'E' and resid 972 through 981 Processing helix chain 'E' and resid 986 through 999 removed outlier: 3.948A pdb=" N LYS E 999 " --> pdb=" O ASN E 995 " (cutoff:3.500A) Processing helix chain 'E' and resid 1003 through 1014 Processing helix chain 'E' and resid 1017 through 1026 Processing helix chain 'E' and resid 1028 through 1037 removed outlier: 3.562A pdb=" N TYR E1032 " --> pdb=" O VAL E1028 " (cutoff:3.500A) Processing helix chain 'E' and resid 1043 through 1053 removed outlier: 3.604A pdb=" N ILE E1047 " --> pdb=" O GLU E1043 " (cutoff:3.500A) Processing helix chain 'E' and resid 1058 through 1066 removed outlier: 4.015A pdb=" N LYS E1062 " --> pdb=" O VAL E1058 " (cutoff:3.500A) Processing helix chain 'E' and resid 1069 through 1079 removed outlier: 4.147A pdb=" N LYS E1079 " --> pdb=" O LYS E1075 " (cutoff:3.500A) Processing helix chain 'E' and resid 1084 through 1095 Processing helix chain 'E' and resid 1099 through 1111 removed outlier: 3.560A pdb=" N GLN E1103 " --> pdb=" O GLU E1099 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU E1111 " --> pdb=" O ASP E1107 " (cutoff:3.500A) Processing helix chain 'E' and resid 1117 through 1129 removed outlier: 4.114A pdb=" N LEU E1121 " --> pdb=" O ASP E1117 " (cutoff:3.500A) Processing helix chain 'E' and resid 1131 through 1149 Processing helix chain 'E' and resid 1150 through 1168 Processing helix chain 'E' and resid 1173 through 1195 Processing sheet with id=AA1, first strand: chain 'A' and resid 1079 through 1082 removed outlier: 3.757A pdb=" N TYR A1197 " --> pdb=" O PHE A1082 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1126 through 1130 Processing sheet with id=AA3, first strand: chain 'A' and resid 1207 through 1210 Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 9 removed outlier: 3.952A pdb=" N ILE D 369 " --> pdb=" O LEU D 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 19 through 22 Processing sheet with id=AA6, first strand: chain 'D' and resid 59 through 64 removed outlier: 3.609A pdb=" N ILE D 80 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 101 through 106 removed outlier: 7.087A pdb=" N ALA D 116 " --> pdb=" O CYS D 102 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ILE D 104 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL D 114 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N PHE D 106 " --> pdb=" O ARG D 112 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ARG D 112 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL D 122 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLN D 133 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL D 124 " --> pdb=" O VAL D 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 140 through 145 removed outlier: 3.944A pdb=" N PHE D 162 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS D 170 " --> pdb=" O PHE D 162 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 169 " --> pdb=" O CYS D 182 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU D 171 " --> pdb=" O ASP D 180 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASP D 180 " --> pdb=" O LEU D 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 188 through 194 removed outlier: 3.907A pdb=" N THR D 204 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 238 through 242 Processing sheet with id=AB2, first strand: chain 'D' and resid 297 through 303 removed outlier: 6.742A pdb=" N GLY D 312 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE D 300 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL D 310 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TYR D 302 " --> pdb=" O VAL D 308 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL D 308 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG D 317 " --> pdb=" O THR D 313 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE D 318 " --> pdb=" O TYR D 342 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR D 342 " --> pdb=" O ILE D 318 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE D 320 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 379 through 382 Processing sheet with id=AB4, first strand: chain 'D' and resid 418 through 421 removed outlier: 6.624A pdb=" N ILE D 434 " --> pdb=" O SER D 453 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER D 453 " --> pdb=" O ILE D 434 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE D 436 " --> pdb=" O VAL D 451 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 460 through 464 removed outlier: 4.440A pdb=" N GLN D 487 " --> pdb=" O VAL D 478 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 498 through 504 removed outlier: 4.253A pdb=" N TYR D 516 " --> pdb=" O THR D 512 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 498 through 504 removed outlier: 4.253A pdb=" N TYR D 516 " --> pdb=" O THR D 512 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 545 through 551 removed outlier: 6.885A pdb=" N THR D 561 " --> pdb=" O ARG D 547 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N CYS D 549 " --> pdb=" O VAL D 559 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 559 " --> pdb=" O CYS D 549 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL D 551 " --> pdb=" O LYS D 557 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LYS D 557 " --> pdb=" O VAL D 551 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN D 585 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 595 through 602 removed outlier: 5.753A pdb=" N ILE D 615 " --> pdb=" O PRO D 597 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN D 599 " --> pdb=" O SER D 613 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASN D 653 " --> pdb=" O ILE D 616 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU D 654 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP D 671 " --> pdb=" O THR D 658 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE D 660 " --> pdb=" O LYS D 669 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LYS D 669 " --> pdb=" O PHE D 660 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR D 662 " --> pdb=" O ILE D 667 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE D 667 " --> pdb=" O THR D 662 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 679 through 685 removed outlier: 6.532A pdb=" N ILE D 693 " --> pdb=" O GLU D 680 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL D 682 " --> pdb=" O TYR D 691 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N TYR D 691 " --> pdb=" O VAL D 682 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA D 684 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LYS D 689 " --> pdb=" O ALA D 684 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN D 705 " --> pdb=" O ASN D 696 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 5 through 10 removed outlier: 6.588A pdb=" N LYS E 6 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU E 352 " --> pdb=" O LYS E 6 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE E 8 " --> pdb=" O GLY E 350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 21 through 24 removed outlier: 6.859A pdb=" N VAL E 40 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU E 52 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL E 42 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 61 through 66 removed outlier: 4.976A pdb=" N GLN E 77 " --> pdb=" O CYS E 82 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N CYS E 82 " --> pdb=" O GLN E 77 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 104 through 109 Processing sheet with id=AC6, first strand: chain 'E' and resid 146 through 150 removed outlier: 3.979A pdb=" N VAL E 165 " --> pdb=" O SER E 161 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU E 166 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE E 180 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 186 through 192 removed outlier: 4.477A pdb=" N LEU E 189 " --> pdb=" O THR E 207 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR E 207 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TRP E 191 " --> pdb=" O THR E 205 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR E 205 " --> pdb=" O TRP E 191 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 238 through 244 removed outlier: 3.560A pdb=" N ASP E 240 " --> pdb=" O GLY E 252 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR E 257 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 284 through 288 removed outlier: 10.444A pdb=" N ILE E 302 " --> pdb=" O SER E 315 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N SER E 315 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE E 304 " --> pdb=" O VAL E 313 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 361 through 362 Processing sheet with id=AD2, first strand: chain 'E' and resid 400 through 403 Processing sheet with id=AD3, first strand: chain 'E' and resid 448 through 450 Processing sheet with id=AD4, first strand: chain 'E' and resid 490 through 493 removed outlier: 3.999A pdb=" N VAL E 519 " --> pdb=" O TYR E 509 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N HIS E 511 " --> pdb=" O PHE E 517 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE E 517 " --> pdb=" O HIS E 511 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 528 through 533 removed outlier: 4.068A pdb=" N GLU E 553 " --> pdb=" O GLN E 558 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN E 558 " --> pdb=" O GLU E 553 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 571 through 574 removed outlier: 4.046A pdb=" N LYS E 571 " --> pdb=" O LEU E 585 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE E 594 " --> pdb=" O GLN E 606 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN E 606 " --> pdb=" O ILE E 594 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 571 through 574 removed outlier: 4.046A pdb=" N LYS E 571 " --> pdb=" O LEU E 585 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 637 through 638 Processing sheet with id=AD9, first strand: chain 'E' and resid 644 through 646 1368 hydrogen bonds defined for protein. 3906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.79 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6985 1.33 - 1.46: 4398 1.46 - 1.58: 14243 1.58 - 1.70: 0 1.70 - 1.82: 176 Bond restraints: 25802 Sorted by residual: bond pdb=" N LYS D 721 " pdb=" CA LYS D 721 " ideal model delta sigma weight residual 1.464 1.488 -0.024 1.36e-02 5.41e+03 3.13e+00 bond pdb=" CA GLY D 666 " pdb=" C GLY D 666 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.37e+00 bond pdb=" CG GLN D 897 " pdb=" CD GLN D 897 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.05e+00 bond pdb=" N GLY D 666 " pdb=" CA GLY D 666 " ideal model delta sigma weight residual 1.464 1.450 0.014 1.12e-02 7.97e+03 1.64e+00 bond pdb=" C GLN E 469 " pdb=" N PRO E 470 " ideal model delta sigma weight residual 1.333 1.348 -0.015 1.20e-02 6.94e+03 1.62e+00 ... (remaining 25797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 34096 1.75 - 3.51: 596 3.51 - 5.26: 92 5.26 - 7.01: 26 7.01 - 8.76: 8 Bond angle restraints: 34818 Sorted by residual: angle pdb=" C ALA D 572 " pdb=" CA ALA D 572 " pdb=" CB ALA D 572 " ideal model delta sigma weight residual 116.54 110.43 6.11 1.15e+00 7.56e-01 2.83e+01 angle pdb=" C GLN E 424 " pdb=" CA GLN E 424 " pdb=" CB GLN E 424 " ideal model delta sigma weight residual 116.54 111.15 5.39 1.15e+00 7.56e-01 2.19e+01 angle pdb=" C GLN E 654 " pdb=" CA GLN E 654 " pdb=" CB GLN E 654 " ideal model delta sigma weight residual 115.79 110.69 5.10 1.19e+00 7.06e-01 1.84e+01 angle pdb=" C ASP E 525 " pdb=" CA ASP E 525 " pdb=" CB ASP E 525 " ideal model delta sigma weight residual 115.89 110.47 5.42 1.32e+00 5.74e-01 1.68e+01 angle pdb=" N SER E 658 " pdb=" CA SER E 658 " pdb=" C SER E 658 " ideal model delta sigma weight residual 112.72 108.17 4.55 1.28e+00 6.10e-01 1.26e+01 ... (remaining 34813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 14196 17.82 - 35.64: 1261 35.64 - 53.45: 217 53.45 - 71.27: 61 71.27 - 89.09: 30 Dihedral angle restraints: 15765 sinusoidal: 6504 harmonic: 9261 Sorted by residual: dihedral pdb=" CA GLU E 744 " pdb=" C GLU E 744 " pdb=" N LYS E 745 " pdb=" CA LYS E 745 " ideal model delta harmonic sigma weight residual -180.00 -151.82 -28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA GLU D 720 " pdb=" C GLU D 720 " pdb=" N LYS D 721 " pdb=" CA LYS D 721 " ideal model delta harmonic sigma weight residual -180.00 -156.38 -23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA SER D1311 " pdb=" C SER D1311 " pdb=" N ASP D1312 " pdb=" CA ASP D1312 " ideal model delta harmonic sigma weight residual -180.00 -156.44 -23.56 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 15762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3348 0.065 - 0.131: 446 0.131 - 0.196: 24 0.196 - 0.261: 0 0.261 - 0.326: 1 Chirality restraints: 3819 Sorted by residual: chirality pdb=" CB VAL E 996 " pdb=" CA VAL E 996 " pdb=" CG1 VAL E 996 " pdb=" CG2 VAL E 996 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA VAL E 341 " pdb=" N VAL E 341 " pdb=" C VAL E 341 " pdb=" CB VAL E 341 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CB VAL E 341 " pdb=" CA VAL E 341 " pdb=" CG1 VAL E 341 " pdb=" CG2 VAL E 341 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.61e-01 ... (remaining 3816 not shown) Planarity restraints: 4498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 720 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C GLU D 720 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU D 720 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS D 721 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 735 " 0.019 2.00e-02 2.50e+03 1.97e-02 9.74e+00 pdb=" CG TRP A 735 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP A 735 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 735 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 735 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 735 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 735 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 735 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 735 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 735 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D1291 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C GLN D1291 " -0.038 2.00e-02 2.50e+03 pdb=" O GLN D1291 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU D1292 " 0.013 2.00e-02 2.50e+03 ... (remaining 4495 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1081 2.73 - 3.27: 26478 3.27 - 3.81: 42582 3.81 - 4.36: 50208 4.36 - 4.90: 82878 Nonbonded interactions: 203227 Sorted by model distance: nonbonded pdb=" OG SER E 214 " pdb=" O LEU E 229 " model vdw 2.183 3.040 nonbonded pdb=" OH TYR A 938 " pdb=" OE1 GLN A 981 " model vdw 2.184 3.040 nonbonded pdb=" OH TYR D 134 " pdb=" O ASP D 173 " model vdw 2.186 3.040 nonbonded pdb=" OG SER D 787 " pdb=" OD2 ASP E 781 " model vdw 2.187 3.040 nonbonded pdb=" OG1 THR D1129 " pdb=" OD1 ASP D1131 " model vdw 2.206 3.040 ... (remaining 203222 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.980 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 : 0.002 0.036 25808 Z= 0.125 Angle : 0.595 8.765 34818 Z= 0.332 Chirality : 0.042 0.326 3819 Planarity : 0.003 0.048 4498 Dihedral : 14.451 89.089 9785 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.03 % Favored : 95.78 % Rotamer: Outliers : 0.04 % Allowed : 0.14 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.15), residues: 3129 helix: 1.15 (0.14), residues: 1380 sheet: 0.43 (0.21), residues: 662 loop : -1.29 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 890 TYR 0.015 0.001 TYR E 898 PHE 0.019 0.001 PHE E 697 TRP 0.054 0.002 TRP A 735 HIS 0.008 0.001 HIS E 741 Details of bonding type rmsd covalent geometry : bond 0.00226 (25802) covalent geometry : angle 0.59521 (34818) hydrogen bonds : bond 0.11836 ( 1350) hydrogen bonds : angle 5.88638 ( 3906) metal coordination : bond 0.00497 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 1.031 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: A 931 ASP cc_start: 0.8195 (m-30) cc_final: 0.7440 (m-30) REVERT: A 1093 PHE cc_start: 0.8915 (t80) cc_final: 0.8537 (t80) REVERT: D 37 HIS cc_start: 0.8357 (m90) cc_final: 0.8146 (m90) REVERT: D 739 MET cc_start: 0.9394 (tpt) cc_final: 0.9035 (tpp) REVERT: D 792 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8834 (tm-30) REVERT: D 812 MET cc_start: 0.8238 (mpp) cc_final: 0.7483 (mpp) REVERT: D 832 MET cc_start: 0.9251 (tmm) cc_final: 0.9004 (tmm) REVERT: D 943 MET cc_start: 0.9455 (mpp) cc_final: 0.9065 (mpp) REVERT: D 1007 MET cc_start: 0.8370 (mpp) cc_final: 0.8113 (mpp) REVERT: E 330 MET cc_start: 0.4742 (tpp) cc_final: 0.4538 (tpp) REVERT: E 500 MET cc_start: 0.9028 (mpp) cc_final: 0.8694 (mpp) REVERT: E 744 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8351 (tm-30) REVERT: E 778 MET cc_start: 0.9418 (tmm) cc_final: 0.9196 (tmm) REVERT: E 926 MET cc_start: 0.6135 (pmm) cc_final: 0.5769 (pmm) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1624 time to fit residues: 30.9574 Evaluate side-chains 93 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 GLN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN E 36 GLN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN E 337 GLN E 415 ASN E 481 GLN E 743 ASN E1035 ASN ** E1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.061266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.041439 restraints weight = 281990.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.042157 restraints weight = 197042.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.042544 restraints weight = 163043.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.042576 restraints weight = 116985.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.042577 restraints weight = 111104.857| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25808 Z= 0.106 Angle : 0.513 8.358 34818 Z= 0.276 Chirality : 0.042 0.235 3819 Planarity : 0.003 0.053 4498 Dihedral : 4.265 25.467 3388 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.12 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.15), residues: 3129 helix: 1.50 (0.14), residues: 1401 sheet: 0.32 (0.21), residues: 670 loop : -1.22 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 565 TYR 0.016 0.001 TYR D1347 PHE 0.017 0.001 PHE E 697 TRP 0.022 0.001 TRP A 735 HIS 0.006 0.001 HIS E 741 Details of bonding type rmsd covalent geometry : bond 0.00211 (25802) covalent geometry : angle 0.51280 (34818) hydrogen bonds : bond 0.03667 ( 1350) hydrogen bonds : angle 4.73981 ( 3906) metal coordination : bond 0.00268 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 GLU cc_start: 0.8778 (pm20) cc_final: 0.8383 (tp30) REVERT: A 931 ASP cc_start: 0.8498 (m-30) cc_final: 0.7737 (m-30) REVERT: A 1093 PHE cc_start: 0.9091 (t80) cc_final: 0.8660 (t80) REVERT: D 781 MET cc_start: 0.7881 (tpp) cc_final: 0.7595 (tpp) REVERT: D 812 MET cc_start: 0.8570 (mpp) cc_final: 0.7887 (mpp) REVERT: D 832 MET cc_start: 0.9294 (tmm) cc_final: 0.8960 (tmm) REVERT: D 943 MET cc_start: 0.9446 (mpp) cc_final: 0.9113 (mpp) REVERT: D 1007 MET cc_start: 0.8391 (mpp) cc_final: 0.8097 (mpp) REVERT: E 217 MET cc_start: 0.6978 (ppp) cc_final: 0.6626 (tmm) REVERT: E 500 MET cc_start: 0.9067 (mpp) cc_final: 0.8704 (mpp) REVERT: E 744 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8484 (tm-30) REVERT: E 778 MET cc_start: 0.9504 (tmm) cc_final: 0.9231 (tmm) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1640 time to fit residues: 29.8373 Evaluate side-chains 94 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 19 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 210 optimal weight: 0.0470 chunk 221 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 chunk 236 optimal weight: 8.9990 chunk 258 optimal weight: 6.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 820 ASN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 455 GLN E 36 GLN E 471 ASN E 558 GLN E 743 ASN E 955 GLN E1035 ASN E1066 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.058191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.039267 restraints weight = 282976.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.039514 restraints weight = 223145.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.039400 restraints weight = 167069.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.039607 restraints weight = 151054.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.039588 restraints weight = 135737.161| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25808 Z= 0.170 Angle : 0.569 8.654 34818 Z= 0.306 Chirality : 0.042 0.268 3819 Planarity : 0.003 0.056 4498 Dihedral : 4.442 24.285 3388 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.15 % Favored : 95.72 % Rotamer: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.15), residues: 3129 helix: 1.60 (0.14), residues: 1396 sheet: 0.22 (0.21), residues: 674 loop : -1.07 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 909 TYR 0.027 0.002 TYR A1191 PHE 0.017 0.002 PHE A1071 TRP 0.012 0.001 TRP D 75 HIS 0.006 0.001 HIS E 686 Details of bonding type rmsd covalent geometry : bond 0.00354 (25802) covalent geometry : angle 0.56939 (34818) hydrogen bonds : bond 0.03757 ( 1350) hydrogen bonds : angle 4.74664 ( 3906) metal coordination : bond 0.01266 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 830 MET cc_start: 0.7627 (mmt) cc_final: 0.7184 (mmt) REVERT: A 841 GLU cc_start: 0.9072 (pm20) cc_final: 0.8690 (tp30) REVERT: A 931 ASP cc_start: 0.9069 (m-30) cc_final: 0.8421 (m-30) REVERT: A 1093 PHE cc_start: 0.9216 (t80) cc_final: 0.8822 (t80) REVERT: A 1151 ASN cc_start: 0.9138 (m-40) cc_final: 0.8895 (t0) REVERT: D 402 ASP cc_start: 0.8399 (m-30) cc_final: 0.7512 (p0) REVERT: D 812 MET cc_start: 0.8880 (mpp) cc_final: 0.8128 (mpp) REVERT: D 832 MET cc_start: 0.9383 (tmm) cc_final: 0.9026 (tmm) REVERT: D 1007 MET cc_start: 0.8488 (mpp) cc_final: 0.8151 (mpp) REVERT: D 1362 MET cc_start: 0.5053 (tpt) cc_final: 0.4702 (tpt) REVERT: E 217 MET cc_start: 0.7387 (ppp) cc_final: 0.7030 (tmm) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.1581 time to fit residues: 29.6757 Evaluate side-chains 90 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 70 optimal weight: 9.9990 chunk 91 optimal weight: 0.0270 chunk 25 optimal weight: 0.9980 chunk 196 optimal weight: 30.0000 chunk 101 optimal weight: 4.9990 chunk 290 optimal weight: 8.9990 chunk 297 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 210 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 301 optimal weight: 3.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 ASN A1049 ASN A1126 GLN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN D1025 GLN E 36 GLN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 GLN ** E 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 743 ASN E 955 GLN E1035 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.058490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.038214 restraints weight = 276545.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.038735 restraints weight = 181883.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.039075 restraints weight = 138728.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.039522 restraints weight = 115726.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.039600 restraints weight = 102392.980| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25808 Z= 0.118 Angle : 0.522 8.321 34818 Z= 0.280 Chirality : 0.042 0.178 3819 Planarity : 0.003 0.058 4498 Dihedral : 4.328 24.421 3388 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.62 % Rotamer: Outliers : 0.07 % Allowed : 3.15 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.15), residues: 3129 helix: 1.67 (0.14), residues: 1405 sheet: 0.18 (0.21), residues: 673 loop : -1.10 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 806 TYR 0.014 0.001 TYR E 676 PHE 0.029 0.001 PHE E1009 TRP 0.036 0.001 TRP A 735 HIS 0.004 0.001 HIS E 741 Details of bonding type rmsd covalent geometry : bond 0.00242 (25802) covalent geometry : angle 0.52178 (34818) hydrogen bonds : bond 0.03396 ( 1350) hydrogen bonds : angle 4.59009 ( 3906) metal coordination : bond 0.00623 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 931 ASP cc_start: 0.8601 (m-30) cc_final: 0.7886 (m-30) REVERT: A 958 MET cc_start: 0.9089 (ptp) cc_final: 0.8671 (ptt) REVERT: A 1093 PHE cc_start: 0.9113 (t80) cc_final: 0.8703 (t80) REVERT: D 402 ASP cc_start: 0.8245 (m-30) cc_final: 0.7298 (p0) REVERT: D 474 MET cc_start: 0.9147 (mmm) cc_final: 0.8780 (mmm) REVERT: D 781 MET cc_start: 0.8015 (tpp) cc_final: 0.7803 (tpp) REVERT: D 812 MET cc_start: 0.8733 (mpp) cc_final: 0.8057 (mpp) REVERT: D 832 MET cc_start: 0.9400 (tmm) cc_final: 0.9024 (tmm) REVERT: D 1007 MET cc_start: 0.8460 (mpp) cc_final: 0.8124 (mpp) REVERT: D 1012 MET cc_start: 0.9345 (pmm) cc_final: 0.9034 (pmm) REVERT: E 217 MET cc_start: 0.6861 (ppp) cc_final: 0.6538 (tmm) REVERT: E 778 MET cc_start: 0.9501 (tmm) cc_final: 0.9232 (tmm) outliers start: 2 outliers final: 0 residues processed: 100 average time/residue: 0.1517 time to fit residues: 25.8149 Evaluate side-chains 85 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 217 optimal weight: 30.0000 chunk 156 optimal weight: 0.7980 chunk 306 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 chunk 251 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 ASN A1066 GLN D 133 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 GLN D 809 GLN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 741 HIS E 743 ASN E1035 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.058389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.038645 restraints weight = 275941.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.039891 restraints weight = 190759.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.039579 restraints weight = 120108.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.039557 restraints weight = 132865.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.039572 restraints weight = 124416.976| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 25808 Z= 0.113 Angle : 0.521 8.773 34818 Z= 0.276 Chirality : 0.042 0.265 3819 Planarity : 0.003 0.056 4498 Dihedral : 4.280 26.454 3388 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.22 % Favored : 95.65 % Rotamer: Outliers : 0.04 % Allowed : 1.86 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.15), residues: 3129 helix: 1.76 (0.14), residues: 1403 sheet: 0.27 (0.21), residues: 663 loop : -1.04 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 806 TYR 0.013 0.001 TYR E 676 PHE 0.016 0.001 PHE E 244 TRP 0.016 0.001 TRP A 735 HIS 0.003 0.001 HIS E 741 Details of bonding type rmsd covalent geometry : bond 0.00229 (25802) covalent geometry : angle 0.52106 (34818) hydrogen bonds : bond 0.03299 ( 1350) hydrogen bonds : angle 4.50577 ( 3906) metal coordination : bond 0.00342 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.831 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 830 MET cc_start: 0.7731 (mmt) cc_final: 0.7379 (mmt) REVERT: A 931 ASP cc_start: 0.8614 (m-30) cc_final: 0.7904 (m-30) REVERT: A 958 MET cc_start: 0.9100 (ptp) cc_final: 0.8813 (ptt) REVERT: A 1093 PHE cc_start: 0.9211 (t80) cc_final: 0.8823 (t80) REVERT: D 402 ASP cc_start: 0.8452 (m-30) cc_final: 0.7539 (p0) REVERT: D 474 MET cc_start: 0.9195 (mmm) cc_final: 0.8852 (mmm) REVERT: D 781 MET cc_start: 0.8101 (tpp) cc_final: 0.7845 (tpp) REVERT: D 812 MET cc_start: 0.8733 (mpp) cc_final: 0.8076 (mpp) REVERT: D 832 MET cc_start: 0.9387 (tmm) cc_final: 0.9070 (tmm) REVERT: D 1007 MET cc_start: 0.8440 (mpp) cc_final: 0.8097 (mpp) REVERT: E 217 MET cc_start: 0.7248 (ppp) cc_final: 0.6952 (tmm) REVERT: E 500 MET cc_start: 0.9043 (mpp) cc_final: 0.8693 (mpp) REVERT: E 778 MET cc_start: 0.9500 (tmm) cc_final: 0.9284 (tmm) REVERT: E 926 MET cc_start: 0.6716 (pmm) cc_final: 0.6498 (pmm) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.1379 time to fit residues: 23.2219 Evaluate side-chains 85 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 219 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 193 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 191 optimal weight: 7.9990 chunk 11 optimal weight: 0.0570 chunk 262 optimal weight: 0.8980 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 407 HIS ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 743 ASN E 955 GLN E1035 ASN E1103 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.057726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.037726 restraints weight = 277706.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.039077 restraints weight = 187284.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.038762 restraints weight = 130733.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.038858 restraints weight = 111991.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.038877 restraints weight = 114312.205| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25808 Z= 0.121 Angle : 0.526 8.489 34818 Z= 0.280 Chirality : 0.042 0.217 3819 Planarity : 0.003 0.056 4498 Dihedral : 4.287 25.863 3388 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.28 % Favored : 95.59 % Rotamer: Outliers : 0.04 % Allowed : 1.97 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.15), residues: 3129 helix: 1.81 (0.14), residues: 1401 sheet: 0.19 (0.20), residues: 690 loop : -1.01 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 806 TYR 0.031 0.001 TYR E1032 PHE 0.032 0.001 PHE D 212 TRP 0.012 0.001 TRP E 332 HIS 0.010 0.001 HIS E 407 Details of bonding type rmsd covalent geometry : bond 0.00250 (25802) covalent geometry : angle 0.52619 (34818) hydrogen bonds : bond 0.03299 ( 1350) hydrogen bonds : angle 4.48814 ( 3906) metal coordination : bond 0.00292 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 830 MET cc_start: 0.7766 (mmt) cc_final: 0.7321 (mmt) REVERT: A 899 MET cc_start: 0.9550 (mmp) cc_final: 0.9329 (mmm) REVERT: A 931 ASP cc_start: 0.8581 (m-30) cc_final: 0.7938 (m-30) REVERT: A 1093 PHE cc_start: 0.9118 (t80) cc_final: 0.8709 (t80) REVERT: D 402 ASP cc_start: 0.8326 (m-30) cc_final: 0.7390 (p0) REVERT: D 474 MET cc_start: 0.9230 (mmm) cc_final: 0.8890 (mmm) REVERT: D 591 MET cc_start: 0.6685 (tmm) cc_final: 0.6468 (tmm) REVERT: D 812 MET cc_start: 0.8782 (mpp) cc_final: 0.8077 (mpp) REVERT: D 832 MET cc_start: 0.9418 (tmm) cc_final: 0.9103 (tmm) REVERT: D 943 MET cc_start: 0.9479 (mpp) cc_final: 0.9213 (mpp) REVERT: D 1007 MET cc_start: 0.8470 (mpp) cc_final: 0.8100 (mpp) REVERT: D 1012 MET cc_start: 0.9375 (pmm) cc_final: 0.9122 (pmm) REVERT: E 217 MET cc_start: 0.7249 (ppp) cc_final: 0.6917 (tmm) REVERT: E 500 MET cc_start: 0.9102 (mpp) cc_final: 0.8753 (mpp) REVERT: E 778 MET cc_start: 0.9511 (tmm) cc_final: 0.9311 (tmm) REVERT: E 926 MET cc_start: 0.6740 (pmm) cc_final: 0.6345 (pmm) REVERT: E 1036 MET cc_start: -0.2959 (mtt) cc_final: -0.3261 (mtp) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1534 time to fit residues: 24.7415 Evaluate side-chains 84 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 181 optimal weight: 3.9990 chunk 302 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 279 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 238 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN A 789 GLN A 820 ASN ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 GLN D 455 GLN ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 743 ASN E 890 GLN E 955 GLN E 966 ASN E1035 ASN E1103 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.056112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.037267 restraints weight = 281706.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.037605 restraints weight = 211905.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.037481 restraints weight = 146952.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.037486 restraints weight = 148262.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.037540 restraints weight = 127110.592| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25808 Z= 0.163 Angle : 0.582 8.345 34818 Z= 0.311 Chirality : 0.043 0.249 3819 Planarity : 0.003 0.055 4498 Dihedral : 4.515 25.821 3388 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.63 % Favored : 95.24 % Rotamer: Outliers : 0.07 % Allowed : 1.75 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.15), residues: 3129 helix: 1.70 (0.14), residues: 1401 sheet: 0.14 (0.21), residues: 677 loop : -1.10 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 806 TYR 0.032 0.002 TYR D1260 PHE 0.020 0.002 PHE E 714 TRP 0.046 0.002 TRP A 735 HIS 0.006 0.001 HIS E 407 Details of bonding type rmsd covalent geometry : bond 0.00336 (25802) covalent geometry : angle 0.58244 (34818) hydrogen bonds : bond 0.03609 ( 1350) hydrogen bonds : angle 4.70582 ( 3906) metal coordination : bond 0.00248 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 1.008 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 830 MET cc_start: 0.8172 (mmt) cc_final: 0.7803 (mmt) REVERT: A 899 MET cc_start: 0.9531 (mmp) cc_final: 0.9324 (mmm) REVERT: A 931 ASP cc_start: 0.8892 (m-30) cc_final: 0.8243 (m-30) REVERT: A 1093 PHE cc_start: 0.9189 (t80) cc_final: 0.8764 (t80) REVERT: D 402 ASP cc_start: 0.8568 (m-30) cc_final: 0.7638 (p0) REVERT: D 781 MET cc_start: 0.8162 (tpp) cc_final: 0.7824 (tpp) REVERT: D 812 MET cc_start: 0.8880 (mpp) cc_final: 0.8200 (mpp) REVERT: D 832 MET cc_start: 0.9446 (tmm) cc_final: 0.9214 (tmm) REVERT: D 1007 MET cc_start: 0.8396 (mpp) cc_final: 0.8045 (mpp) REVERT: E 217 MET cc_start: 0.7469 (ppp) cc_final: 0.7141 (tmm) REVERT: E 500 MET cc_start: 0.9195 (mpp) cc_final: 0.8845 (mpp) REVERT: E 778 MET cc_start: 0.9524 (tmm) cc_final: 0.9295 (tmm) REVERT: E 903 MET cc_start: 0.9163 (ppp) cc_final: 0.8732 (ppp) REVERT: E 926 MET cc_start: 0.6881 (pmm) cc_final: 0.6537 (pmm) REVERT: E 1084 TYR cc_start: 0.6601 (m-80) cc_final: 0.6369 (m-80) outliers start: 2 outliers final: 0 residues processed: 95 average time/residue: 0.1486 time to fit residues: 23.9562 Evaluate side-chains 85 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 GLN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 743 ASN E 955 GLN E1035 ASN E1103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.055744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.037214 restraints weight = 289868.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.036811 restraints weight = 209839.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.036958 restraints weight = 185409.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.037067 restraints weight = 144778.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.037097 restraints weight = 128923.931| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25808 Z= 0.166 Angle : 0.575 9.203 34818 Z= 0.306 Chirality : 0.042 0.312 3819 Planarity : 0.003 0.054 4498 Dihedral : 4.552 30.119 3388 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.73 % Favored : 95.14 % Rotamer: Outliers : 0.04 % Allowed : 1.50 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.15), residues: 3129 helix: 1.65 (0.14), residues: 1397 sheet: 0.12 (0.21), residues: 683 loop : -1.05 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1083 TYR 0.021 0.001 TYR E 661 PHE 0.023 0.002 PHE A1249 TRP 0.034 0.002 TRP A 826 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00343 (25802) covalent geometry : angle 0.57467 (34818) hydrogen bonds : bond 0.03587 ( 1350) hydrogen bonds : angle 4.72116 ( 3906) metal coordination : bond 0.02267 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 830 MET cc_start: 0.8656 (mmt) cc_final: 0.8298 (mmm) REVERT: A 931 ASP cc_start: 0.8922 (m-30) cc_final: 0.8263 (m-30) REVERT: A 1093 PHE cc_start: 0.9194 (t80) cc_final: 0.8746 (t80) REVERT: D 402 ASP cc_start: 0.8319 (m-30) cc_final: 0.7322 (p0) REVERT: D 474 MET cc_start: 0.9230 (mmm) cc_final: 0.8913 (mmm) REVERT: D 781 MET cc_start: 0.8282 (tpp) cc_final: 0.7827 (tpp) REVERT: D 812 MET cc_start: 0.8896 (mpp) cc_final: 0.8153 (mpp) REVERT: D 832 MET cc_start: 0.9480 (tmm) cc_final: 0.9278 (tmm) REVERT: D 864 MET cc_start: 0.9119 (tmm) cc_final: 0.8917 (tmm) REVERT: D 943 MET cc_start: 0.9445 (mpp) cc_final: 0.9162 (mpp) REVERT: D 1007 MET cc_start: 0.8460 (mpp) cc_final: 0.8084 (mpp) REVERT: D 1362 MET cc_start: 0.5651 (tpt) cc_final: 0.5264 (tpt) REVERT: E 217 MET cc_start: 0.7587 (ppp) cc_final: 0.7286 (tmm) REVERT: E 778 MET cc_start: 0.9547 (tmm) cc_final: 0.9285 (tmm) REVERT: E 926 MET cc_start: 0.6861 (pmm) cc_final: 0.6657 (pmm) REVERT: E 1084 TYR cc_start: 0.6492 (m-80) cc_final: 0.6278 (m-80) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1426 time to fit residues: 22.8429 Evaluate side-chains 82 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 245 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 276 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 310 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 ASN ** A 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 HIS ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 GLN ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 GLN E 190 GLN ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 601 ASN E 955 GLN E1035 ASN E1103 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.055165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.036828 restraints weight = 289345.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.036545 restraints weight = 205992.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.036376 restraints weight = 190191.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.036472 restraints weight = 161152.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.036569 restraints weight = 129643.474| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25808 Z= 0.169 Angle : 0.595 9.495 34818 Z= 0.314 Chirality : 0.043 0.257 3819 Planarity : 0.004 0.069 4498 Dihedral : 4.633 30.357 3388 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.15 % Favored : 94.73 % Rotamer: Outliers : 0.07 % Allowed : 0.86 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.15), residues: 3129 helix: 1.50 (0.14), residues: 1402 sheet: 0.05 (0.21), residues: 674 loop : -1.13 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 929 TYR 0.027 0.002 TYR E 704 PHE 0.020 0.002 PHE D 212 TRP 0.029 0.002 TRP A 826 HIS 0.005 0.001 HIS A1090 Details of bonding type rmsd covalent geometry : bond 0.00348 (25802) covalent geometry : angle 0.59480 (34818) hydrogen bonds : bond 0.03698 ( 1350) hydrogen bonds : angle 4.78462 ( 3906) metal coordination : bond 0.00577 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 1.006 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 830 MET cc_start: 0.8699 (mmt) cc_final: 0.8295 (mmm) REVERT: A 931 ASP cc_start: 0.8850 (m-30) cc_final: 0.8184 (m-30) REVERT: A 1093 PHE cc_start: 0.9198 (t80) cc_final: 0.8743 (t80) REVERT: D 474 MET cc_start: 0.9257 (mmm) cc_final: 0.8962 (mmm) REVERT: D 591 MET cc_start: 0.6617 (tmm) cc_final: 0.6404 (tmm) REVERT: D 781 MET cc_start: 0.8241 (tpp) cc_final: 0.7884 (tpp) REVERT: D 812 MET cc_start: 0.8895 (mpp) cc_final: 0.8219 (mpp) REVERT: D 832 MET cc_start: 0.9479 (tmm) cc_final: 0.9271 (tmm) REVERT: D 943 MET cc_start: 0.9439 (mpp) cc_final: 0.9126 (mpp) REVERT: D 1007 MET cc_start: 0.8492 (mpp) cc_final: 0.8111 (mpp) REVERT: D 1012 MET cc_start: 0.9375 (pmm) cc_final: 0.9132 (pmm) REVERT: E 718 ASP cc_start: 0.9264 (p0) cc_final: 0.9056 (p0) REVERT: E 778 MET cc_start: 0.9568 (tmm) cc_final: 0.9274 (tmm) REVERT: E 903 MET cc_start: 0.9147 (ppp) cc_final: 0.8532 (ppp) REVERT: E 925 SER cc_start: 0.8870 (m) cc_final: 0.8582 (p) REVERT: E 926 MET cc_start: 0.7180 (pmm) cc_final: 0.6822 (pmm) outliers start: 2 outliers final: 0 residues processed: 95 average time/residue: 0.1673 time to fit residues: 26.5885 Evaluate side-chains 83 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 292 optimal weight: 0.5980 chunk 125 optimal weight: 0.0010 chunk 136 optimal weight: 1.9990 chunk 269 optimal weight: 0.7980 chunk 227 optimal weight: 9.9990 chunk 254 optimal weight: 0.4980 chunk 215 optimal weight: 10.0000 chunk 278 optimal weight: 0.9990 chunk 277 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 GLN D 252 HIS D 437 HIS ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 GLN ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1035 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.056326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.036490 restraints weight = 282148.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.037328 restraints weight = 190589.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.037263 restraints weight = 127090.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.037335 restraints weight = 121285.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.037346 restraints weight = 118589.465| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25808 Z= 0.108 Angle : 0.556 9.483 34818 Z= 0.291 Chirality : 0.043 0.295 3819 Planarity : 0.003 0.053 4498 Dihedral : 4.424 32.291 3388 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.31 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.15), residues: 3129 helix: 1.66 (0.14), residues: 1399 sheet: 0.21 (0.21), residues: 659 loop : -1.14 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 806 TYR 0.031 0.001 TYR E1032 PHE 0.017 0.001 PHE D 212 TRP 0.036 0.001 TRP A 826 HIS 0.004 0.001 HIS D 437 Details of bonding type rmsd covalent geometry : bond 0.00214 (25802) covalent geometry : angle 0.55554 (34818) hydrogen bonds : bond 0.03312 ( 1350) hydrogen bonds : angle 4.52920 ( 3906) metal coordination : bond 0.00201 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 830 MET cc_start: 0.8703 (mmt) cc_final: 0.8302 (mmm) REVERT: A 876 MET cc_start: 0.9080 (ppp) cc_final: 0.8837 (ppp) REVERT: A 931 ASP cc_start: 0.8432 (m-30) cc_final: 0.7780 (m-30) REVERT: A 958 MET cc_start: 0.9108 (ptp) cc_final: 0.8581 (mpp) REVERT: A 1064 MET cc_start: 0.8459 (tpt) cc_final: 0.8221 (tpp) REVERT: A 1093 PHE cc_start: 0.9197 (t80) cc_final: 0.8779 (t80) REVERT: D 474 MET cc_start: 0.9283 (mmm) cc_final: 0.8999 (mmm) REVERT: D 781 MET cc_start: 0.8276 (tpp) cc_final: 0.7918 (tpp) REVERT: D 812 MET cc_start: 0.8692 (mpp) cc_final: 0.8016 (mpp) REVERT: D 943 MET cc_start: 0.9407 (mpp) cc_final: 0.9082 (mpp) REVERT: D 1007 MET cc_start: 0.8560 (mpp) cc_final: 0.8132 (mpp) REVERT: D 1012 MET cc_start: 0.9361 (pmm) cc_final: 0.9105 (pmm) REVERT: D 1362 MET cc_start: 0.5546 (tpt) cc_final: 0.5123 (tpt) REVERT: E 718 ASP cc_start: 0.9191 (p0) cc_final: 0.8964 (p0) REVERT: E 778 MET cc_start: 0.9523 (tmm) cc_final: 0.9302 (tmm) REVERT: E 903 MET cc_start: 0.9105 (ppp) cc_final: 0.8460 (ppp) REVERT: E 925 SER cc_start: 0.8879 (m) cc_final: 0.8626 (p) REVERT: E 926 MET cc_start: 0.7115 (pmm) cc_final: 0.6770 (pmm) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1637 time to fit residues: 26.3489 Evaluate side-chains 79 residues out of total 2797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 111 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 233 optimal weight: 8.9990 chunk 252 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 GLN ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 GLN ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 955 GLN ** E1035 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 = 0.3550 r_free = 0.3550 target = 0.054916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.036891 restraints weight = 293987.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.036301 restraints weight = 203056.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.036373 restraints weight = 164220.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.036392 restraints weight = 149088.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.036686 restraints weight = 128274.986| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25808 Z= 0.164 Angle : 0.588 8.198 34818 Z= 0.311 Chirality : 0.043 0.282 3819 Planarity : 0.003 0.053 4498 Dihedral : 4.572 29.380 3388 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.08 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.15), residues: 3129 helix: 1.55 (0.14), residues: 1403 sheet: 0.05 (0.20), residues: 675 loop : -1.11 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1083 TYR 0.030 0.002 TYR E1032 PHE 0.017 0.001 PHE A1093 TRP 0.027 0.002 TRP A 826 HIS 0.006 0.001 HIS A1090 Details of bonding type rmsd covalent geometry : bond 0.00338 (25802) covalent geometry : angle 0.58778 (34818) hydrogen bonds : bond 0.03664 ( 1350) hydrogen bonds : angle 4.69529 ( 3906) metal coordination : bond 0.00497 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4399.78 seconds wall clock time: 77 minutes 9.29 seconds (4629.29 seconds total)