Starting phenix.real_space_refine on Fri Aug 9 09:53:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmf_34898/08_2024/8hmf_34898.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmf_34898/08_2024/8hmf_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmf_34898/08_2024/8hmf_34898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmf_34898/08_2024/8hmf_34898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmf_34898/08_2024/8hmf_34898.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmf_34898/08_2024/8hmf_34898.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A GLU 734": "OE1" <-> "OE2" Residue "A ASP 855": "OD1" <-> "OD2" Residue "A ASP 871": "OD1" <-> "OD2" Residue "A GLU 887": "OE1" <-> "OE2" Residue "A TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1152": "OE1" <-> "OE2" Residue "A ASP 1220": "OD1" <-> "OD2" Residue "A GLU 1225": "OE1" <-> "OE2" Residue "D TYR 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/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: 14.00, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 9.13 Conformation dependent library (CDL) restraints added in 4.7 seconds 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: 3.28 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: 13.16 Time building geometry restraints manager: 10.11 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: 97.04 - 104.45: 265 104.45 - 111.86: 11985 111.86 - 119.27: 9229 119.27 - 126.68: 13062 126.68 - 134.09: 277 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.070 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 75.310 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.200 ------------------------------------------------------------------------------- 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 25802 Z= 0.146 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.054 0.002 TRP A 735 HIS 0.008 0.001 HIS E 741 PHE 0.019 0.001 PHE E 697 TYR 0.015 0.001 TYR E 898 ARG 0.004 0.000 ARG D 890 *********************** 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 fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 2.787 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: 0.3456 time to fit residues: 66.0941 Evaluate side-chains 93 residues out of total 2797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 148 optimal weight: 0.8980 chunk 182 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: