Starting phenix.real_space_refine on Thu Jun 19 13:08:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hme_34897/06_2025/8hme_34897.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hme_34897/06_2025/8hme_34897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hme_34897/06_2025/8hme_34897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hme_34897/06_2025/8hme_34897.map" model { file = "/net/cci-nas-00/data/ceres_data/8hme_34897/06_2025/8hme_34897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hme_34897/06_2025/8hme_34897.cif" } resolution = 4.2 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 100 5.16 5 C 14062 2.51 5 N 3755 2.21 5 O 4250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22169 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4380 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 19, 'TRANS': 512} Chain: "D" Number of atoms: 8740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8740 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 23, 'TRANS': 1060} Chain: "E" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9047 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 31, 'TRANS': 1097} 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 2680 SG CYS A1044 126.757 77.297 86.001 1.00145.03 S ATOM 2705 SG CYS A1047 129.888 77.999 88.231 1.00132.36 S ATOM 2807 SG CYS A1060 126.118 78.850 89.347 1.00147.36 S ATOM 2825 SG CYS A1063 128.369 80.763 87.127 1.00147.20 S ATOM 4039 SG CYS A1210 113.063 81.160 64.380 1.00124.68 S ATOM 4063 SG CYS A1213 111.902 82.188 67.639 1.00124.37 S ATOM 4225 SG CYS A1232 109.907 79.486 65.624 1.00134.93 S ATOM 4249 SG CYS A1235 109.937 83.431 64.829 1.00138.82 S Time building chain proxies: 13.35, per 1000 atoms: 0.60 Number of scatterers: 22169 At special positions: 0 Unit cell: (163.9, 220, 177.1, 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 100 16.00 O 4250 8.00 N 3755 7.00 C 14062 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: 6.02 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1047 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1063 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1060 " pdb="ZN ZN A2001 " - pdb=" SG CYS A1044 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A1213 " pdb="ZN ZN A2002 " - pdb=" SG CYS A1210 " pdb="ZN ZN A2002 " - pdb=" SG CYS A1235 " pdb="ZN ZN A2002 " - pdb=" SG CYS A1232 " Number of angles added : 12 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5222 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 36 sheets defined 41.2% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 720 through 740 removed outlier: 3.663A pdb=" N LYS A 738 " --> pdb=" O GLU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 751 removed outlier: 3.609A pdb=" N GLY A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN A 751 " --> pdb=" O GLU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 766 Processing helix chain 'A' and resid 767 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 908 Processing helix chain 'A' and resid 915 through 947 removed outlier: 3.544A pdb=" N ILE A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 3.952A 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 1018 through 1031 removed outlier: 4.052A pdb=" N SER A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1104 removed outlier: 3.840A pdb=" N GLU A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1123 removed outlier: 3.694A pdb=" N ASP A1115 " --> pdb=" O LYS A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1161 Processing helix chain 'A' and resid 1169 through 1176 Processing helix chain 'A' and resid 1219 through 1229 Processing helix chain 'D' and resid 271 through 282 Processing helix chain 'D' and resid 617 through 630 removed outlier: 3.694A pdb=" N GLN D 621 " --> pdb=" O ASN D 617 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN D 630 " --> pdb=" O ALA D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 649 removed outlier: 4.184A pdb=" N LYS D 649 " --> pdb=" O ASP D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 717 removed outlier: 3.837A pdb=" N VAL D 717 " --> pdb=" O ASN D 714 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 714 through 717' Processing helix chain 'D' and resid 725 through 739 removed outlier: 3.964A pdb=" N ALA D 729 " --> pdb=" O GLN D 725 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET D 739 " --> pdb=" O PHE D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 751 removed outlier: 4.256A pdb=" N GLN D 751 " --> pdb=" O LYS D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 754 through 768 Processing helix chain 'D' and resid 771 through 781 Processing helix chain 'D' and resid 783 through 794 Processing helix chain 'D' and resid 798 through 810 removed outlier: 3.748A pdb=" N GLN D 802 " --> pdb=" O GLU D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 823 removed outlier: 3.636A pdb=" N ALA D 816 " --> pdb=" O MET D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 826 through 837 removed outlier: 3.511A pdb=" N GLY D 837 " --> pdb=" O LEU D 833 " (cutoff:3.500A) 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 880 Processing helix chain 'D' and resid 886 through 896 Processing helix chain 'D' and resid 897 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 Processing helix chain 'D' and resid 952 through 964 removed outlier: 3.602A pdb=" N ALA D 956 " --> pdb=" O ASP D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 980 removed outlier: 3.789A 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: 3.925A pdb=" N ALA D 998 " --> pdb=" O HIS D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1008 through 1018 removed outlier: 3.786A pdb=" N GLN D1017 " --> pdb=" O SER D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1033 Processing helix chain 'D' and resid 1036 through 1045 Processing helix chain 'D' and resid 1048 through 1060 removed outlier: 3.878A pdb=" N ALA D1052 " --> pdb=" O ASN D1048 " (cutoff:3.500A) Processing helix chain 'D' and resid 1062 through 1081 Processing helix chain 'E' and resid 11 through 16 removed outlier: 3.869A pdb=" N ASN E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 102 Processing helix chain 'E' and resid 264 through 269 removed outlier: 4.373A 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 671 through 686 Processing helix chain 'E' and resid 687 through 698 removed outlier: 3.548A 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: 3.608A pdb=" N THR E 735 " --> pdb=" O SER E 731 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS E 741 " --> pdb=" O GLN E 737 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE E 742 " --> pdb=" O SER E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 744 through 757 removed outlier: 3.723A pdb=" N ILE E 748 " --> pdb=" O GLU E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 769 Processing helix chain 'E' and resid 771 through 783 removed outlier: 4.026A pdb=" N ALA E 775 " --> pdb=" O GLN E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 795 Processing helix chain 'E' and resid 796 through 798 No H-bonds generated for 'chain 'E' and resid 796 through 798' Processing helix chain 'E' and resid 799 through 814 removed outlier: 3.794A pdb=" N ILE E 803 " --> pdb=" O GLU E 799 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 834 removed outlier: 3.645A pdb=" N ALA E 820 " --> pdb=" O ASN E 816 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG E 821 " --> pdb=" O ASN E 817 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS E 822 " --> pdb=" O GLN E 818 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG E 834 " --> pdb=" O ASN E 830 " (cutoff:3.500A) Processing helix chain 'E' and resid 837 through 859 removed outlier: 3.539A pdb=" N ILE E 841 " --> pdb=" O ASP E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 872 Processing helix chain 'E' and resid 874 through 889 removed outlier: 3.547A 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 removed outlier: 3.814A pdb=" N ALA E 949 " --> pdb=" O ALA E 945 " (cutoff:3.500A) Processing helix chain 'E' and resid 959 through 969 Processing helix chain 'E' and resid 972 through 983 Processing helix chain 'E' and resid 986 through 999 removed outlier: 3.885A 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 removed outlier: 3.595A pdb=" N GLN E1021 " --> pdb=" O GLU E1017 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1037 removed outlier: 4.025A pdb=" N TYR E1032 " --> pdb=" O VAL E1028 " (cutoff:3.500A) Processing helix chain 'E' and resid 1043 through 1053 removed outlier: 3.554A pdb=" N ILE E1047 " --> pdb=" O GLU E1043 " (cutoff:3.500A) Processing helix chain 'E' and resid 1057 through 1067 removed outlier: 3.900A pdb=" N LYS E1062 " --> pdb=" O VAL E1058 " (cutoff:3.500A) Processing helix chain 'E' and resid 1069 through 1078 Processing helix chain 'E' and resid 1084 through 1095 Processing helix chain 'E' and resid 1099 through 1111 removed outlier: 3.509A pdb=" N GLN E1103 " --> pdb=" O GLU E1099 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU E1111 " --> pdb=" O ASP E1107 " (cutoff:3.500A) Processing helix chain 'E' and resid 1117 through 1129 removed outlier: 3.917A pdb=" N LEU E1121 " --> pdb=" O ASP E1117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1049 through 1050 removed outlier: 3.808A pdb=" N GLN A1135 " --> pdb=" O GLN A1050 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A1136 " --> pdb=" O THR A1129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1069 through 1070 removed outlier: 3.848A pdb=" N GLU A1075 " --> pdb=" O CYS A1070 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1167 through 1168 removed outlier: 8.535A pdb=" N LEU A1168 " --> pdb=" O GLU A1081 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LYS A1083 " --> pdb=" O LEU A1168 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A1197 " --> pdb=" O PHE A1082 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU A1084 " --> pdb=" O ILE A1195 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N ILE A1195 " --> pdb=" O LEU A1084 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1207 through 1210 Processing sheet with id=AA5, first strand: chain 'D' and resid 2 through 9 removed outlier: 4.683A pdb=" N ILE D 369 " --> pdb=" O LEU D 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 19 through 22 Processing sheet with id=AA7, first strand: chain 'D' and resid 59 through 64 removed outlier: 3.564A pdb=" N ILE D 80 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 106 removed outlier: 7.329A pdb=" N ALA D 116 " --> pdb=" O CYS D 102 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE D 104 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL D 114 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N PHE D 106 " --> pdb=" O ARG D 112 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ARG D 112 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D 132 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ARG D 126 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 142 through 145 removed outlier: 4.222A pdb=" N PHE D 162 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS D 170 " --> pdb=" O PHE D 162 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL D 169 " --> pdb=" O VAL D 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 188 through 194 removed outlier: 4.451A pdb=" N THR D 204 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS D 213 " --> pdb=" O THR D 220 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR D 220 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 188 through 194 removed outlier: 4.451A pdb=" N THR D 204 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 238 through 242 Processing sheet with id=AB4, first strand: chain 'D' and resid 297 through 303 removed outlier: 6.537A pdb=" N GLY D 312 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE D 300 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL D 310 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR D 302 " --> pdb=" O VAL D 308 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL D 308 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG D 317 " --> pdb=" O THR D 313 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE D 318 " --> pdb=" O TYR D 342 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR D 342 " --> pdb=" O ILE D 318 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE D 320 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 379 through 382 Processing sheet with id=AB6, first strand: chain 'D' and resid 418 through 421 removed outlier: 6.540A pdb=" N ILE D 434 " --> pdb=" O SER D 453 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER D 453 " --> pdb=" O ILE D 434 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE D 436 " --> pdb=" O VAL D 451 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 460 through 464 removed outlier: 4.602A pdb=" N GLN D 487 " --> pdb=" O VAL D 478 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 500 through 504 removed outlier: 4.415A pdb=" N ASN D 500 " --> pdb=" O TRP D 511 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP D 511 " --> pdb=" O ASN D 500 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE D 517 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL D 532 " --> pdb=" O ILE D 517 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU D 519 " --> pdb=" O ILE D 530 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 545 through 551 removed outlier: 6.833A pdb=" N THR D 561 " --> pdb=" O ARG D 547 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N CYS D 549 " --> pdb=" O VAL D 559 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 559 " --> pdb=" O CYS D 549 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL D 551 " --> pdb=" O LYS D 557 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LYS D 557 " --> pdb=" O VAL D 551 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ALA D 562 " --> pdb=" O LYS D 575 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LYS D 575 " --> pdb=" O ALA D 562 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN D 585 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 595 through 602 removed outlier: 5.747A pdb=" N ILE D 615 " --> pdb=" O PRO D 597 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN D 599 " --> pdb=" O SER D 613 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN D 653 " --> pdb=" O ILE D 616 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER D 652 " --> pdb=" O GLU D 676 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLU D 676 " --> pdb=" O SER D 652 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU D 654 " --> pdb=" O GLN D 674 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLN D 674 " --> pdb=" O LEU D 654 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE D 656 " --> pdb=" O GLN D 672 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN D 672 " --> pdb=" O PHE D 656 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR D 658 " --> pdb=" O GLN D 670 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 679 through 685 removed outlier: 6.468A pdb=" N ILE D 693 " --> pdb=" O GLU D 680 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL D 682 " --> pdb=" O TYR D 691 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N TYR D 691 " --> pdb=" O VAL D 682 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA D 684 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LYS D 689 " --> pdb=" O ALA D 684 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN D 705 " --> pdb=" O ASN D 696 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 5 through 10 removed outlier: 6.129A pdb=" N LYS E 6 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU E 352 " --> pdb=" O LYS E 6 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE E 8 " --> pdb=" O GLY E 350 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 21 through 24 removed outlier: 6.788A pdb=" N VAL E 40 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU E 52 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL E 42 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 61 through 66 removed outlier: 5.158A pdb=" N GLN E 77 " --> pdb=" O CYS E 82 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N CYS E 82 " --> pdb=" O GLN E 77 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 104 through 109 Processing sheet with id=AC7, first strand: chain 'E' and resid 146 through 151 removed outlier: 3.640A pdb=" N SER E 161 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL E 165 " --> pdb=" O SER E 161 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 186 through 192 removed outlier: 4.463A pdb=" N LEU E 189 " --> pdb=" O THR E 207 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR E 207 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TRP E 191 " --> pdb=" O THR E 205 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR E 205 " --> pdb=" O TRP E 191 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 238 through 244 removed outlier: 4.299A pdb=" N TYR E 257 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 284 through 288 removed outlier: 5.202A pdb=" N ILE E 304 " --> pdb=" O GLN E 316 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN E 316 " --> pdb=" O ILE E 304 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 365 through 368 Processing sheet with id=AD3, first strand: chain 'E' and resid 400 through 403 Processing sheet with id=AD4, first strand: chain 'E' and resid 447 through 450 removed outlier: 3.841A pdb=" N ASP E 447 " --> pdb=" O LEU E 458 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 488 through 493 removed outlier: 4.057A pdb=" N VAL E 519 " --> pdb=" O TYR E 509 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N HIS E 511 " --> pdb=" O PHE E 517 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE E 517 " --> pdb=" O HIS E 511 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 528 through 533 removed outlier: 4.180A pdb=" N GLU E 553 " --> pdb=" O GLN E 558 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN E 558 " --> pdb=" O GLU E 553 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 571 through 574 removed outlier: 4.007A pdb=" N LYS E 571 " --> pdb=" O LEU E 585 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE E 594 " --> pdb=" O GLN E 606 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN E 606 " --> pdb=" O ILE E 594 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 571 through 574 removed outlier: 4.007A pdb=" N LYS E 571 " --> pdb=" O LEU E 585 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 633 through 638 removed outlier: 6.462A pdb=" N PHE E 645 " --> pdb=" O PRO E 634 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR E 636 " --> pdb=" O LYS E 643 " (cutoff:3.500A) 1115 hydrogen bonds defined for protein. 3168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.68 Time building geometry restraints manager: 7.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7272 1.34 - 1.46: 4775 1.46 - 1.58: 10386 1.58 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 22585 Sorted by residual: bond pdb=" CA ILE D 687 " pdb=" CB ILE D 687 " ideal model delta sigma weight residual 1.539 1.527 0.012 5.40e-03 3.43e+04 5.19e+00 bond pdb=" N LYS D 721 " pdb=" CA LYS D 721 " ideal model delta sigma weight residual 1.462 1.489 -0.027 1.40e-02 5.10e+03 3.70e+00 bond pdb=" C ILE D 982 " pdb=" N PRO D 983 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.74e+00 bond pdb=" CZ TYR E 661 " pdb=" OH TYR E 661 " ideal model delta sigma weight residual 1.376 1.351 0.025 2.10e-02 2.27e+03 1.42e+00 bond pdb=" C LYS E 522 " pdb=" N PRO E 523 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.32e+00 ... (remaining 22580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 29650 1.52 - 3.04: 670 3.04 - 4.56: 116 4.56 - 6.08: 32 6.08 - 7.60: 11 Bond angle restraints: 30479 Sorted by residual: angle pdb=" C ILE D 752 " pdb=" N GLN D 753 " pdb=" CA GLN D 753 " ideal model delta sigma weight residual 121.54 127.08 -5.54 1.91e+00 2.74e-01 8.41e+00 angle pdb=" N ILE E 782 " pdb=" CA ILE E 782 " pdb=" C ILE E 782 " ideal model delta sigma weight residual 112.50 108.48 4.02 1.39e+00 5.18e-01 8.35e+00 angle pdb=" N GLU D 879 " pdb=" CA GLU D 879 " pdb=" CB GLU D 879 " ideal model delta sigma weight residual 110.28 114.59 -4.31 1.55e+00 4.16e-01 7.73e+00 angle pdb=" C TYR D 878 " pdb=" N GLU D 879 " pdb=" CA GLU D 879 " ideal model delta sigma weight residual 120.31 116.21 4.10 1.52e+00 4.33e-01 7.29e+00 angle pdb=" CA MET E 754 " pdb=" CB MET E 754 " pdb=" CG MET E 754 " ideal model delta sigma weight residual 114.10 119.36 -5.26 2.00e+00 2.50e-01 6.92e+00 ... (remaining 30474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 12328 17.63 - 35.26: 1164 35.26 - 52.89: 201 52.89 - 70.53: 47 70.53 - 88.16: 27 Dihedral angle restraints: 13767 sinusoidal: 5673 harmonic: 8094 Sorted by residual: 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 -156.05 -23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA ASN D 811 " pdb=" C ASN D 811 " pdb=" N MET D 812 " pdb=" CA MET D 812 " ideal model delta harmonic sigma weight residual 180.00 156.70 23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA PHE E 93 " pdb=" C PHE E 93 " pdb=" N GLU E 94 " pdb=" CA GLU E 94 " ideal model delta harmonic sigma weight residual 180.00 160.19 19.81 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 13764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2534 0.045 - 0.090: 606 0.090 - 0.135: 191 0.135 - 0.180: 6 0.180 - 0.225: 2 Chirality restraints: 3339 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 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL E 715 " pdb=" CA VAL E 715 " pdb=" CG1 VAL E 715 " pdb=" CG2 VAL E 715 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA ILE D 982 " pdb=" N ILE D 982 " pdb=" C ILE D 982 " pdb=" CB ILE D 982 " both_signs ideal model delta sigma weight residual False 2.43 2.28 0.15 2.00e-01 2.50e+01 5.73e-01 ... (remaining 3336 not shown) Planarity restraints: 3933 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 720 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C GLU D 720 " 0.061 2.00e-02 2.50e+03 pdb=" O GLU D 720 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS D 721 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS E 113 " -0.048 5.00e-02 4.00e+02 7.43e-02 8.83e+00 pdb=" N PRO E 114 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO E 114 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 114 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E1077 " 0.017 2.00e-02 2.50e+03 1.25e-02 3.11e+00 pdb=" CG TYR E1077 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR E1077 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR E1077 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR E1077 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR E1077 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E1077 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR E1077 " 0.005 2.00e-02 2.50e+03 ... (remaining 3930 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 469 2.69 - 3.25: 22249 3.25 - 3.80: 34911 3.80 - 4.35: 45247 4.35 - 4.90: 72424 Nonbonded interactions: 175300 Sorted by model distance: nonbonded pdb=" OH TYR E 406 " pdb=" O LYS E 425 " model vdw 2.143 3.040 nonbonded pdb=" OH TYR D 51 " pdb=" OE2 GLU D 85 " model vdw 2.180 3.040 nonbonded pdb=" OH TYR A 938 " pdb=" OE1 GLN A 981 " model vdw 2.186 3.040 nonbonded pdb=" OH TYR D 134 " pdb=" O ASP D 173 " model vdw 2.196 3.040 nonbonded pdb=" O PHE D 735 " pdb=" OG1 THR D 738 " model vdw 2.212 3.040 ... (remaining 175295 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 59.450 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.090 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 0.031 22593 Z= 0.119 Angle : 0.601 17.389 30491 Z= 0.320 Chirality : 0.043 0.225 3339 Planarity : 0.003 0.074 3933 Dihedral : 14.513 88.157 8545 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.60 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -0.01 (0.16), residues: 2739 helix: 1.14 (0.16), residues: 1047 sheet: 0.68 (0.22), residues: 615 loop : -1.59 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 959 HIS 0.006 0.000 HIS E 142 PHE 0.015 0.001 PHE D 576 TYR 0.030 0.001 TYR E1077 ARG 0.005 0.000 ARG E1046 Details of bonding type rmsd hydrogen bonds : bond 0.11882 ( 1098) hydrogen bonds : angle 5.74124 ( 3168) metal coordination : bond 0.01077 ( 8) metal coordination : angle 7.85451 ( 12) covalent geometry : bond 0.00220 (22585) covalent geometry : angle 0.58107 (30479) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 2.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 MET cc_start: 0.8320 (pmm) cc_final: 0.8005 (mmm) REVERT: A 876 MET cc_start: 0.9096 (ppp) cc_final: 0.8651 (ppp) REVERT: A 909 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7539 (tmm160) REVERT: A 988 SER cc_start: 0.9458 (m) cc_final: 0.9233 (p) REVERT: D 113 MET cc_start: 0.9344 (tmm) cc_final: 0.9045 (tmm) REVERT: D 426 MET cc_start: 0.8306 (tmm) cc_final: 0.8002 (tmm) REVERT: D 603 ASP cc_start: 0.8180 (t0) cc_final: 0.7921 (t0) REVERT: D 739 MET cc_start: 0.8765 (mpp) cc_final: 0.8532 (mpp) REVERT: D 761 MET cc_start: 0.8981 (mmm) cc_final: 0.8508 (mmm) REVERT: D 832 MET cc_start: 0.9033 (tmm) cc_final: 0.8740 (tmm) REVERT: D 943 MET cc_start: 0.9224 (mpp) cc_final: 0.8587 (mpp) REVERT: E 1009 PHE cc_start: 0.9048 (m-10) cc_final: 0.8791 (m-10) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.4179 time to fit residues: 75.6113 Evaluate side-chains 85 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1126 GLN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN D1071 GLN E 15 ASN E 113 HIS ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 ASN ** E 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1035 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.062560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.044708 restraints weight = 203432.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.045063 restraints weight = 139261.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.044776 restraints weight = 108521.542| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22593 Z= 0.151 Angle : 0.568 14.845 30491 Z= 0.295 Chirality : 0.043 0.199 3339 Planarity : 0.003 0.057 3933 Dihedral : 4.279 25.243 2965 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.29 % Favored : 94.52 % Rotamer: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.52 % 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: 0.15 (0.16), residues: 2739 helix: 1.31 (0.16), residues: 1078 sheet: 0.54 (0.22), residues: 603 loop : -1.47 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 959 HIS 0.003 0.001 HIS E 699 PHE 0.021 0.002 PHE D1030 TYR 0.016 0.001 TYR E 785 ARG 0.009 0.000 ARG E1046 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 1098) hydrogen bonds : angle 4.74842 ( 3168) metal coordination : bond 0.01124 ( 8) metal coordination : angle 7.86110 ( 12) covalent geometry : bond 0.00325 (22585) covalent geometry : angle 0.54601 (30479) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 MET cc_start: 0.8737 (pmm) cc_final: 0.8387 (mmm) REVERT: A 876 MET cc_start: 0.9142 (ppp) cc_final: 0.8703 (ppp) REVERT: A 909 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.7838 (tmm160) REVERT: A 1201 MET cc_start: 0.9162 (mmm) cc_final: 0.8926 (mmp) REVERT: D 1 MET cc_start: 0.7379 (pmm) cc_final: 0.6859 (mmp) REVERT: D 113 MET cc_start: 0.9315 (tmm) cc_final: 0.8864 (tmm) REVERT: D 426 MET cc_start: 0.8526 (tmm) cc_final: 0.8031 (tmm) REVERT: D 474 MET cc_start: 0.9328 (tpp) cc_final: 0.9012 (tpp) REVERT: D 603 ASP cc_start: 0.8219 (t0) cc_final: 0.7959 (t0) REVERT: D 943 MET cc_start: 0.9097 (mpp) cc_final: 0.8456 (mpp) REVERT: E 778 MET cc_start: 0.8828 (tmm) cc_final: 0.8554 (tmm) REVERT: E 1009 PHE cc_start: 0.9041 (m-10) cc_final: 0.8785 (m-10) REVERT: E 1084 TYR cc_start: 0.7596 (m-80) cc_final: 0.7375 (m-80) outliers start: 2 outliers final: 0 residues processed: 110 average time/residue: 0.3609 time to fit residues: 63.8545 Evaluate side-chains 80 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 178 optimal weight: 0.0070 chunk 192 optimal weight: 5.9990 chunk 240 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 193 optimal weight: 9.9990 chunk 164 optimal weight: 20.0000 chunk 188 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 overall best weight: 2.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 ASN A1126 GLN D 133 GLN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 GLN E 203 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 GLN ** E 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 955 GLN ** E1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1035 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.077332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.057998 restraints weight = 196905.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.059724 restraints weight = 123414.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.059821 restraints weight = 72892.126| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22593 Z= 0.187 Angle : 0.619 14.558 30491 Z= 0.319 Chirality : 0.044 0.215 3339 Planarity : 0.003 0.066 3933 Dihedral : 4.545 24.879 2965 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.59 % Favored : 94.23 % Rotamer: Outliers : 0.04 % Allowed : 4.77 % Favored : 95.19 % 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: 0.10 (0.16), residues: 2739 helix: 1.28 (0.16), residues: 1076 sheet: 0.44 (0.22), residues: 602 loop : -1.44 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 959 HIS 0.005 0.001 HIS E 347 PHE 0.016 0.002 PHE D1030 TYR 0.022 0.002 TYR D1053 ARG 0.006 0.001 ARG D1003 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 1098) hydrogen bonds : angle 4.81322 ( 3168) metal coordination : bond 0.01159 ( 8) metal coordination : angle 8.71304 ( 12) covalent geometry : bond 0.00399 (22585) covalent geometry : angle 0.59479 (30479) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 2.393 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 840 MET cc_start: 0.8702 (pmm) cc_final: 0.8492 (mmm) REVERT: A 876 MET cc_start: 0.9065 (ppp) cc_final: 0.8611 (ppp) REVERT: A 909 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7812 (tmm160) REVERT: A 1201 MET cc_start: 0.9209 (mmm) cc_final: 0.8972 (mmp) REVERT: D 1 MET cc_start: 0.7101 (pmm) cc_final: 0.6638 (mmm) REVERT: D 113 MET cc_start: 0.9330 (tmm) cc_final: 0.8960 (tmm) REVERT: D 426 MET cc_start: 0.8419 (tmm) cc_final: 0.7929 (tmm) REVERT: D 739 MET cc_start: 0.8896 (mpp) cc_final: 0.8625 (mpp) REVERT: E 778 MET cc_start: 0.8810 (tmm) cc_final: 0.8494 (tmm) REVERT: E 903 MET cc_start: 0.9294 (tmm) cc_final: 0.8909 (tmm) REVERT: E 1009 PHE cc_start: 0.8929 (m-10) cc_final: 0.8608 (m-10) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.3230 time to fit residues: 52.2488 Evaluate side-chains 73 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 108 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 208 optimal weight: 0.0270 chunk 171 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 0.0470 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 ASN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 743 ASN E1035 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.060745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.043056 restraints weight = 202479.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.044151 restraints weight = 117485.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.044933 restraints weight = 83884.609| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22593 Z= 0.121 Angle : 0.562 16.832 30491 Z= 0.286 Chirality : 0.042 0.152 3339 Planarity : 0.003 0.057 3933 Dihedral : 4.399 25.273 2965 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.97 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: 0.16 (0.16), residues: 2739 helix: 1.34 (0.16), residues: 1080 sheet: 0.41 (0.22), residues: 609 loop : -1.41 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 959 HIS 0.004 0.001 HIS E 699 PHE 0.015 0.001 PHE E 678 TYR 0.019 0.001 TYR D 194 ARG 0.007 0.000 ARG E1046 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 1098) hydrogen bonds : angle 4.59936 ( 3168) metal coordination : bond 0.01148 ( 8) metal coordination : angle 8.70511 ( 12) covalent geometry : bond 0.00257 (22585) covalent geometry : angle 0.53477 (30479) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 2.705 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 876 MET cc_start: 0.9082 (ppp) cc_final: 0.8625 (ppp) REVERT: A 909 ARG cc_start: 0.8127 (mmm-85) cc_final: 0.7765 (tmm160) REVERT: D 113 MET cc_start: 0.9314 (tmm) cc_final: 0.9006 (tmm) REVERT: D 426 MET cc_start: 0.8536 (tmm) cc_final: 0.8050 (tmm) REVERT: D 1012 MET cc_start: 0.9106 (ptp) cc_final: 0.8873 (ptt) REVERT: E 778 MET cc_start: 0.8859 (tmm) cc_final: 0.8452 (tmm) REVERT: E 903 MET cc_start: 0.9296 (tmm) cc_final: 0.8838 (tmm) REVERT: E 1009 PHE cc_start: 0.8884 (m-10) cc_final: 0.8605 (m-10) REVERT: E 1050 TYR cc_start: 0.8730 (m-10) cc_final: 0.8498 (m-10) REVERT: E 1088 MET cc_start: 0.7273 (tpt) cc_final: 0.7059 (mpp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.3516 time to fit residues: 56.0403 Evaluate side-chains 79 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 69 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 249 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 HIS ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 686 HIS ** E 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 955 GLN E1035 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.080989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.063472 restraints weight = 192417.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.064440 restraints weight = 114642.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.065221 restraints weight = 84318.640| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22593 Z= 0.170 Angle : 0.597 15.206 30491 Z= 0.307 Chirality : 0.043 0.205 3339 Planarity : 0.003 0.053 3933 Dihedral : 4.545 22.260 2965 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.66 % Favored : 94.16 % Rotamer: Outliers : 0.04 % Allowed : 2.85 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.09 (0.16), residues: 2739 helix: 1.29 (0.16), residues: 1079 sheet: 0.39 (0.22), residues: 602 loop : -1.44 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 959 HIS 0.005 0.001 HIS A 870 PHE 0.022 0.002 PHE D 783 TYR 0.020 0.001 TYR D1053 ARG 0.005 0.000 ARG E1046 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 1098) hydrogen bonds : angle 4.67432 ( 3168) metal coordination : bond 0.01237 ( 8) metal coordination : angle 8.47184 ( 12) covalent geometry : bond 0.00362 (22585) covalent geometry : angle 0.57263 (30479) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 2.930 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 876 MET cc_start: 0.9095 (ppp) cc_final: 0.8613 (ppp) REVERT: A 909 ARG cc_start: 0.8225 (mmm-85) cc_final: 0.7878 (tmm160) REVERT: D 1 MET cc_start: 0.7927 (mmt) cc_final: 0.7717 (mmp) REVERT: D 113 MET cc_start: 0.9331 (tmm) cc_final: 0.8997 (tmm) REVERT: D 426 MET cc_start: 0.8629 (tmm) cc_final: 0.8167 (tmm) REVERT: D 739 MET cc_start: 0.8876 (mpp) cc_final: 0.8611 (mpp) REVERT: D 1012 MET cc_start: 0.9106 (ptp) cc_final: 0.8893 (ptt) REVERT: E 778 MET cc_start: 0.8879 (tmm) cc_final: 0.8485 (tmm) REVERT: E 903 MET cc_start: 0.9199 (tmm) cc_final: 0.8647 (tmm) REVERT: E 1009 PHE cc_start: 0.8839 (m-10) cc_final: 0.8569 (m-10) REVERT: E 1120 TYR cc_start: 0.7611 (t80) cc_final: 0.7409 (t80) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.3632 time to fit residues: 56.0274 Evaluate side-chains 73 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 201 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 208 optimal weight: 0.6980 chunk 114 optimal weight: 7.9990 chunk 212 optimal weight: 0.4980 chunk 234 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 217 optimal weight: 0.0030 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 743 ASN E1035 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.060506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.042858 restraints weight = 196087.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.044439 restraints weight = 119253.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.044312 restraints weight = 68539.212| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22593 Z= 0.103 Angle : 0.562 15.378 30491 Z= 0.283 Chirality : 0.043 0.183 3339 Planarity : 0.003 0.051 3933 Dihedral : 4.347 24.001 2965 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.71 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: 0.17 (0.16), residues: 2739 helix: 1.36 (0.16), residues: 1082 sheet: 0.43 (0.22), residues: 606 loop : -1.43 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 429 HIS 0.004 0.001 HIS E 741 PHE 0.030 0.001 PHE E 697 TYR 0.017 0.001 TYR E1050 ARG 0.004 0.000 ARG A1092 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 1098) hydrogen bonds : angle 4.45804 ( 3168) metal coordination : bond 0.01275 ( 8) metal coordination : angle 9.21143 ( 12) covalent geometry : bond 0.00211 (22585) covalent geometry : angle 0.53146 (30479) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 2.650 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 876 MET cc_start: 0.9039 (ppp) cc_final: 0.8593 (ppp) REVERT: A 909 ARG cc_start: 0.8282 (mmm-85) cc_final: 0.7870 (tmm160) REVERT: D 113 MET cc_start: 0.9288 (tmm) cc_final: 0.9004 (tmm) REVERT: D 426 MET cc_start: 0.8575 (tmm) cc_final: 0.8055 (tmm) REVERT: D 510 MET cc_start: 0.9383 (pmm) cc_final: 0.8415 (pmm) REVERT: D 739 MET cc_start: 0.8815 (mpp) cc_final: 0.8604 (mpp) REVERT: D 1012 MET cc_start: 0.9165 (ptp) cc_final: 0.8949 (ptt) REVERT: E 732 MET cc_start: 0.9161 (mmp) cc_final: 0.8940 (mmp) REVERT: E 778 MET cc_start: 0.8831 (tmm) cc_final: 0.8445 (tmm) REVERT: E 903 MET cc_start: 0.9347 (tmm) cc_final: 0.8773 (tmm) REVERT: E 987 SER cc_start: 0.9371 (m) cc_final: 0.9165 (p) REVERT: E 1009 PHE cc_start: 0.8930 (m-10) cc_final: 0.8643 (m-10) REVERT: E 1050 TYR cc_start: 0.7908 (t80) cc_final: 0.7531 (t80) REVERT: E 1088 MET cc_start: 0.7441 (tpt) cc_final: 0.7125 (mmt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.3205 time to fit residues: 51.1339 Evaluate side-chains 76 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 132 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 228 optimal weight: 4.9990 chunk 85 optimal weight: 0.3980 chunk 245 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 59 optimal weight: 0.2980 chunk 258 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1114 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 ASN ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 743 ASN E1035 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.060771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.043040 restraints weight = 201647.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.044641 restraints weight = 122579.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.044852 restraints weight = 70877.248| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22593 Z= 0.101 Angle : 0.553 12.927 30491 Z= 0.281 Chirality : 0.043 0.240 3339 Planarity : 0.003 0.050 3933 Dihedral : 4.258 23.171 2965 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.04 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: 0.19 (0.16), residues: 2739 helix: 1.38 (0.16), residues: 1083 sheet: 0.42 (0.22), residues: 602 loop : -1.40 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP E 332 HIS 0.004 0.001 HIS A 904 PHE 0.016 0.001 PHE E 697 TYR 0.036 0.001 TYR E1077 ARG 0.005 0.000 ARG E1046 Details of bonding type rmsd hydrogen bonds : bond 0.03188 ( 1098) hydrogen bonds : angle 4.38438 ( 3168) metal coordination : bond 0.01099 ( 8) metal coordination : angle 8.39903 ( 12) covalent geometry : bond 0.00207 (22585) covalent geometry : angle 0.52705 (30479) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 876 MET cc_start: 0.8989 (ppp) cc_final: 0.8609 (ppp) REVERT: A 909 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7828 (tmm160) REVERT: D 1 MET cc_start: 0.6990 (pmm) cc_final: 0.6550 (mmm) REVERT: D 113 MET cc_start: 0.9277 (tmm) cc_final: 0.9008 (tmm) REVERT: D 237 LEU cc_start: 0.9160 (tp) cc_final: 0.8795 (pp) REVERT: D 426 MET cc_start: 0.8543 (tmm) cc_final: 0.7983 (tmm) REVERT: D 510 MET cc_start: 0.9403 (pmm) cc_final: 0.8411 (pmm) REVERT: D 1012 MET cc_start: 0.9179 (ptp) cc_final: 0.8932 (ptt) REVERT: E 732 MET cc_start: 0.9149 (mmp) cc_final: 0.8927 (mmp) REVERT: E 778 MET cc_start: 0.8635 (tmm) cc_final: 0.8435 (tmm) REVERT: E 903 MET cc_start: 0.9304 (tmm) cc_final: 0.8699 (tmm) REVERT: E 987 SER cc_start: 0.9350 (m) cc_final: 0.9113 (p) REVERT: E 1009 PHE cc_start: 0.8921 (m-10) cc_final: 0.8627 (m-10) REVERT: E 1050 TYR cc_start: 0.7950 (t80) cc_final: 0.7652 (t80) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3349 time to fit residues: 55.2037 Evaluate side-chains 76 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 154 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 193 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 743 ASN E1035 ASN E1049 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.060040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.042404 restraints weight = 204498.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.044101 restraints weight = 124851.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.044246 restraints weight = 72812.398| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22593 Z= 0.124 Angle : 0.569 12.415 30491 Z= 0.289 Chirality : 0.042 0.184 3339 Planarity : 0.003 0.049 3933 Dihedral : 4.297 22.937 2965 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.44 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: 0.18 (0.16), residues: 2739 helix: 1.39 (0.16), residues: 1081 sheet: 0.41 (0.22), residues: 595 loop : -1.39 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 332 HIS 0.004 0.001 HIS E 741 PHE 0.014 0.001 PHE D 733 TYR 0.029 0.001 TYR A 749 ARG 0.004 0.000 ARG E1046 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 1098) hydrogen bonds : angle 4.42491 ( 3168) metal coordination : bond 0.01076 ( 8) metal coordination : angle 8.36870 ( 12) covalent geometry : bond 0.00265 (22585) covalent geometry : angle 0.54436 (30479) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 2.876 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 876 MET cc_start: 0.9033 (ppp) cc_final: 0.8562 (ppp) REVERT: A 909 ARG cc_start: 0.8205 (mmm-85) cc_final: 0.7933 (tmm160) REVERT: D 1 MET cc_start: 0.6942 (pmm) cc_final: 0.6576 (mmm) REVERT: D 113 MET cc_start: 0.9280 (tmm) cc_final: 0.8976 (tmm) REVERT: D 237 LEU cc_start: 0.9168 (tp) cc_final: 0.8806 (pp) REVERT: D 426 MET cc_start: 0.8499 (tmm) cc_final: 0.7942 (tmm) REVERT: D 510 MET cc_start: 0.9393 (pmm) cc_final: 0.8418 (pmm) REVERT: D 739 MET cc_start: 0.8857 (mpp) cc_final: 0.8545 (mpp) REVERT: D 1012 MET cc_start: 0.9150 (ptp) cc_final: 0.8929 (ptt) REVERT: E 1 MET cc_start: 0.3584 (tpt) cc_final: 0.3360 (tpt) REVERT: E 732 MET cc_start: 0.9150 (mmp) cc_final: 0.8948 (mmp) REVERT: E 778 MET cc_start: 0.8751 (tmm) cc_final: 0.8547 (tmm) REVERT: E 903 MET cc_start: 0.9284 (tmm) cc_final: 0.8689 (tmm) REVERT: E 1009 PHE cc_start: 0.8959 (m-10) cc_final: 0.8665 (m-10) REVERT: E 1050 TYR cc_start: 0.7931 (t80) cc_final: 0.7709 (t80) REVERT: E 1084 TYR cc_start: 0.8048 (m-80) cc_final: 0.7837 (m-80) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.3422 time to fit residues: 53.2738 Evaluate side-chains 78 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 208 optimal weight: 0.7980 chunk 61 optimal weight: 0.3980 chunk 174 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 200 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 23 optimal weight: 0.0040 chunk 39 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 HIS ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 743 ASN E1035 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.060262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.042457 restraints weight = 196074.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.043931 restraints weight = 121757.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.043797 restraints weight = 70616.428| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22593 Z= 0.103 Angle : 0.561 12.260 30491 Z= 0.284 Chirality : 0.043 0.184 3339 Planarity : 0.003 0.048 3933 Dihedral : 4.256 23.071 2965 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.67 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 0.20 (0.16), residues: 2739 helix: 1.39 (0.16), residues: 1082 sheet: 0.43 (0.22), residues: 595 loop : -1.39 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 332 HIS 0.004 0.001 HIS A 904 PHE 0.013 0.001 PHE D 576 TYR 0.023 0.001 TYR A 749 ARG 0.007 0.000 ARG E 382 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 1098) hydrogen bonds : angle 4.36020 ( 3168) metal coordination : bond 0.01077 ( 8) metal coordination : angle 8.07933 ( 12) covalent geometry : bond 0.00216 (22585) covalent geometry : angle 0.53731 (30479) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 3.129 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 876 MET cc_start: 0.9046 (ppp) cc_final: 0.8606 (ppp) REVERT: A 909 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.7961 (tmm160) REVERT: D 113 MET cc_start: 0.9235 (tmm) cc_final: 0.8993 (tmm) REVERT: D 237 LEU cc_start: 0.9145 (tp) cc_final: 0.8811 (pp) REVERT: D 426 MET cc_start: 0.8579 (tmm) cc_final: 0.7995 (tmm) REVERT: D 510 MET cc_start: 0.9514 (pmm) cc_final: 0.8523 (pmm) REVERT: D 739 MET cc_start: 0.8813 (mpp) cc_final: 0.8484 (mpp) REVERT: D 761 MET cc_start: 0.9109 (mmm) cc_final: 0.8533 (mmm) REVERT: D 1012 MET cc_start: 0.9105 (ptp) cc_final: 0.8887 (ptt) REVERT: E 1 MET cc_start: 0.3709 (tpt) cc_final: 0.3476 (tpt) REVERT: E 330 MET cc_start: 0.6394 (tmm) cc_final: 0.6131 (tmm) REVERT: E 732 MET cc_start: 0.9138 (mmp) cc_final: 0.8931 (mmp) REVERT: E 778 MET cc_start: 0.8755 (tmm) cc_final: 0.8531 (tmm) REVERT: E 903 MET cc_start: 0.9336 (tmm) cc_final: 0.8743 (tmm) REVERT: E 1009 PHE cc_start: 0.8939 (m-10) cc_final: 0.8665 (m-10) REVERT: E 1050 TYR cc_start: 0.8056 (t80) cc_final: 0.7821 (t80) REVERT: E 1084 TYR cc_start: 0.8015 (m-80) cc_final: 0.7768 (m-80) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.4241 time to fit residues: 67.6185 Evaluate side-chains 76 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 262 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 ASN ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 743 ASN E 955 GLN E1035 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.059293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.042767 restraints weight = 203968.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.042892 restraints weight = 132853.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.042898 restraints weight = 102977.679| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22593 Z= 0.144 Angle : 0.586 12.739 30491 Z= 0.299 Chirality : 0.043 0.249 3339 Planarity : 0.003 0.048 3933 Dihedral : 4.410 23.249 2965 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.59 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 0.15 (0.16), residues: 2739 helix: 1.32 (0.16), residues: 1084 sheet: 0.36 (0.22), residues: 617 loop : -1.37 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 332 HIS 0.006 0.001 HIS E 741 PHE 0.018 0.001 PHE D 733 TYR 0.022 0.001 TYR A 749 ARG 0.004 0.000 ARG E1046 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 1098) hydrogen bonds : angle 4.49604 ( 3168) metal coordination : bond 0.01142 ( 8) metal coordination : angle 8.55859 ( 12) covalent geometry : bond 0.00309 (22585) covalent geometry : angle 0.56051 (30479) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 4.353 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 876 MET cc_start: 0.9112 (ppp) cc_final: 0.8672 (ppp) REVERT: A 899 MET cc_start: 0.9257 (tpt) cc_final: 0.9050 (tpp) REVERT: A 909 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.8000 (tmm160) REVERT: D 113 MET cc_start: 0.9239 (tmm) cc_final: 0.8964 (tmm) REVERT: D 426 MET cc_start: 0.8662 (tmm) cc_final: 0.8126 (tmm) REVERT: D 510 MET cc_start: 0.9448 (pmm) cc_final: 0.8446 (pmm) REVERT: D 739 MET cc_start: 0.8909 (mpp) cc_final: 0.8573 (mpp) REVERT: D 812 MET cc_start: 0.8565 (pmm) cc_final: 0.8335 (pmm) REVERT: D 1012 MET cc_start: 0.9162 (ptp) cc_final: 0.8946 (ptt) REVERT: E 1 MET cc_start: 0.3612 (tpt) cc_final: 0.3399 (tpt) REVERT: E 778 MET cc_start: 0.8819 (tmm) cc_final: 0.8578 (tmm) REVERT: E 903 MET cc_start: 0.9363 (tmm) cc_final: 0.8749 (tmm) REVERT: E 1009 PHE cc_start: 0.9016 (m-10) cc_final: 0.8774 (m-10) REVERT: E 1084 TYR cc_start: 0.8207 (m-80) cc_final: 0.8000 (m-80) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.4785 time to fit residues: 74.0360 Evaluate side-chains 76 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 8 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 196 optimal weight: 0.3980 chunk 213 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 141 optimal weight: 0.4980 chunk 61 optimal weight: 0.0470 chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 HIS ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 743 ASN E1035 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.060128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.042271 restraints weight = 201661.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.043912 restraints weight = 121886.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.044048 restraints weight = 72976.383| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22593 Z= 0.101 Angle : 0.561 12.538 30491 Z= 0.283 Chirality : 0.043 0.225 3339 Planarity : 0.003 0.047 3933 Dihedral : 4.288 23.128 2965 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.75 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: 0.20 (0.16), residues: 2739 helix: 1.37 (0.16), residues: 1084 sheet: 0.40 (0.22), residues: 615 loop : -1.37 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 332 HIS 0.004 0.001 HIS E 741 PHE 0.022 0.001 PHE A 767 TYR 0.019 0.001 TYR A 749 ARG 0.003 0.000 ARG E 382 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 1098) hydrogen bonds : angle 4.34514 ( 3168) metal coordination : bond 0.01077 ( 8) metal coordination : angle 8.10457 ( 12) covalent geometry : bond 0.00212 (22585) covalent geometry : angle 0.53767 (30479) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8165.17 seconds wall clock time: 146 minutes 35.52 seconds (8795.52 seconds total)