Starting phenix.real_space_refine on Fri Jan 16 21:33:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f5o_28866/01_2026/8f5o_28866.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f5o_28866/01_2026/8f5o_28866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f5o_28866/01_2026/8f5o_28866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f5o_28866/01_2026/8f5o_28866.map" model { file = "/net/cci-nas-00/data/ceres_data/8f5o_28866/01_2026/8f5o_28866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f5o_28866/01_2026/8f5o_28866.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.020 sd= 1.359 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 273 5.16 5 C 27385 2.51 5 N 7581 2.21 5 O 8155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43398 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 8965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 8965 Classifications: {'peptide': 1134} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1095} Chain breaks: 3 Chain: "C" Number of atoms: 9354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1179, 9354 Classifications: {'peptide': 1179} Link IDs: {'PTRANS': 44, 'TRANS': 1134} Chain breaks: 2 Chain: "E" Number of atoms: 8380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8380 Classifications: {'peptide': 1076} Link IDs: {'PCIS': 4, 'PTRANS': 39, 'TRANS': 1032} Chain breaks: 5 Chain: "A" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 427 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "F" Number of atoms: 7045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 911, 7045 Classifications: {'peptide': 911} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 872} Chain breaks: 1 Chain: "D" Number of atoms: 9223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9223 Classifications: {'peptide': 1180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 1134} Chain breaks: 7 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8752 SG CYS B1214 110.641 122.750 250.398 1.00466.26 S ATOM 8771 SG CYS B1217 106.967 123.543 250.152 1.00464.25 S ATOM 8896 SG CYS B1232 108.005 120.739 252.405 1.00435.55 S ATOM 8917 SG CYS B1235 108.395 120.354 248.605 1.00447.96 S ATOM 8448 SG CYS B1174 106.140 141.377 266.504 1.00437.60 S ATOM 8468 SG CYS B1177 105.351 144.578 268.405 1.00448.87 S ATOM 8560 SG CYS B1188 102.521 142.380 267.243 1.00421.45 S ATOM 8583 SG CYS B1191 104.539 144.266 264.673 1.00441.81 S ATOM 16908 SG CYS C1044 74.825 115.555 51.248 1.00229.34 S ATOM 16936 SG CYS C1047 76.679 116.114 47.962 1.00232.95 S ATOM 17040 SG CYS C1061 77.107 112.975 49.917 1.00205.05 S ATOM 17061 SG CYS C1064 78.571 116.247 51.299 1.00216.45 S ATOM 17903 SG CYS C1232 56.895 115.722 68.902 1.00137.53 S ATOM 17921 SG CYS C1235 60.187 114.294 68.058 1.00128.37 S ATOM 18072 SG CYS C1254 56.874 112.367 67.323 1.00115.60 S ATOM 18093 SG CYS C1257 58.052 112.597 70.818 1.00127.61 S Time building chain proxies: 9.37, per 1000 atoms: 0.22 Number of scatterers: 43398 At special positions: 0 Unit cell: (138.61, 211.65, 314.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 273 16.00 O 8155 8.00 N 7581 7.00 C 27385 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: 4.32 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1217 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1214 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1235 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1232 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1188 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1177 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1191 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1174 " pdb=" ZN C2000 " pdb="ZN ZN C2000 " - pdb=" SG CYS C1061 " pdb="ZN ZN C2000 " - pdb=" SG CYS C1044 " pdb="ZN ZN C2000 " - pdb=" SG CYS C1047 " pdb="ZN ZN C2000 " - pdb=" SG CYS C1064 " pdb=" ZN C2001 " pdb="ZN ZN C2001 " - pdb=" SG CYS C1232 " pdb="ZN ZN C2001 " - pdb=" SG CYS C1254 " pdb="ZN ZN C2001 " - pdb=" SG CYS C1257 " pdb="ZN ZN C2001 " - pdb=" SG CYS C1235 " Number of angles added : 24 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10494 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 63 sheets defined 43.4% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'B' and resid 12 through 15 removed outlier: 3.920A pdb=" N VAL B 15 " --> pdb=" O PRO B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 12 through 15' Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.728A pdb=" N ARG B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 52' Processing helix chain 'B' and resid 207 through 210 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 626 through 631 removed outlier: 3.668A pdb=" N LEU B 630 " --> pdb=" O GLN B 626 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 626 through 631' Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 647 through 659 Processing helix chain 'B' and resid 661 through 673 Processing helix chain 'B' and resid 674 through 688 Processing helix chain 'B' and resid 690 through 693 Processing helix chain 'B' and resid 694 through 702 Processing helix chain 'B' and resid 703 through 716 Processing helix chain 'B' and resid 720 through 730 Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.528A pdb=" N ALA B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 743 " --> pdb=" O LEU B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 757 removed outlier: 4.049A pdb=" N ASP B 751 " --> pdb=" O ASP B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 775 through 790 Processing helix chain 'B' and resid 792 through 804 Processing helix chain 'B' and resid 805 through 817 Processing helix chain 'B' and resid 818 through 823 Processing helix chain 'B' and resid 824 through 829 removed outlier: 3.808A pdb=" N GLY B 829 " --> pdb=" O ILE B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 847 removed outlier: 4.220A pdb=" N VAL B 837 " --> pdb=" O LYS B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 859 Processing helix chain 'B' and resid 861 through 872 removed outlier: 3.874A pdb=" N ALA B 865 " --> pdb=" O GLU B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 885 removed outlier: 3.551A pdb=" N ALA B 880 " --> pdb=" O ASN B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 904 removed outlier: 3.511A pdb=" N LEU B 893 " --> pdb=" O ASP B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 918 Processing helix chain 'B' and resid 920 through 936 removed outlier: 3.725A pdb=" N LEU B 930 " --> pdb=" O LEU B 926 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 933 " --> pdb=" O GLN B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 961 removed outlier: 4.036A pdb=" N ARG B 957 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 961 " --> pdb=" O ARG B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 997 removed outlier: 3.573A pdb=" N ALA B 990 " --> pdb=" O THR B 986 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TRP B 991 " --> pdb=" O LEU B 987 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR B 997 " --> pdb=" O GLY B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1006 removed outlier: 4.390A pdb=" N MET B1002 " --> pdb=" O HIS B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1020 removed outlier: 3.891A pdb=" N LEU B1016 " --> pdb=" O PHE B1012 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B1017 " --> pdb=" O LYS B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1045 removed outlier: 3.588A pdb=" N GLY B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER B1036 " --> pdb=" O VAL B1032 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B1037 " --> pdb=" O ASP B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1067 Processing helix chain 'B' and resid 1149 through 1162 removed outlier: 4.202A pdb=" N ASP B1153 " --> pdb=" O ARG B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1209 No H-bonds generated for 'chain 'B' and resid 1207 through 1209' Processing helix chain 'B' and resid 1223 through 1227 Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.672A pdb=" N GLY C 193 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 572 removed outlier: 4.012A pdb=" N ALA C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 568 " --> pdb=" O HIS C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 583 removed outlier: 3.573A pdb=" N ALA C 578 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU C 580 " --> pdb=" O ASP C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 601 Processing helix chain 'C' and resid 603 through 611 removed outlier: 3.551A pdb=" N ALA C 607 " --> pdb=" O ARG C 603 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 621 removed outlier: 3.729A pdb=" N VAL C 620 " --> pdb=" O ASP C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 625 Processing helix chain 'C' and resid 626 through 632 removed outlier: 3.568A pdb=" N GLN C 632 " --> pdb=" O LEU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 689 removed outlier: 3.608A pdb=" N TYR C 681 " --> pdb=" O ASP C 677 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU C 685 " --> pdb=" O TYR C 681 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA C 686 " --> pdb=" O GLY C 682 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C 687 " --> pdb=" O SER C 683 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C 688 " --> pdb=" O ILE C 684 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY C 689 " --> pdb=" O LEU C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 701 Processing helix chain 'C' and resid 703 through 715 removed outlier: 3.593A pdb=" N ALA C 707 " --> pdb=" O CYS C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 724 removed outlier: 4.060A pdb=" N ALA C 720 " --> pdb=" O MET C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 744 removed outlier: 3.817A pdb=" N GLU C 743 " --> pdb=" O ARG C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 758 removed outlier: 3.640A pdb=" N ALA C 750 " --> pdb=" O ASN C 746 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER C 752 " --> pdb=" O VAL C 748 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY C 758 " --> pdb=" O TYR C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 771 removed outlier: 4.191A pdb=" N GLN C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA C 770 " --> pdb=" O MET C 766 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 771 " --> pdb=" O MET C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 783 removed outlier: 3.648A pdb=" N LYS C 778 " --> pdb=" O GLU C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 801 removed outlier: 3.515A pdb=" N ILE C 791 " --> pdb=" O GLU C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 814 Processing helix chain 'C' and resid 816 through 828 Processing helix chain 'C' and resid 830 through 840 removed outlier: 3.725A pdb=" N LYS C 839 " --> pdb=" O THR C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 858 Proline residue: C 850 - end of helix Processing helix chain 'C' and resid 860 through 871 Processing helix chain 'C' and resid 873 through 891 Processing helix chain 'C' and resid 893 through 908 removed outlier: 3.672A pdb=" N GLU C 906 " --> pdb=" O ILE C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 951 removed outlier: 4.020A pdb=" N ARG C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY C 944 " --> pdb=" O TYR C 940 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL C 945 " --> pdb=" O ALA C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 971 Processing helix chain 'C' and resid 981 through 996 removed outlier: 3.609A pdb=" N ILE C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1010 removed outlier: 3.642A pdb=" N GLN C1010 " --> pdb=" O PHE C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1032 removed outlier: 3.578A pdb=" N ARG C1030 " --> pdb=" O THR C1026 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER C1031 " --> pdb=" O LEU C1027 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS C1032 " --> pdb=" O LEU C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1060 removed outlier: 3.823A pdb=" N ARG C1060 " --> pdb=" O ALA C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1090 through 1101 Processing helix chain 'C' and resid 1168 through 1176 removed outlier: 3.996A pdb=" N GLN C1173 " --> pdb=" O PHE C1169 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR C1174 " --> pdb=" O THR C1170 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C1175 " --> pdb=" O GLN C1171 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU C1176 " --> pdb=" O LEU C1172 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1198 Processing helix chain 'C' and resid 1199 through 1201 No H-bonds generated for 'chain 'C' and resid 1199 through 1201' Processing helix chain 'C' and resid 1241 through 1249 removed outlier: 3.726A pdb=" N MET C1249 " --> pdb=" O GLU C1245 " (cutoff:3.500A) Processing helix chain 'C' and resid 1269 through 1284 removed outlier: 3.771A pdb=" N LEU C1273 " --> pdb=" O MET C1269 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 98 removed outlier: 3.607A pdb=" N ALA E 98 " --> pdb=" O SER E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 119 Processing helix chain 'E' and resid 127 through 133 Processing helix chain 'E' and resid 410 through 412 No H-bonds generated for 'chain 'E' and resid 410 through 412' Processing helix chain 'E' and resid 686 through 688 No H-bonds generated for 'chain 'E' and resid 686 through 688' Processing helix chain 'E' and resid 709 through 712 Processing helix chain 'E' and resid 867 through 883 Processing helix chain 'E' and resid 884 through 889 removed outlier: 4.310A pdb=" N ALA E 888 " --> pdb=" O ASN E 884 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 912 removed outlier: 3.772A pdb=" N TRP E 901 " --> pdb=" O ASN E 897 " (cutoff:3.500A) Processing helix chain 'E' and resid 914 through 923 removed outlier: 3.805A pdb=" N VAL E 919 " --> pdb=" O ASP E 915 " (cutoff:3.500A) Processing helix chain 'E' and resid 926 through 940 Processing helix chain 'E' and resid 944 through 955 Processing helix chain 'E' and resid 959 through 965 removed outlier: 4.059A pdb=" N GLU E 963 " --> pdb=" O GLU E 959 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU E 965 " --> pdb=" O ALA E 961 " (cutoff:3.500A) Processing helix chain 'E' and resid 970 through 981 removed outlier: 3.541A pdb=" N LEU E 974 " --> pdb=" O ARG E 970 " (cutoff:3.500A) Processing helix chain 'E' and resid 983 through 994 removed outlier: 4.202A pdb=" N ARG E 989 " --> pdb=" O GLU E 985 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG E 993 " --> pdb=" O ARG E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 995 through 997 No H-bonds generated for 'chain 'E' and resid 995 through 997' Processing helix chain 'E' and resid 998 through 1012 removed outlier: 3.806A pdb=" N VAL E1002 " --> pdb=" O ARG E 998 " (cutoff:3.500A) Processing helix chain 'E' and resid 1015 through 1026 Processing helix chain 'E' and resid 1032 through 1040 Processing helix chain 'E' and resid 1042 through 1051 Processing helix chain 'E' and resid 1075 through 1083 removed outlier: 3.838A pdb=" N PHE E1079 " --> pdb=" O GLN E1075 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE E1082 " --> pdb=" O THR E1078 " (cutoff:3.500A) Processing helix chain 'E' and resid 1086 through 1100 Processing helix chain 'E' and resid 1102 through 1113 Processing helix chain 'E' and resid 1115 through 1126 Processing helix chain 'E' and resid 1130 through 1157 Processing helix chain 'E' and resid 1176 through 1186 removed outlier: 4.256A pdb=" N VAL E1180 " --> pdb=" O SER E1176 " (cutoff:3.500A) Processing helix chain 'E' and resid 1189 through 1201 removed outlier: 3.877A pdb=" N GLN E1195 " --> pdb=" O GLN E1191 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR E1196 " --> pdb=" O LEU E1192 " (cutoff:3.500A) Processing helix chain 'E' and resid 1202 through 1212 removed outlier: 4.587A pdb=" N LYS E1212 " --> pdb=" O ARG E1208 " (cutoff:3.500A) Processing helix chain 'E' and resid 1216 through 1227 removed outlier: 3.796A pdb=" N SER E1227 " --> pdb=" O ALA E1223 " (cutoff:3.500A) Processing helix chain 'E' and resid 1228 through 1234 removed outlier: 3.939A pdb=" N MET E1232 " --> pdb=" O ASP E1228 " (cutoff:3.500A) Processing helix chain 'E' and resid 1234 through 1242 removed outlier: 3.604A pdb=" N HIS E1242 " --> pdb=" O ALA E1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 162 Processing helix chain 'A' and resid 163 through 171 removed outlier: 3.611A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N MET A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 183 removed outlier: 4.397A pdb=" N SER A 181 " --> pdb=" O CYS A 178 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS A 182 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 183 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'F' and resid 10 through 14 Processing helix chain 'F' and resid 224 through 228 removed outlier: 3.512A pdb=" N GLY F 228 " --> pdb=" O SER F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 663 through 673 Processing helix chain 'F' and resid 675 through 680 Processing helix chain 'F' and resid 681 through 683 No H-bonds generated for 'chain 'F' and resid 681 through 683' Processing helix chain 'F' and resid 685 through 699 Processing helix chain 'F' and resid 701 through 713 removed outlier: 4.000A pdb=" N GLN F 711 " --> pdb=" O ARG F 707 " (cutoff:3.500A) Processing helix chain 'F' and resid 714 through 725 removed outlier: 3.941A pdb=" N LYS F 723 " --> pdb=" O LEU F 719 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE F 724 " --> pdb=" O CYS F 720 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 742 Processing helix chain 'F' and resid 743 through 753 removed outlier: 3.501A pdb=" N ASN F 749 " --> pdb=" O LYS F 745 " (cutoff:3.500A) Processing helix chain 'F' and resid 759 through 766 removed outlier: 3.780A pdb=" N ASP F 766 " --> pdb=" O GLU F 762 " (cutoff:3.500A) Processing helix chain 'F' and resid 769 through 778 Processing helix chain 'F' and resid 784 through 798 removed outlier: 3.690A pdb=" N ILE F 788 " --> pdb=" O GLU F 784 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER F 789 " --> pdb=" O VAL F 785 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR F 798 " --> pdb=" O GLN F 794 " (cutoff:3.500A) Processing helix chain 'F' and resid 801 through 805 removed outlier: 3.905A pdb=" N LYS F 804 " --> pdb=" O VAL F 801 " (cutoff:3.500A) Processing helix chain 'F' and resid 806 through 812 Processing helix chain 'F' and resid 823 through 851 removed outlier: 4.411A pdb=" N THR F 828 " --> pdb=" O GLU F 824 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL F 829 " --> pdb=" O LEU F 825 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN F 830 " --> pdb=" O SER F 826 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU F 831 " --> pdb=" O VAL F 827 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE F 848 " --> pdb=" O ALA F 844 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG F 849 " --> pdb=" O ARG F 845 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE F 850 " --> pdb=" O SER F 846 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY F 851 " --> pdb=" O GLN F 847 " (cutoff:3.500A) Processing helix chain 'F' and resid 852 through 862 removed outlier: 4.061A pdb=" N LYS F 858 " --> pdb=" O ALA F 854 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR F 859 " --> pdb=" O ASP F 855 " (cutoff:3.500A) Processing helix chain 'F' and resid 865 through 874 removed outlier: 3.676A pdb=" N LYS F 874 " --> pdb=" O LYS F 870 " (cutoff:3.500A) Processing helix chain 'F' and resid 881 through 891 removed outlier: 3.709A pdb=" N GLU F 890 " --> pdb=" O ALA F 886 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS F 891 " --> pdb=" O GLN F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 895 through 905 Processing helix chain 'F' and resid 908 through 915 removed outlier: 3.567A pdb=" N ALA F 912 " --> pdb=" O ASN F 908 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG F 914 " --> pdb=" O LYS F 910 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU F 915 " --> pdb=" O ALA F 911 " (cutoff:3.500A) Processing helix chain 'F' and resid 916 through 919 Processing helix chain 'F' and resid 921 through 929 removed outlier: 3.816A pdb=" N ILE F 927 " --> pdb=" O ASN F 923 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 302 Processing helix chain 'D' and resid 303 through 316 removed outlier: 3.681A pdb=" N VAL D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 336 removed outlier: 3.632A pdb=" N MET D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 353 removed outlier: 3.737A pdb=" N GLU D 344 " --> pdb=" O GLU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 370 Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 376 through 392 removed outlier: 3.535A pdb=" N ARG D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU D 392 " --> pdb=" O VAL D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 411 removed outlier: 3.630A pdb=" N ALA D 410 " --> pdb=" O PHE D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 431 removed outlier: 3.745A pdb=" N GLN D 422 " --> pdb=" O SER D 418 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D 424 " --> pdb=" O THR D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 449 removed outlier: 4.243A pdb=" N LEU D 438 " --> pdb=" O ASN D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 removed outlier: 3.866A pdb=" N GLU D 456 " --> pdb=" O LYS D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 482 Processing helix chain 'D' and resid 483 through 497 Processing helix chain 'D' and resid 504 through 517 removed outlier: 3.607A pdb=" N SER D 508 " --> pdb=" O ASN D 504 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS D 517 " --> pdb=" O GLN D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 545 removed outlier: 3.750A pdb=" N ALA D 534 " --> pdb=" O TYR D 530 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA D 537 " --> pdb=" O GLN D 533 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 542 " --> pdb=" O ILE D 538 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS D 543 " --> pdb=" O LYS D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 557 removed outlier: 3.712A pdb=" N VAL D 552 " --> pdb=" O VAL D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 572 removed outlier: 3.775A pdb=" N ALA D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET D 570 " --> pdb=" O HIS D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 602 removed outlier: 3.525A pdb=" N HIS D 594 " --> pdb=" O LYS D 590 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 595 " --> pdb=" O CYS D 591 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU D 596 " --> pdb=" O GLY D 592 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N HIS D 601 " --> pdb=" O PHE D 597 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU D 602 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 620 removed outlier: 3.705A pdb=" N MET D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE D 617 " --> pdb=" O ALA D 613 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL D 618 " --> pdb=" O LYS D 614 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR D 619 " --> pdb=" O VAL D 615 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY D 620 " --> pdb=" O TRP D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 636 removed outlier: 3.527A pdb=" N LEU D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 635 " --> pdb=" O SER D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 655 removed outlier: 3.896A pdb=" N LEU D 645 " --> pdb=" O PRO D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 671 removed outlier: 3.773A pdb=" N LEU D 664 " --> pdb=" O ALA D 660 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA D 665 " --> pdb=" O CYS D 661 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU D 670 " --> pdb=" O GLN D 666 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP D 671 " --> pdb=" O ALA D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 677 Processing helix chain 'D' and resid 678 through 688 removed outlier: 3.859A pdb=" N LEU D 682 " --> pdb=" O PRO D 678 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL D 687 " --> pdb=" O LEU D 683 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS D 688 " --> pdb=" O LEU D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 744 removed outlier: 3.799A pdb=" N ARG D 744 " --> pdb=" O GLN D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 760 Processing helix chain 'D' and resid 765 through 778 removed outlier: 3.640A pdb=" N VAL D 769 " --> pdb=" O GLN D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 781 through 791 Processing helix chain 'D' and resid 796 through 807 removed outlier: 4.353A pdb=" N ILE D 800 " --> pdb=" O SER D 796 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA D 801 " --> pdb=" O GLU D 797 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 811 Processing helix chain 'D' and resid 817 through 831 Processing helix chain 'D' and resid 833 through 847 removed outlier: 3.700A pdb=" N GLY D 841 " --> pdb=" O TYR D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 864 removed outlier: 3.637A pdb=" N SER D 864 " --> pdb=" O ALA D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 881 removed outlier: 3.887A pdb=" N ARG D 873 " --> pdb=" O GLU D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 898 removed outlier: 3.813A pdb=" N ILE D 888 " --> pdb=" O TYR D 884 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG D 889 " --> pdb=" O ALA D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 915 removed outlier: 3.760A pdb=" N ASP D 907 " --> pdb=" O ILE D 903 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 927 Processing helix chain 'D' and resid 955 through 972 removed outlier: 4.159A pdb=" N ILE D 959 " --> pdb=" O VAL D 955 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG D 961 " --> pdb=" O THR D 957 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR D 965 " --> pdb=" O ARG D 961 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 997 removed outlier: 4.164A pdb=" N GLY D 996 " --> pdb=" O ASP D 992 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP D 997 " --> pdb=" O ASP D 993 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 992 through 997' Processing helix chain 'D' and resid 997 through 1018 Processing helix chain 'D' and resid 1023 through 1031 removed outlier: 3.836A pdb=" N ILE D1027 " --> pdb=" O ALA D1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 1032 through 1047 removed outlier: 3.658A pdb=" N ARG D1036 " --> pdb=" O VAL D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1063 through 1069 Processing helix chain 'D' and resid 1071 through 1094 removed outlier: 4.510A pdb=" N ARG D1088 " --> pdb=" O ARG D1084 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU D1089 " --> pdb=" O GLU D1085 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP D1094 " --> pdb=" O ALA D1090 " (cutoff:3.500A) Processing helix chain 'D' and resid 1097 through 1112 Processing helix chain 'D' and resid 1113 through 1128 Processing helix chain 'D' and resid 1133 through 1146 removed outlier: 3.710A pdb=" N LEU D1140 " --> pdb=" O ASP D1136 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR D1146 " --> pdb=" O ALA D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1152 through 1165 removed outlier: 4.454A pdb=" N ASN D1156 " --> pdb=" O GLU D1152 " (cutoff:3.500A) Processing helix chain 'D' and resid 1168 through 1183 removed outlier: 3.990A pdb=" N TYR D1174 " --> pdb=" O GLU D1170 " (cutoff:3.500A) Processing helix chain 'D' and resid 1184 through 1187 removed outlier: 3.585A pdb=" N GLU D1187 " --> pdb=" O GLN D1184 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1184 through 1187' Processing helix chain 'D' and resid 1188 through 1199 removed outlier: 4.307A pdb=" N ARG D1194 " --> pdb=" O GLU D1190 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D1195 " --> pdb=" O ALA D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1206 through 1220 Processing helix chain 'D' and resid 1222 through 1235 removed outlier: 3.667A pdb=" N ARG D1228 " --> pdb=" O ALA D1224 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU D1235 " --> pdb=" O ASN D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1239 through 1255 removed outlier: 4.266A pdb=" N THR D1243 " --> pdb=" O ASN D1239 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG D1244 " --> pdb=" O PRO D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1302 through 1319 removed outlier: 3.743A pdb=" N GLU D1306 " --> pdb=" O THR D1302 " (cutoff:3.500A) Processing helix chain 'D' and resid 1326 through 1340 removed outlier: 4.058A pdb=" N ILE D1330 " --> pdb=" O GLU D1326 " (cutoff:3.500A) Processing helix chain 'D' and resid 1343 through 1360 removed outlier: 4.027A pdb=" N THR D1347 " --> pdb=" O GLU D1343 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE D1356 " --> pdb=" O PHE D1352 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL D1357 " --> pdb=" O LEU D1353 " (cutoff:3.500A) Processing helix chain 'D' and resid 1426 through 1434 Processing helix chain 'D' and resid 1439 through 1453 Processing helix chain 'D' and resid 1456 through 1470 removed outlier: 3.570A pdb=" N LYS D1470 " --> pdb=" O LEU D1466 " (cutoff:3.500A) Processing helix chain 'D' and resid 1475 through 1485 removed outlier: 4.312A pdb=" N LYS D1480 " --> pdb=" O MET D1476 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN D1481 " --> pdb=" O SER D1477 " (cutoff:3.500A) Processing helix chain 'D' and resid 1520 through 1537 Processing helix chain 'D' and resid 1538 through 1553 removed outlier: 3.833A pdb=" N ALA D1542 " --> pdb=" O ARG D1538 " (cutoff:3.500A) Processing helix chain 'D' and resid 1556 through 1570 Processing helix chain 'D' and resid 1572 through 1588 removed outlier: 3.626A pdb=" N ALA D1576 " --> pdb=" O LYS D1572 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN D1578 " --> pdb=" O LYS D1574 " (cutoff:3.500A) Processing helix chain 'D' and resid 1592 through 1606 Processing helix chain 'D' and resid 1608 through 1622 removed outlier: 4.515A pdb=" N ASP D1613 " --> pdb=" O VAL D1609 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL D1614 " --> pdb=" O LYS D1610 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS D1621 " --> pdb=" O ARG D1617 " (cutoff:3.500A) Processing helix chain 'D' and resid 1632 through 1641 Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 10 removed outlier: 5.673A pdb=" N VAL B 3 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ARG B 324 " --> pdb=" O VAL B 3 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU B 5 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASN B 322 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 7 " --> pdb=" O PHE B 320 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG B 309 " --> pdb=" O TRP B 303 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TRP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA B 311 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE B 301 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY B 313 " --> pdb=" O GLY B 299 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 22 removed outlier: 3.728A pdb=" N SER B 19 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 38 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 74 removed outlier: 6.414A pdb=" N ILE B 89 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL B 104 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B 91 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 117 removed outlier: 4.018A pdb=" N ASP B 114 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B 132 " --> pdb=" O TYR B 128 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 133 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY B 145 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 135 " --> pdb=" O TYR B 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 157 removed outlier: 6.513A pdb=" N GLY B 167 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL B 155 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU B 165 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TRP B 157 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N SER B 163 " --> pdb=" O TRP B 157 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP B 177 " --> pdb=" O HIS B 183 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N HIS B 183 " --> pdb=" O ASP B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 200 through 205 removed outlier: 3.575A pdb=" N CYS B 222 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS B 227 " --> pdb=" O TYR B 223 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 228 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 250 through 253 removed outlier: 3.755A pdb=" N PHE B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 276 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG B 292 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR B 278 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR B 290 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE B 280 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 332 Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 374 removed outlier: 6.619A pdb=" N ILE B 381 " --> pdb=" O GLN B 369 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET B 371 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 379 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA B 373 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG B 391 " --> pdb=" O PHE B 407 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE B 407 " --> pdb=" O ARG B 391 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B 393 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR B 405 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 395 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 414 through 417 Processing sheet with id=AB2, first strand: chain 'B' and resid 487 through 492 removed outlier: 6.933A pdb=" N SER B 500 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N MET B 490 " --> pdb=" O PHE B 498 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE B 498 " --> pdb=" O MET B 490 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL B 492 " --> pdb=" O HIS B 496 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N HIS B 496 " --> pdb=" O VAL B 492 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLN B 510 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU B 516 " --> pdb=" O GLN B 510 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N CYS B 562 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 526 through 531 removed outlier: 6.542A pdb=" N ILE B 541 " --> pdb=" O GLN B 527 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET B 529 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA B 539 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL B 531 " --> pdb=" O GLN B 537 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLN B 537 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE B 546 " --> pdb=" O HIS B 542 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP B 565 " --> pdb=" O CYS B 551 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 526 through 531 removed outlier: 6.542A pdb=" N ILE B 541 " --> pdb=" O GLN B 527 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET B 529 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA B 539 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL B 531 " --> pdb=" O GLN B 537 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLN B 537 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE B 546 " --> pdb=" O HIS B 542 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 572 " --> pdb=" O THR B 547 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 575 through 578 removed outlier: 6.686A pdb=" N MET B 591 " --> pdb=" O TRP B 576 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 613 through 618 removed outlier: 5.225A pdb=" N LEU B 614 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 625 " --> pdb=" O LEU B 614 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1170 through 1173 removed outlier: 3.865A pdb=" N VAL B1172 " --> pdb=" O ASN B1181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1211 through 1213 Processing sheet with id=AB9, first strand: chain 'C' and resid 4 through 10 removed outlier: 4.961A pdb=" N VAL C 5 " --> pdb=" O ASP C 292 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASP C 292 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP C 7 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR C 283 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER C 289 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR C 281 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN C 278 " --> pdb=" O GLN C 272 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLN C 272 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS C 280 " --> pdb=" O ALA C 270 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA C 270 " --> pdb=" O CYS C 280 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY C 282 " --> pdb=" O TRP C 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 25 through 26 removed outlier: 6.652A pdb=" N ALA C 45 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 51 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 64 through 67 removed outlier: 4.269A pdb=" N CYS C 64 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY C 77 " --> pdb=" O CYS C 64 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP C 66 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA C 75 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR C 96 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL C 85 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL C 94 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 106 through 107 removed outlier: 3.777A pdb=" N ALA C 106 " --> pdb=" O ALA C 115 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 144 through 146 Processing sheet with id=AC5, first strand: chain 'C' and resid 181 through 186 removed outlier: 5.488A pdb=" N ALA C 183 " --> pdb=" O GLY C 200 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY C 200 " --> pdb=" O ALA C 183 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 230 through 232 removed outlier: 3.530A pdb=" N SER C 230 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL C 247 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 258 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 299 through 300 Processing sheet with id=AC8, first strand: chain 'C' and resid 336 through 340 removed outlier: 4.591A pdb=" N LYS C 336 " --> pdb=" O GLN C 347 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 371 " --> pdb=" O VAL C 354 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLU C 356 " --> pdb=" O ASP C 369 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASP C 369 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 381 through 383 Processing sheet with id=AD1, first strand: chain 'C' and resid 416 through 423 removed outlier: 6.427A pdb=" N MET C 419 " --> pdb=" O GLY C 434 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N GLY C 434 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL C 421 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU C 432 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY C 423 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS C 442 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU C 452 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 460 through 465 removed outlier: 4.132A pdb=" N SER C 462 " --> pdb=" O ILE C 475 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR C 480 " --> pdb=" O ASP C 476 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU C 481 " --> pdb=" O SER C 495 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER C 495 " --> pdb=" O LEU C 481 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL C 483 " --> pdb=" O LEU C 493 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 499 through 504 removed outlier: 6.540A pdb=" N THR C 515 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL C 502 " --> pdb=" O ALA C 513 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA C 513 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.464A pdb=" N PHE C 548 " --> pdb=" O VAL C 540 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1043 through 1044 Processing sheet with id=AD6, first strand: chain 'C' and resid 1188 through 1190 removed outlier: 3.913A pdb=" N PHE C1188 " --> pdb=" O GLU C1082 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR C1219 " --> pdb=" O PHE C1083 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1229 through 1231 Processing sheet with id=AD8, first strand: chain 'E' and resid 2 through 7 removed outlier: 6.703A pdb=" N ALA E 438 " --> pdb=" O VAL E 429 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL E 429 " --> pdb=" O ALA E 438 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N CYS E 440 " --> pdb=" O ASP E 427 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 14 through 22 removed outlier: 5.304A pdb=" N ALA E 32 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N GLN E 18 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N ALA E 30 " --> pdb=" O GLN E 18 " (cutoff:3.500A) removed outlier: 10.443A pdb=" N ILE E 20 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 11.527A pdb=" N LEU E 28 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ASN E 43 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL E 48 " --> pdb=" O ASN E 43 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 67 through 70 Processing sheet with id=AE2, first strand: chain 'E' and resid 137 through 142 removed outlier: 4.244A pdb=" N HIS E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL E 158 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER E 181 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N MET E 160 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 190 through 193 removed outlier: 7.455A pdb=" N VAL E 235 " --> pdb=" O CYS E 247 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 254 through 260 removed outlier: 4.688A pdb=" N SER E 256 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU E 269 " --> pdb=" O SER E 256 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL E 277 " --> pdb=" O THR E 289 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 314 through 319 removed outlier: 5.462A pdb=" N MET E 315 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY E 326 " --> pdb=" O MET E 315 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP E 317 " --> pdb=" O ALA E 324 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALA E 324 " --> pdb=" O TRP E 317 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 354 through 360 removed outlier: 3.697A pdb=" N SER E 356 " --> pdb=" O GLY E 369 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE E 374 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU E 375 " --> pdb=" O VAL E 419 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL E 419 " --> pdb=" O LEU E 375 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL E 377 " --> pdb=" O MET E 417 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 456 through 458 Processing sheet with id=AE8, first strand: chain 'E' and resid 492 through 496 removed outlier: 6.361A pdb=" N ILE E 508 " --> pdb=" O PHE E 525 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE E 525 " --> pdb=" O ILE E 508 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE E 510 " --> pdb=" O ILE E 523 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE E 523 " --> pdb=" O PHE E 510 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET E 512 " --> pdb=" O THR E 521 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR E 521 " --> pdb=" O MET E 512 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 533 through 535 Processing sheet with id=AF1, first strand: chain 'E' and resid 570 through 576 Processing sheet with id=AF2, first strand: chain 'E' and resid 640 through 647 removed outlier: 5.748A pdb=" N VAL E 642 " --> pdb=" O THR E 659 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR E 659 " --> pdb=" O VAL E 642 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY E 644 " --> pdb=" O MET E 657 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL E 654 " --> pdb=" O TRP E 671 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP E 671 " --> pdb=" O VAL E 654 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU E 656 " --> pdb=" O ARG E 669 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ARG E 669 " --> pdb=" O LEU E 656 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N SER E 658 " --> pdb=" O ASP E 667 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP E 667 " --> pdb=" O SER E 658 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 690 through 697 removed outlier: 6.267A pdb=" N TYR E 720 " --> pdb=" O PRO E 692 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER E 694 " --> pdb=" O GLU E 718 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N HIS E 796 " --> pdb=" O PRO E 815 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE E 798 " --> pdb=" O PHE E 813 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE E 813 " --> pdb=" O ILE E 798 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR E 800 " --> pdb=" O GLN E 811 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 825 through 827 Processing sheet with id=AF5, first strand: chain 'F' and resid 69 through 72 removed outlier: 3.597A pdb=" N LEU F 69 " --> pdb=" O TYR F 82 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP F 90 " --> pdb=" O LEU F 81 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 120 through 124 removed outlier: 4.465A pdb=" N PHE F 120 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL F 133 " --> pdb=" O PHE F 120 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 162 through 166 removed outlier: 4.329A pdb=" N ILE F 165 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR F 174 " --> pdb=" O ILE F 165 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 199 through 203 removed outlier: 4.815A pdb=" N ILE F 210 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA F 219 " --> pdb=" O ILE F 210 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 233 through 235 removed outlier: 4.674A pdb=" N PHE F 241 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU F 253 " --> pdb=" O PHE F 241 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA F 243 " --> pdb=" O ALA F 251 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA F 251 " --> pdb=" O ALA F 243 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 275 through 277 removed outlier: 4.337A pdb=" N MET F 275 " --> pdb=" O VAL F 288 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL F 288 " --> pdb=" O MET F 275 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN F 277 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA F 286 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL F 293 " --> pdb=" O ALA F 310 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA F 310 " --> pdb=" O VAL F 293 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 322 through 324 removed outlier: 4.208A pdb=" N ALA F 323 " --> pdb=" O PHE F 332 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE F 332 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 352 through 354 removed outlier: 3.890A pdb=" N CYS F 379 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASN F 371 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL F 377 " --> pdb=" O ASN F 371 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 389 through 391 removed outlier: 6.584A pdb=" N VAL F 405 " --> pdb=" O THR F 441 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR F 441 " --> pdb=" O VAL F 405 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR F 407 " --> pdb=" O LEU F 439 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 450 through 453 removed outlier: 3.741A pdb=" N ASP F 450 " --> pdb=" O VAL F 461 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 491 through 496 removed outlier: 4.493A pdb=" N ARG F 508 " --> pdb=" O THR F 505 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA F 521 " --> pdb=" O VAL F 511 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA F 513 " --> pdb=" O GLN F 519 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLN F 519 " --> pdb=" O ALA F 513 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 531 through 534 Processing sheet with id=AG8, first strand: chain 'F' and resid 572 through 575 removed outlier: 4.763A pdb=" N HIS F 599 " --> pdb=" O GLY F 603 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY F 603 " --> pdb=" O HIS F 599 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 629 through 633 removed outlier: 5.955A pdb=" N GLN F 640 " --> pdb=" O PRO F 629 " (cutoff:3.500A) 1981 hydrogen bonds defined for protein. 5652 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: 17.06 Time building geometry restraints manager: 5.45 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: 14482 1.34 - 1.46: 8354 1.46 - 1.58: 20975 1.58 - 1.69: 0 1.69 - 1.81: 421 Bond restraints: 44232 Sorted by residual: bond pdb=" CA ILE D 323 " pdb=" CB ILE D 323 " ideal model delta sigma weight residual 1.539 1.554 -0.015 5.40e-03 3.43e+04 8.12e+00 bond pdb=" CA PRO D1053 " pdb=" C PRO D1053 " ideal model delta sigma weight residual 1.517 1.533 -0.016 6.70e-03 2.23e+04 5.61e+00 bond pdb=" CA PRO E 55 " pdb=" C PRO E 55 " ideal model delta sigma weight residual 1.514 1.503 0.012 5.50e-03 3.31e+04 4.46e+00 bond pdb=" CA VAL F 785 " pdb=" CB VAL F 785 " ideal model delta sigma weight residual 1.539 1.528 0.011 5.40e-03 3.43e+04 4.40e+00 bond pdb=" C TRP C 873 " pdb=" O TRP C 873 " ideal model delta sigma weight residual 1.234 1.244 -0.010 5.00e-03 4.00e+04 3.95e+00 ... (remaining 44227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 59164 2.14 - 4.29: 704 4.29 - 6.43: 91 6.43 - 8.57: 20 8.57 - 10.72: 3 Bond angle restraints: 59982 Sorted by residual: angle pdb=" N ARG E 966 " pdb=" CA ARG E 966 " pdb=" C ARG E 966 " ideal model delta sigma weight residual 111.02 116.10 -5.08 1.22e+00 6.72e-01 1.73e+01 angle pdb=" CA SER E 968 " pdb=" C SER E 968 " pdb=" N LYS E 969 " ideal model delta sigma weight residual 118.44 112.76 5.68 1.41e+00 5.03e-01 1.62e+01 angle pdb=" O SER E 968 " pdb=" C SER E 968 " pdb=" N LYS E 969 " ideal model delta sigma weight residual 122.39 128.21 -5.82 1.48e+00 4.57e-01 1.55e+01 angle pdb=" N GLY E 57 " pdb=" CA GLY E 57 " pdb=" C GLY E 57 " ideal model delta sigma weight residual 114.85 110.30 4.55 1.35e+00 5.49e-01 1.14e+01 angle pdb=" C GLY E1113 " pdb=" N GLU E1114 " pdb=" CA GLU E1114 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 9.99e+00 ... (remaining 59977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 24275 17.90 - 35.81: 1918 35.81 - 53.71: 485 53.71 - 71.61: 83 71.61 - 89.52: 27 Dihedral angle restraints: 26788 sinusoidal: 10594 harmonic: 16194 Sorted by residual: dihedral pdb=" CA HIS D 374 " pdb=" C HIS D 374 " pdb=" N ASP D 375 " pdb=" CA ASP D 375 " ideal model delta harmonic sigma weight residual -180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ALA D 958 " pdb=" C ALA D 958 " pdb=" N ILE D 959 " pdb=" CA ILE D 959 " ideal model delta harmonic sigma weight residual -180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PRO C 954 " pdb=" C PRO C 954 " pdb=" N TYR C 955 " pdb=" CA TYR C 955 " ideal model delta harmonic sigma weight residual 180.00 -155.56 -24.44 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 26785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 5139 0.047 - 0.095: 1312 0.095 - 0.142: 367 0.142 - 0.189: 9 0.189 - 0.237: 1 Chirality restraints: 6828 Sorted by residual: chirality pdb=" CB ILE C 293 " pdb=" CA ILE C 293 " pdb=" CG1 ILE C 293 " pdb=" CG2 ILE C 293 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA LEU D1003 " pdb=" N LEU D1003 " pdb=" C LEU D1003 " pdb=" CB LEU D1003 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CB ILE E 548 " pdb=" CA ILE E 548 " pdb=" CG1 ILE E 548 " pdb=" CG2 ILE E 548 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 6825 not shown) Planarity restraints: 7739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 953 " 0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO C 954 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 954 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 954 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 961 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.33e+00 pdb=" C ARG D 961 " -0.047 2.00e-02 2.50e+03 pdb=" O ARG D 961 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE D 962 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 768 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C ARG D 768 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG D 768 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL D 769 " 0.011 2.00e-02 2.50e+03 ... (remaining 7736 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1575 2.71 - 3.26: 44393 3.26 - 3.80: 73650 3.80 - 4.35: 89584 4.35 - 4.90: 145432 Nonbonded interactions: 354634 Sorted by model distance: nonbonded pdb=" O VAL D1032 " pdb=" OG SER D1035 " model vdw 2.162 3.040 nonbonded pdb=" O THR D1336 " pdb=" OG1 THR D1339 " model vdw 2.169 3.040 nonbonded pdb=" O LEU D1466 " pdb=" OG SER D1469 " model vdw 2.180 3.040 nonbonded pdb=" O ALA D1002 " pdb=" OG1 THR D1005 " model vdw 2.185 3.040 nonbonded pdb=" O ILE E1036 " pdb=" OG1 THR E1040 " model vdw 2.189 3.040 ... (remaining 354629 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: 22.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 54.460 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.110 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: 0.020 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 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 : 0.004 0.052 44248 Z= 0.182 Angle : 0.620 10.715 60006 Z= 0.327 Chirality : 0.044 0.237 6828 Planarity : 0.005 0.098 7739 Dihedral : 14.210 89.516 16294 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.55 % Allowed : 11.48 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.11), residues: 5485 helix: -0.22 (0.11), residues: 2079 sheet: -0.13 (0.16), residues: 1073 loop : -0.78 (0.13), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 593 TYR 0.017 0.002 TYR F 503 PHE 0.021 0.002 PHE F 583 TRP 0.011 0.001 TRP B 576 HIS 0.010 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00388 (44232) covalent geometry : angle 0.61788 (59982) hydrogen bonds : bond 0.15741 ( 1975) hydrogen bonds : angle 6.27169 ( 5652) metal coordination : bond 0.00801 ( 16) metal coordination : angle 2.56735 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 313 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 351 MET cc_start: 0.7800 (tmm) cc_final: 0.7065 (tmm) REVERT: B 410 MET cc_start: 0.8397 (ppp) cc_final: 0.8006 (ppp) REVERT: B 450 MET cc_start: 0.8730 (mtm) cc_final: 0.8479 (mtm) REVERT: B 522 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.6979 (mm) REVERT: B 624 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8607 (t) REVERT: B 653 MET cc_start: 0.9049 (tpp) cc_final: 0.8827 (tpp) REVERT: B 842 MET cc_start: 0.9406 (mtp) cc_final: 0.9086 (mtp) REVERT: C 1 MET cc_start: 0.6461 (tpt) cc_final: 0.6174 (tpt) REVERT: C 56 MET cc_start: 0.7793 (mmm) cc_final: 0.7484 (mmm) REVERT: C 435 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7052 (pt) REVERT: C 441 MET cc_start: 0.8056 (mmt) cc_final: 0.7264 (mmt) REVERT: C 970 MET cc_start: 0.8087 (mmt) cc_final: 0.7865 (mmt) REVERT: E 1 MET cc_start: 0.7442 (mmt) cc_final: 0.7168 (mmt) REVERT: E 91 MET cc_start: 0.8515 (ppp) cc_final: 0.8164 (ppp) REVERT: E 471 MET cc_start: 0.7547 (mmt) cc_final: 0.7298 (mmt) REVERT: E 1010 MET cc_start: 0.8412 (mmt) cc_final: 0.8206 (mmt) REVERT: E 1147 MET cc_start: 0.8329 (tmm) cc_final: 0.8076 (tmm) REVERT: E 1165 ASP cc_start: 0.3127 (OUTLIER) cc_final: 0.2882 (t0) REVERT: D 458 PHE cc_start: 0.7643 (m-80) cc_final: 0.7429 (m-80) REVERT: D 751 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7704 (pt0) REVERT: D 1253 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8237 (m-80) REVERT: D 1354 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7835 (pt0) outliers start: 166 outliers final: 81 residues processed: 457 average time/residue: 0.2398 time to fit residues: 188.7247 Evaluate side-chains 356 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 268 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1044 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 902 ILE Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 1096 ARG Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 325 PHE Chi-restraints excluded: chain E residue 381 HIS Chi-restraints excluded: chain E residue 436 ASP Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 482 CYS Chi-restraints excluded: chain E residue 499 ASN Chi-restraints excluded: chain E residue 548 ILE Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 916 VAL Chi-restraints excluded: chain E residue 970 ARG Chi-restraints excluded: chain E residue 1040 THR Chi-restraints excluded: chain E residue 1165 ASP Chi-restraints excluded: chain E residue 1234 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 613 ASP Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain F residue 702 VAL Chi-restraints excluded: chain F residue 766 ASP Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 814 ARG Chi-restraints excluded: chain F residue 833 GLU Chi-restraints excluded: chain D residue 339 TRP Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 751 GLU Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 957 THR Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 994 ASN Chi-restraints excluded: chain D residue 1008 SER Chi-restraints excluded: chain D residue 1029 GLU Chi-restraints excluded: chain D residue 1045 CYS Chi-restraints excluded: chain D residue 1098 GLU Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1139 ILE Chi-restraints excluded: chain D residue 1158 PHE Chi-restraints excluded: chain D residue 1221 ASN Chi-restraints excluded: chain D residue 1227 LEU Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1257 THR Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 ILE Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1593 ASP Chi-restraints excluded: chain D residue 1624 THR Chi-restraints excluded: chain D residue 1634 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 551 random chunks: chunk 394 optimal weight: 4.9990 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 0.6980 chunk 497 optimal weight: 8.9990 chunk 414 optimal weight: 0.8980 chunk 310 optimal weight: 0.9980 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 20.0000 chunk 223 optimal weight: 2.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1151 GLN F 106 GLN F 674 ASN D 308 GLN D 352 HIS D 400 HIS D 492 GLN ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 566 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.099049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.073822 restraints weight = 180411.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.073176 restraints weight = 114065.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.073685 restraints weight = 80558.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.074079 restraints weight = 63524.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.074564 restraints weight = 56459.675| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 44248 Z= 0.200 Angle : 0.598 14.354 60006 Z= 0.315 Chirality : 0.043 0.186 6828 Planarity : 0.004 0.097 7739 Dihedral : 6.651 81.493 6202 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.31 % Allowed : 14.20 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.11), residues: 5485 helix: 0.09 (0.11), residues: 2160 sheet: -0.20 (0.16), residues: 1075 loop : -0.74 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1126 TYR 0.020 0.002 TYR D1109 PHE 0.027 0.002 PHE D 315 TRP 0.014 0.001 TRP C 873 HIS 0.009 0.001 HIS D1181 Details of bonding type rmsd covalent geometry : bond 0.00410 (44232) covalent geometry : angle 0.59606 (59982) hydrogen bonds : bond 0.04698 ( 1975) hydrogen bonds : angle 5.25204 ( 5652) metal coordination : bond 0.00951 ( 16) metal coordination : angle 2.34308 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 296 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 351 MET cc_start: 0.7706 (tmm) cc_final: 0.7040 (tmm) REVERT: B 410 MET cc_start: 0.8396 (ppp) cc_final: 0.7942 (ppp) REVERT: B 450 MET cc_start: 0.8809 (mtm) cc_final: 0.8276 (mtm) REVERT: B 497 MET cc_start: 0.8397 (tmm) cc_final: 0.8067 (tmm) REVERT: B 624 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8864 (t) REVERT: B 653 MET cc_start: 0.9051 (tpp) cc_final: 0.8831 (tpp) REVERT: B 842 MET cc_start: 0.9438 (mtp) cc_final: 0.9204 (mtp) REVERT: B 1044 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7615 (mm) REVERT: C 1 MET cc_start: 0.6969 (tpt) cc_final: 0.6717 (tpt) REVERT: C 266 TRP cc_start: 0.7277 (t-100) cc_final: 0.6185 (t-100) REVERT: C 441 MET cc_start: 0.7909 (mmt) cc_final: 0.7195 (mmt) REVERT: C 481 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8943 (mt) REVERT: E 1 MET cc_start: 0.7563 (mmt) cc_final: 0.7063 (mmt) REVERT: E 91 MET cc_start: 0.8643 (ppp) cc_final: 0.8300 (ppp) REVERT: E 669 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8391 (ptt90) REVERT: F 579 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6159 (mp0) REVERT: D 368 MET cc_start: 0.2037 (tpp) cc_final: 0.1584 (tpp) REVERT: D 439 CYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6760 (p) REVERT: D 458 PHE cc_start: 0.6723 (m-80) cc_final: 0.6455 (m-80) REVERT: D 568 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6826 (m-80) REVERT: D 644 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8485 (t80) REVERT: D 1126 ARG cc_start: 0.7381 (mtm110) cc_final: 0.7180 (mtm110) REVERT: D 1127 MET cc_start: 0.7228 (mmm) cc_final: 0.6951 (mmm) REVERT: D 1354 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7596 (pt0) outliers start: 155 outliers final: 94 residues processed: 424 average time/residue: 0.2422 time to fit residues: 174.6043 Evaluate side-chains 378 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 275 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 903 HIS Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1044 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 902 ILE Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 1174 TYR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 PHE Chi-restraints excluded: chain E residue 381 HIS Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 482 CYS Chi-restraints excluded: chain E residue 499 ASN Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 669 ARG Chi-restraints excluded: chain E residue 885 MET Chi-restraints excluded: chain E residue 916 VAL Chi-restraints excluded: chain E residue 990 HIS Chi-restraints excluded: chain E residue 1234 GLU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 579 GLU Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 678 TRP Chi-restraints excluded: chain F residue 702 VAL Chi-restraints excluded: chain F residue 788 ILE Chi-restraints excluded: chain F residue 814 ARG Chi-restraints excluded: chain F residue 828 THR Chi-restraints excluded: chain D residue 339 TRP Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 492 GLN Chi-restraints excluded: chain D residue 568 TYR Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 644 PHE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 994 ASN Chi-restraints excluded: chain D residue 1008 SER Chi-restraints excluded: chain D residue 1029 GLU Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1045 CYS Chi-restraints excluded: chain D residue 1098 GLU Chi-restraints excluded: chain D residue 1189 LYS Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 ILE Chi-restraints excluded: chain D residue 1431 PHE Chi-restraints excluded: chain D residue 1439 HIS Chi-restraints excluded: chain D residue 1467 LEU Chi-restraints excluded: chain D residue 1473 THR Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1557 SER Chi-restraints excluded: chain D residue 1593 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 551 random chunks: chunk 175 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 333 optimal weight: 0.0060 chunk 218 optimal weight: 9.9990 chunk 265 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 445 optimal weight: 2.9990 chunk 320 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 340 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1151 GLN D 481 GLN D 492 GLN ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.098608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.073636 restraints weight = 183898.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.075594 restraints weight = 115562.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.074999 restraints weight = 74568.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.074928 restraints weight = 74529.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.074940 restraints weight = 67826.430| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 44248 Z= 0.197 Angle : 0.595 12.336 60006 Z= 0.310 Chirality : 0.043 0.202 6828 Planarity : 0.004 0.093 7739 Dihedral : 6.153 80.279 6137 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.32 % Allowed : 15.12 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.11), residues: 5485 helix: 0.14 (0.11), residues: 2159 sheet: -0.32 (0.16), residues: 1073 loop : -0.74 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 668 TYR 0.022 0.002 TYR D 733 PHE 0.022 0.002 PHE D 315 TRP 0.010 0.001 TRP E1093 HIS 0.008 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00414 (44232) covalent geometry : angle 0.59338 (59982) hydrogen bonds : bond 0.04272 ( 1975) hydrogen bonds : angle 5.12807 ( 5652) metal coordination : bond 0.00963 ( 16) metal coordination : angle 2.48175 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 288 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8836 (p) REVERT: B 241 ASN cc_start: 0.7631 (OUTLIER) cc_final: 0.7410 (t0) REVERT: B 351 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7104 (tmm) REVERT: B 410 MET cc_start: 0.8391 (ppp) cc_final: 0.7853 (ppp) REVERT: B 450 MET cc_start: 0.8790 (mtm) cc_final: 0.8345 (mtm) REVERT: B 653 MET cc_start: 0.9051 (tpp) cc_final: 0.8821 (tpp) REVERT: B 842 MET cc_start: 0.9395 (mtp) cc_final: 0.9134 (mtp) REVERT: B 1044 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7609 (mm) REVERT: C 1 MET cc_start: 0.6847 (tpt) cc_final: 0.6604 (tpt) REVERT: C 266 TRP cc_start: 0.7319 (t-100) cc_final: 0.6316 (t-100) REVERT: C 441 MET cc_start: 0.7833 (mmt) cc_final: 0.7159 (mmt) REVERT: C 481 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8992 (mt) REVERT: C 556 MET cc_start: 0.8719 (ppp) cc_final: 0.8425 (ppp) REVERT: E 1 MET cc_start: 0.7632 (mmt) cc_final: 0.7192 (mmt) REVERT: E 91 MET cc_start: 0.8667 (ppp) cc_final: 0.8313 (ppp) REVERT: E 381 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.6627 (t-90) REVERT: F 579 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6348 (mp0) REVERT: D 368 MET cc_start: 0.1946 (tpp) cc_final: 0.1526 (tpp) REVERT: D 439 CYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6899 (p) REVERT: D 458 PHE cc_start: 0.6800 (m-10) cc_final: 0.6463 (m-80) REVERT: D 611 MET cc_start: 0.8268 (mpp) cc_final: 0.7780 (mpp) REVERT: D 644 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8598 (t80) REVERT: D 827 MET cc_start: 0.7696 (ppp) cc_final: 0.7245 (ppp) REVERT: D 857 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.6853 (m-10) REVERT: D 1085 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: D 1253 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: D 1354 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7152 (pt0) outliers start: 202 outliers final: 126 residues processed: 459 average time/residue: 0.2435 time to fit residues: 191.5222 Evaluate side-chains 412 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 273 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 746 LYS Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 903 HIS Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1044 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 902 ILE Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 1174 TYR Chi-restraints excluded: chain C residue 1269 MET Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 PHE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 381 HIS Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 482 CYS Chi-restraints excluded: chain E residue 548 ILE Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 879 TYR Chi-restraints excluded: chain E residue 885 MET Chi-restraints excluded: chain E residue 916 VAL Chi-restraints excluded: chain E residue 990 HIS Chi-restraints excluded: chain E residue 1234 GLU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 579 GLU Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 678 TRP Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain F residue 702 VAL Chi-restraints excluded: chain F residue 788 ILE Chi-restraints excluded: chain F residue 814 ARG Chi-restraints excluded: chain F residue 828 THR Chi-restraints excluded: chain F residue 833 GLU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 339 TRP Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 644 PHE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 857 TYR Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 907 ASP Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 957 THR Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 994 ASN Chi-restraints excluded: chain D residue 1008 SER Chi-restraints excluded: chain D residue 1029 GLU Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1085 GLU Chi-restraints excluded: chain D residue 1098 GLU Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1158 PHE Chi-restraints excluded: chain D residue 1189 LYS Chi-restraints excluded: chain D residue 1228 ARG Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1317 LEU Chi-restraints excluded: chain D residue 1319 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 ILE Chi-restraints excluded: chain D residue 1439 HIS Chi-restraints excluded: chain D residue 1467 LEU Chi-restraints excluded: chain D residue 1473 THR Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1561 ASN Chi-restraints excluded: chain D residue 1593 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 551 random chunks: chunk 306 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 56 optimal weight: 0.0570 chunk 534 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 285 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 319 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 258 optimal weight: 6.9990 chunk 370 optimal weight: 3.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 ASN E 600 GLN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1151 GLN D 481 GLN D 492 GLN ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.097895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.072729 restraints weight = 181813.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.073316 restraints weight = 112436.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.073869 restraints weight = 76579.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.074189 restraints weight = 62520.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.074275 restraints weight = 53514.444| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 44248 Z= 0.214 Angle : 0.613 11.447 60006 Z= 0.318 Chirality : 0.043 0.193 6828 Planarity : 0.004 0.096 7739 Dihedral : 6.144 80.401 6129 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.47 % Allowed : 16.08 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.11), residues: 5485 helix: 0.08 (0.11), residues: 2156 sheet: -0.42 (0.16), residues: 1067 loop : -0.74 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 636 TYR 0.025 0.002 TYR D 733 PHE 0.024 0.002 PHE D 315 TRP 0.035 0.001 TRP B 353 HIS 0.008 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00449 (44232) covalent geometry : angle 0.61062 (59982) hydrogen bonds : bond 0.04132 ( 1975) hydrogen bonds : angle 5.16033 ( 5652) metal coordination : bond 0.01034 ( 16) metal coordination : angle 2.57097 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 293 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.5762 (ppp) REVERT: B 72 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.8998 (p) REVERT: B 241 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7561 (t0) REVERT: B 351 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7089 (tmm) REVERT: B 410 MET cc_start: 0.8379 (ppp) cc_final: 0.7803 (ppp) REVERT: B 450 MET cc_start: 0.8895 (mtm) cc_final: 0.8374 (mtm) REVERT: B 653 MET cc_start: 0.9071 (tpp) cc_final: 0.8848 (tpp) REVERT: B 1044 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7635 (mm) REVERT: C 1 MET cc_start: 0.7281 (tpt) cc_final: 0.7069 (tpt) REVERT: C 182 TRP cc_start: 0.8075 (OUTLIER) cc_final: 0.7732 (m100) REVERT: C 266 TRP cc_start: 0.7331 (t-100) cc_final: 0.6852 (t-100) REVERT: C 441 MET cc_start: 0.7939 (mmt) cc_final: 0.7117 (mmt) REVERT: C 481 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8986 (mt) REVERT: E 1 MET cc_start: 0.7640 (mmt) cc_final: 0.6903 (mmt) REVERT: E 91 MET cc_start: 0.8733 (ppp) cc_final: 0.8405 (ppp) REVERT: E 381 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.6793 (t-90) REVERT: E 591 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6491 (tt) REVERT: E 669 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8384 (ptt90) REVERT: E 796 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6710 (t-90) REVERT: E 988 GLN cc_start: 0.5465 (pt0) cc_final: 0.4917 (tm-30) REVERT: A 171 ARG cc_start: 0.5520 (OUTLIER) cc_final: 0.4442 (ttp80) REVERT: F 579 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6350 (mp0) REVERT: F 699 MET cc_start: 0.8251 (mpp) cc_final: 0.7973 (mpp) REVERT: D 368 MET cc_start: 0.2427 (tpp) cc_final: 0.2011 (tpp) REVERT: D 439 CYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6896 (p) REVERT: D 458 PHE cc_start: 0.6831 (m-10) cc_final: 0.6477 (m-80) REVERT: D 611 MET cc_start: 0.8274 (mpp) cc_final: 0.7752 (mpp) REVERT: D 644 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8561 (t80) REVERT: D 822 GLN cc_start: 0.8651 (mt0) cc_final: 0.8274 (mp10) REVERT: D 827 MET cc_start: 0.7644 (ppp) cc_final: 0.7302 (ppp) REVERT: D 857 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.6952 (m-10) REVERT: D 1085 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: D 1140 LEU cc_start: 0.8659 (tp) cc_final: 0.8451 (tp) REVERT: D 1253 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7940 (m-80) outliers start: 209 outliers final: 146 residues processed: 471 average time/residue: 0.2427 time to fit residues: 195.3129 Evaluate side-chains 443 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 279 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 533 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 746 LYS Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 903 HIS Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1044 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 182 TRP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 902 ILE Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 1174 TYR Chi-restraints excluded: chain C residue 1198 PHE Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 PHE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 381 HIS Chi-restraints excluded: chain E residue 436 ASP Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 482 CYS Chi-restraints excluded: chain E residue 548 ILE Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 669 ARG Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 821 ILE Chi-restraints excluded: chain E residue 833 LEU Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 879 TYR Chi-restraints excluded: chain E residue 885 MET Chi-restraints excluded: chain E residue 916 VAL Chi-restraints excluded: chain E residue 927 CYS Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain E residue 974 LEU Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 579 GLU Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain F residue 702 VAL Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 788 ILE Chi-restraints excluded: chain F residue 789 SER Chi-restraints excluded: chain F residue 814 ARG Chi-restraints excluded: chain F residue 828 THR Chi-restraints excluded: chain F residue 833 GLU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 339 TRP Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 644 PHE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain D residue 857 TYR Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 907 ASP Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 957 THR Chi-restraints excluded: chain D residue 962 ILE Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 994 ASN Chi-restraints excluded: chain D residue 1008 SER Chi-restraints excluded: chain D residue 1029 GLU Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1085 GLU Chi-restraints excluded: chain D residue 1098 GLU Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1158 PHE Chi-restraints excluded: chain D residue 1189 LYS Chi-restraints excluded: chain D residue 1228 ARG Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1317 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1330 ILE Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 ILE Chi-restraints excluded: chain D residue 1431 PHE Chi-restraints excluded: chain D residue 1439 HIS Chi-restraints excluded: chain D residue 1467 LEU Chi-restraints excluded: chain D residue 1473 THR Chi-restraints excluded: chain D residue 1474 THR Chi-restraints excluded: chain D residue 1521 THR Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1557 SER Chi-restraints excluded: chain D residue 1561 ASN Chi-restraints excluded: chain D residue 1593 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 551 random chunks: chunk 384 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 486 optimal weight: 4.9990 chunk 478 optimal weight: 8.9990 chunk 509 optimal weight: 0.7980 chunk 291 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 124 optimal weight: 40.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 HIS ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 ASN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1151 GLN D 481 GLN D 492 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1621 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.099635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.074913 restraints weight = 180133.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.075930 restraints weight = 118116.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.077015 restraints weight = 79828.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.076093 restraints weight = 85273.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.076264 restraints weight = 68203.648| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 44248 Z= 0.130 Angle : 0.570 11.623 60006 Z= 0.288 Chirality : 0.042 0.237 6828 Planarity : 0.004 0.092 7739 Dihedral : 5.874 75.965 6126 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.74 % Allowed : 17.38 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.11), residues: 5485 helix: 0.31 (0.11), residues: 2157 sheet: -0.42 (0.16), residues: 1076 loop : -0.68 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 593 TYR 0.020 0.001 TYR D1109 PHE 0.022 0.001 PHE D 315 TRP 0.017 0.001 TRP B 353 HIS 0.006 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00282 (44232) covalent geometry : angle 0.56822 (59982) hydrogen bonds : bond 0.03690 ( 1975) hydrogen bonds : angle 4.93479 ( 5652) metal coordination : bond 0.00623 ( 16) metal coordination : angle 2.09464 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 312 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.5559 (ppp) REVERT: B 72 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.8845 (p) REVERT: B 211 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8748 (pm20) REVERT: B 241 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7436 (t0) REVERT: B 347 GLU cc_start: 0.7791 (pp20) cc_final: 0.7555 (pp20) REVERT: B 351 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7112 (tmm) REVERT: B 410 MET cc_start: 0.8286 (ppp) cc_final: 0.7623 (ppp) REVERT: B 416 ASP cc_start: 0.8596 (t0) cc_final: 0.8350 (t0) REVERT: B 450 MET cc_start: 0.8878 (mtm) cc_final: 0.8339 (mtm) REVERT: B 653 MET cc_start: 0.9053 (tpp) cc_final: 0.8823 (tpp) REVERT: B 1044 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7688 (mm) REVERT: C 182 TRP cc_start: 0.8073 (OUTLIER) cc_final: 0.7677 (m100) REVERT: C 266 TRP cc_start: 0.7397 (t-100) cc_final: 0.7000 (t-100) REVERT: C 441 MET cc_start: 0.7784 (mmt) cc_final: 0.7063 (mmt) REVERT: C 453 LEU cc_start: 0.6955 (mt) cc_final: 0.6706 (mm) REVERT: C 481 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8979 (mt) REVERT: C 716 MET cc_start: 0.7347 (pmm) cc_final: 0.6972 (pmm) REVERT: C 931 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: E 1 MET cc_start: 0.7550 (mmt) cc_final: 0.6954 (mmt) REVERT: E 91 MET cc_start: 0.8698 (ppp) cc_final: 0.8348 (ppp) REVERT: E 381 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.6737 (t-90) REVERT: E 417 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7188 (mmt) REVERT: E 591 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6340 (tt) REVERT: E 669 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8235 (ptt90) REVERT: E 796 HIS cc_start: 0.6977 (OUTLIER) cc_final: 0.6654 (t-90) REVERT: E 988 GLN cc_start: 0.5412 (pt0) cc_final: 0.4933 (tm-30) REVERT: D 368 MET cc_start: 0.2329 (tpp) cc_final: 0.1642 (tpp) REVERT: D 458 PHE cc_start: 0.6828 (m-10) cc_final: 0.6480 (m-80) REVERT: D 568 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.6992 (m-80) REVERT: D 606 MET cc_start: 0.4842 (tpt) cc_final: 0.4433 (mmm) REVERT: D 611 MET cc_start: 0.8212 (mpp) cc_final: 0.7666 (mpp) REVERT: D 644 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8583 (t80) REVERT: D 827 MET cc_start: 0.7733 (ppp) cc_final: 0.7381 (ppp) REVERT: D 857 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.6946 (m-10) REVERT: D 901 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6408 (mm) REVERT: D 1085 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7456 (tm-30) REVERT: D 1253 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: D 1354 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7383 (pt0) REVERT: D 1617 ARG cc_start: 0.8559 (tpm170) cc_final: 0.8090 (tpm170) outliers start: 175 outliers final: 118 residues processed: 457 average time/residue: 0.2540 time to fit residues: 197.6229 Evaluate side-chains 420 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 281 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 533 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 746 LYS Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 903 HIS Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1044 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 182 TRP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 902 ILE Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain C residue 931 GLU Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 1198 PHE Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1269 MET Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 PHE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 381 HIS Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 548 ILE Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 669 ARG Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 833 LEU Chi-restraints excluded: chain E residue 879 TYR Chi-restraints excluded: chain E residue 885 MET Chi-restraints excluded: chain E residue 916 VAL Chi-restraints excluded: chain E residue 974 LEU Chi-restraints excluded: chain E residue 990 HIS Chi-restraints excluded: chain E residue 1234 GLU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 678 TRP Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain F residue 788 ILE Chi-restraints excluded: chain F residue 789 SER Chi-restraints excluded: chain F residue 797 GLU Chi-restraints excluded: chain F residue 814 ARG Chi-restraints excluded: chain F residue 828 THR Chi-restraints excluded: chain F residue 833 GLU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 339 TRP Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 568 TYR Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 644 PHE Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 857 TYR Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 994 ASN Chi-restraints excluded: chain D residue 1029 GLU Chi-restraints excluded: chain D residue 1085 GLU Chi-restraints excluded: chain D residue 1098 GLU Chi-restraints excluded: chain D residue 1158 PHE Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1317 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 ILE Chi-restraints excluded: chain D residue 1439 HIS Chi-restraints excluded: chain D residue 1467 LEU Chi-restraints excluded: chain D residue 1473 THR Chi-restraints excluded: chain D residue 1474 THR Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1557 SER Chi-restraints excluded: chain D residue 1593 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 551 random chunks: chunk 495 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 419 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 436 optimal weight: 0.0060 chunk 518 optimal weight: 4.9990 chunk 500 optimal weight: 0.0370 chunk 483 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 overall best weight: 2.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 HIS ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1151 GLN D 492 GLN D 803 HIS ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.097742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.073644 restraints weight = 181880.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.074085 restraints weight = 114195.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.074893 restraints weight = 78790.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.074698 restraints weight = 74436.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.074974 restraints weight = 67907.608| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 44248 Z= 0.201 Angle : 0.619 12.876 60006 Z= 0.316 Chirality : 0.043 0.310 6828 Planarity : 0.004 0.094 7739 Dihedral : 5.966 79.089 6122 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.51 % Allowed : 17.30 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.11), residues: 5485 helix: 0.25 (0.11), residues: 2161 sheet: -0.52 (0.16), residues: 1090 loop : -0.69 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 593 TYR 0.022 0.002 TYR D1109 PHE 0.022 0.002 PHE D 315 TRP 0.013 0.001 TRP B 353 HIS 0.009 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00428 (44232) covalent geometry : angle 0.61684 (59982) hydrogen bonds : bond 0.03885 ( 1975) hydrogen bonds : angle 5.06862 ( 5652) metal coordination : bond 0.00967 ( 16) metal coordination : angle 2.56773 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 292 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.5753 (ppp) REVERT: B 72 THR cc_start: 0.9357 (OUTLIER) cc_final: 0.8970 (p) REVERT: B 211 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8783 (pm20) REVERT: B 241 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7476 (t0) REVERT: B 351 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7143 (tmm) REVERT: B 410 MET cc_start: 0.8194 (ppp) cc_final: 0.7514 (ppp) REVERT: B 428 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7671 (pt0) REVERT: B 450 MET cc_start: 0.8922 (mtm) cc_final: 0.8425 (mtm) REVERT: B 653 MET cc_start: 0.9053 (tpp) cc_final: 0.8823 (tpp) REVERT: B 1044 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7643 (mm) REVERT: C 182 TRP cc_start: 0.7895 (OUTLIER) cc_final: 0.7441 (m100) REVERT: C 266 TRP cc_start: 0.7306 (t-100) cc_final: 0.6921 (t-100) REVERT: C 441 MET cc_start: 0.8074 (mmt) cc_final: 0.7217 (mmt) REVERT: C 481 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8979 (mt) REVERT: C 777 MET cc_start: 0.9146 (tmm) cc_final: 0.8930 (tmm) REVERT: C 1018 MET cc_start: 0.8343 (tpp) cc_final: 0.8058 (tpp) REVERT: C 1184 THR cc_start: 0.7562 (m) cc_final: 0.7200 (p) REVERT: E 1 MET cc_start: 0.7647 (mmt) cc_final: 0.6955 (mmt) REVERT: E 91 MET cc_start: 0.8736 (ppp) cc_final: 0.8397 (ppp) REVERT: E 381 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.6904 (t-90) REVERT: E 417 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7366 (mmt) REVERT: E 591 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6350 (tt) REVERT: E 669 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8206 (ptt90) REVERT: E 796 HIS cc_start: 0.7104 (OUTLIER) cc_final: 0.6690 (t-90) REVERT: E 988 GLN cc_start: 0.5641 (pt0) cc_final: 0.5111 (tm-30) REVERT: A 189 GLU cc_start: 0.6425 (pp20) cc_final: 0.6201 (pp20) REVERT: F 579 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: F 699 MET cc_start: 0.8221 (mpp) cc_final: 0.7994 (mpp) REVERT: D 439 CYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7085 (p) REVERT: D 458 PHE cc_start: 0.6856 (m-10) cc_final: 0.6530 (m-80) REVERT: D 531 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8969 (mm) REVERT: D 568 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: D 575 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7248 (mp0) REVERT: D 606 MET cc_start: 0.5135 (tpt) cc_final: 0.4925 (tpt) REVERT: D 611 MET cc_start: 0.8389 (mpp) cc_final: 0.7841 (mpp) REVERT: D 644 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8521 (t80) REVERT: D 827 MET cc_start: 0.7595 (ppp) cc_final: 0.7312 (ppp) REVERT: D 857 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7028 (m-10) REVERT: D 901 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6389 (mm) REVERT: D 1085 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: D 1253 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7827 (m-80) REVERT: D 1617 ARG cc_start: 0.8572 (tpm170) cc_final: 0.8084 (tpm170) outliers start: 211 outliers final: 148 residues processed: 471 average time/residue: 0.2449 time to fit residues: 196.5056 Evaluate side-chains 450 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 279 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 533 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 687 PHE Chi-restraints excluded: chain B residue 746 LYS Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 903 HIS Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1044 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1055 PHE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 182 TRP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 760 TYR Chi-restraints excluded: chain C residue 767 MET Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 1174 TYR Chi-restraints excluded: chain C residue 1198 PHE Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 PHE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 349 GLN Chi-restraints excluded: chain E residue 381 HIS Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain E residue 436 ASP Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 548 ILE Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 669 ARG Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 821 ILE Chi-restraints excluded: chain E residue 833 LEU Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 879 TYR Chi-restraints excluded: chain E residue 904 LEU Chi-restraints excluded: chain E residue 916 VAL Chi-restraints excluded: chain E residue 927 CYS Chi-restraints excluded: chain E residue 974 LEU Chi-restraints excluded: chain E residue 990 HIS Chi-restraints excluded: chain E residue 1234 GLU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 361 PHE Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 579 GLU Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 648 THR Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 788 ILE Chi-restraints excluded: chain F residue 789 SER Chi-restraints excluded: chain F residue 797 GLU Chi-restraints excluded: chain F residue 814 ARG Chi-restraints excluded: chain F residue 828 THR Chi-restraints excluded: chain F residue 833 GLU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 339 TRP Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 568 TYR Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 644 PHE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain D residue 857 TYR Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 895 LEU Chi-restraints excluded: chain D residue 897 THR Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 957 THR Chi-restraints excluded: chain D residue 962 ILE Chi-restraints excluded: chain D residue 994 ASN Chi-restraints excluded: chain D residue 1029 GLU Chi-restraints excluded: chain D residue 1085 GLU Chi-restraints excluded: chain D residue 1098 GLU Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1161 LEU Chi-restraints excluded: chain D residue 1189 LYS Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1228 ARG Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1317 LEU Chi-restraints excluded: chain D residue 1319 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 ILE Chi-restraints excluded: chain D residue 1431 PHE Chi-restraints excluded: chain D residue 1439 HIS Chi-restraints excluded: chain D residue 1467 LEU Chi-restraints excluded: chain D residue 1473 THR Chi-restraints excluded: chain D residue 1474 THR Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1557 SER Chi-restraints excluded: chain D residue 1561 ASN Chi-restraints excluded: chain D residue 1593 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 551 random chunks: chunk 262 optimal weight: 0.7980 chunk 216 optimal weight: 4.9990 chunk 507 optimal weight: 0.6980 chunk 305 optimal weight: 0.9980 chunk 278 optimal weight: 9.9990 chunk 385 optimal weight: 4.9990 chunk 125 optimal weight: 0.0270 chunk 107 optimal weight: 20.0000 chunk 208 optimal weight: 0.0870 chunk 147 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 420 HIS ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1151 GLN D 308 GLN D 492 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.100550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.076597 restraints weight = 185767.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.078513 restraints weight = 111121.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.078523 restraints weight = 69584.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.078623 restraints weight = 58726.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.078343 restraints weight = 55192.960| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 44248 Z= 0.107 Angle : 0.581 12.071 60006 Z= 0.289 Chirality : 0.042 0.226 6828 Planarity : 0.004 0.088 7739 Dihedral : 5.699 72.790 6120 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.51 % Allowed : 18.49 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.11), residues: 5485 helix: 0.45 (0.11), residues: 2165 sheet: -0.33 (0.16), residues: 1079 loop : -0.63 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 593 TYR 0.021 0.001 TYR D1109 PHE 0.022 0.001 PHE D 315 TRP 0.022 0.001 TRP D1560 HIS 0.005 0.001 HIS B 672 Details of bonding type rmsd covalent geometry : bond 0.00234 (44232) covalent geometry : angle 0.57968 (59982) hydrogen bonds : bond 0.03453 ( 1975) hydrogen bonds : angle 4.77067 ( 5652) metal coordination : bond 0.00425 ( 16) metal coordination : angle 1.99537 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 305 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.5606 (ppp) REVERT: B 211 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8761 (pm20) REVERT: B 351 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7116 (tmm) REVERT: B 410 MET cc_start: 0.8213 (ppp) cc_final: 0.7541 (ppp) REVERT: B 450 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8342 (mtm) REVERT: B 653 MET cc_start: 0.9048 (tpp) cc_final: 0.8817 (tpp) REVERT: B 1044 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7724 (mm) REVERT: C 182 TRP cc_start: 0.8056 (OUTLIER) cc_final: 0.7672 (m100) REVERT: C 266 TRP cc_start: 0.7394 (t-100) cc_final: 0.7061 (t-100) REVERT: C 441 MET cc_start: 0.7854 (mmt) cc_final: 0.7059 (mmt) REVERT: C 556 MET cc_start: 0.8459 (ppp) cc_final: 0.8139 (ppp) REVERT: C 716 MET cc_start: 0.7454 (pmm) cc_final: 0.7023 (pmm) REVERT: C 878 MET cc_start: 0.5496 (mmt) cc_final: 0.5221 (mmt) REVERT: C 1018 MET cc_start: 0.8344 (tpp) cc_final: 0.8023 (tpp) REVERT: E 1 MET cc_start: 0.7658 (mmt) cc_final: 0.7145 (mmt) REVERT: E 91 MET cc_start: 0.8740 (ppp) cc_final: 0.8427 (ppp) REVERT: E 274 MET cc_start: 0.7962 (mmm) cc_final: 0.7703 (mmm) REVERT: E 366 MET cc_start: 0.7981 (mpp) cc_final: 0.7752 (mpp) REVERT: E 417 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7289 (mmt) REVERT: E 573 MET cc_start: 0.6642 (ptp) cc_final: 0.6121 (ptp) REVERT: E 591 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6287 (tt) REVERT: E 669 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8038 (ptt90) REVERT: E 796 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.6685 (t-90) REVERT: E 885 MET cc_start: 0.7356 (ptp) cc_final: 0.6939 (pmm) REVERT: E 988 GLN cc_start: 0.5654 (pt0) cc_final: 0.5320 (tm-30) REVERT: A 189 GLU cc_start: 0.6640 (pp20) cc_final: 0.6439 (pp20) REVERT: D 439 CYS cc_start: 0.7356 (OUTLIER) cc_final: 0.7049 (p) REVERT: D 458 PHE cc_start: 0.6786 (m-10) cc_final: 0.6431 (m-80) REVERT: D 568 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: D 611 MET cc_start: 0.8185 (mpp) cc_final: 0.7685 (mpp) REVERT: D 644 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8430 (t80) REVERT: D 733 TYR cc_start: 0.7050 (t80) cc_final: 0.6560 (m-80) REVERT: D 751 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7596 (pt0) REVERT: D 827 MET cc_start: 0.7655 (ppp) cc_final: 0.7409 (ppp) REVERT: D 857 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.6988 (m-10) REVERT: D 901 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6417 (mm) REVERT: D 1085 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: D 1228 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8182 (ptm160) REVERT: D 1253 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: D 1354 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7666 (pt0) REVERT: D 1475 LYS cc_start: 0.4261 (mttt) cc_final: 0.4010 (ttmt) REVERT: D 1617 ARG cc_start: 0.8522 (tpm170) cc_final: 0.8018 (tpm170) outliers start: 164 outliers final: 113 residues processed: 446 average time/residue: 0.2406 time to fit residues: 182.7462 Evaluate side-chains 412 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 279 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 746 LYS Chi-restraints excluded: chain B residue 903 HIS Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1044 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1055 PHE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1230 ARG Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 182 TRP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 760 TYR Chi-restraints excluded: chain C residue 902 ILE Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 1198 PHE Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1269 MET Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 PHE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 381 HIS Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain E residue 436 ASP Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 548 ILE Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 669 ARG Chi-restraints excluded: chain E residue 670 ILE Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 879 TYR Chi-restraints excluded: chain E residue 916 VAL Chi-restraints excluded: chain E residue 927 CYS Chi-restraints excluded: chain E residue 974 LEU Chi-restraints excluded: chain E residue 1234 GLU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 361 PHE Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 678 TRP Chi-restraints excluded: chain F residue 788 ILE Chi-restraints excluded: chain F residue 814 ARG Chi-restraints excluded: chain F residue 828 THR Chi-restraints excluded: chain F residue 833 GLU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 339 TRP Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 568 TYR Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 644 PHE Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 751 GLU Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain D residue 857 TYR Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 957 THR Chi-restraints excluded: chain D residue 994 ASN Chi-restraints excluded: chain D residue 1029 GLU Chi-restraints excluded: chain D residue 1085 GLU Chi-restraints excluded: chain D residue 1098 GLU Chi-restraints excluded: chain D residue 1158 PHE Chi-restraints excluded: chain D residue 1189 LYS Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1228 ARG Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1317 LEU Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 ILE Chi-restraints excluded: chain D residue 1431 PHE Chi-restraints excluded: chain D residue 1439 HIS Chi-restraints excluded: chain D residue 1467 LEU Chi-restraints excluded: chain D residue 1473 THR Chi-restraints excluded: chain D residue 1521 THR Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1593 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 551 random chunks: chunk 332 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 401 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 379 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 257 optimal weight: 0.2980 chunk 45 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1151 GLN D 422 GLN D 492 GLN D 636 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.098961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.074552 restraints weight = 181741.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.074158 restraints weight = 117127.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 75)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.073581 restraints weight = 87824.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.074057 restraints weight = 68841.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.074259 restraints weight = 58958.931| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 44248 Z= 0.159 Angle : 0.607 13.975 60006 Z= 0.304 Chirality : 0.043 0.268 6828 Planarity : 0.004 0.089 7739 Dihedral : 5.690 74.875 6113 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.51 % Allowed : 18.77 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.11), residues: 5485 helix: 0.40 (0.11), residues: 2164 sheet: -0.37 (0.16), residues: 1084 loop : -0.63 (0.13), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 636 TYR 0.018 0.001 TYR D 733 PHE 0.022 0.001 PHE D 315 TRP 0.058 0.001 TRP B 353 HIS 0.007 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00345 (44232) covalent geometry : angle 0.60542 (59982) hydrogen bonds : bond 0.03592 ( 1975) hydrogen bonds : angle 4.84934 ( 5652) metal coordination : bond 0.00756 ( 16) metal coordination : angle 2.42031 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 284 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.5731 (ppp) REVERT: B 72 THR cc_start: 0.9341 (OUTLIER) cc_final: 0.8991 (p) REVERT: B 211 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8738 (pm20) REVERT: B 351 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7115 (tmm) REVERT: B 410 MET cc_start: 0.8157 (ppp) cc_final: 0.7441 (ppp) REVERT: B 450 MET cc_start: 0.8928 (mtm) cc_final: 0.8545 (mtm) REVERT: B 653 MET cc_start: 0.9027 (tpp) cc_final: 0.8796 (tpp) REVERT: B 1044 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7652 (mm) REVERT: C 182 TRP cc_start: 0.8093 (OUTLIER) cc_final: 0.7746 (m100) REVERT: C 266 TRP cc_start: 0.7371 (t-100) cc_final: 0.7045 (t-100) REVERT: C 441 MET cc_start: 0.8030 (mmt) cc_final: 0.7177 (mmt) REVERT: C 556 MET cc_start: 0.8491 (ppp) cc_final: 0.8164 (ppp) REVERT: C 716 MET cc_start: 0.7697 (pmm) cc_final: 0.7299 (pmm) REVERT: E 1 MET cc_start: 0.7613 (mmt) cc_final: 0.6963 (mmt) REVERT: E 91 MET cc_start: 0.8758 (ppp) cc_final: 0.8455 (ppp) REVERT: E 381 HIS cc_start: 0.7596 (OUTLIER) cc_final: 0.6891 (t-90) REVERT: E 417 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7188 (mmt) REVERT: E 554 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8638 (tp-100) REVERT: E 591 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6398 (tt) REVERT: E 669 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8175 (ptt90) REVERT: E 796 HIS cc_start: 0.7083 (OUTLIER) cc_final: 0.6707 (t-90) REVERT: E 988 GLN cc_start: 0.5594 (pt0) cc_final: 0.5170 (tm-30) REVERT: A 170 MET cc_start: 0.7274 (pmm) cc_final: 0.6937 (pmm) REVERT: D 380 ARG cc_start: 0.9086 (mmt90) cc_final: 0.8856 (mtm-85) REVERT: D 439 CYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7073 (p) REVERT: D 458 PHE cc_start: 0.6876 (m-10) cc_final: 0.6503 (m-80) REVERT: D 568 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.6814 (m-80) REVERT: D 575 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7212 (mp0) REVERT: D 606 MET cc_start: 0.4773 (tpt) cc_final: 0.4564 (mmt) REVERT: D 611 MET cc_start: 0.8213 (mpp) cc_final: 0.7721 (mpp) REVERT: D 644 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8499 (t80) REVERT: D 751 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7575 (pt0) REVERT: D 857 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.6892 (m-10) REVERT: D 901 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6408 (mm) REVERT: D 1085 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: D 1253 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7796 (m-80) REVERT: D 1354 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7410 (pt0) outliers start: 164 outliers final: 124 residues processed: 425 average time/residue: 0.2279 time to fit residues: 166.8187 Evaluate side-chains 422 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 277 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 533 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 746 LYS Chi-restraints excluded: chain B residue 903 HIS Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1044 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1055 PHE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1225 VAL Chi-restraints excluded: chain B residue 1230 ARG Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 182 TRP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 760 TYR Chi-restraints excluded: chain C residue 902 ILE Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain C residue 1198 PHE Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 PHE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 349 GLN Chi-restraints excluded: chain E residue 381 HIS Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain E residue 436 ASP Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 548 ILE Chi-restraints excluded: chain E residue 554 GLN Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 669 ARG Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 879 TYR Chi-restraints excluded: chain E residue 916 VAL Chi-restraints excluded: chain E residue 927 CYS Chi-restraints excluded: chain E residue 974 LEU Chi-restraints excluded: chain E residue 990 HIS Chi-restraints excluded: chain E residue 1234 GLU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 361 PHE Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 788 ILE Chi-restraints excluded: chain F residue 797 GLU Chi-restraints excluded: chain F residue 814 ARG Chi-restraints excluded: chain F residue 828 THR Chi-restraints excluded: chain F residue 833 GLU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 339 TRP Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 422 GLN Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 568 TYR Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 644 PHE Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 751 GLU Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain D residue 857 TYR Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 957 THR Chi-restraints excluded: chain D residue 994 ASN Chi-restraints excluded: chain D residue 1029 GLU Chi-restraints excluded: chain D residue 1085 GLU Chi-restraints excluded: chain D residue 1098 GLU Chi-restraints excluded: chain D residue 1158 PHE Chi-restraints excluded: chain D residue 1189 LYS Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1228 ARG Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1317 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 ILE Chi-restraints excluded: chain D residue 1431 PHE Chi-restraints excluded: chain D residue 1439 HIS Chi-restraints excluded: chain D residue 1467 LEU Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1561 ASN Chi-restraints excluded: chain D residue 1593 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 551 random chunks: chunk 247 optimal weight: 5.9990 chunk 493 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 267 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 461 optimal weight: 2.9990 chunk 330 optimal weight: 5.9990 chunk 462 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 HIS ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 674 ASN F 726 HIS D 308 GLN D 492 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.096801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.073273 restraints weight = 184832.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.073609 restraints weight = 116666.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.074068 restraints weight = 80716.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.074146 restraints weight = 79091.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.073906 restraints weight = 74442.315| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 44248 Z= 0.239 Angle : 0.680 11.614 60006 Z= 0.347 Chirality : 0.045 0.262 6828 Planarity : 0.004 0.091 7739 Dihedral : 6.006 81.560 6112 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.68 % Allowed : 18.69 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.11), residues: 5485 helix: 0.12 (0.11), residues: 2160 sheet: -0.58 (0.16), residues: 1083 loop : -0.71 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 593 TYR 0.021 0.002 TYR D 733 PHE 0.026 0.002 PHE F 583 TRP 0.051 0.002 TRP B 353 HIS 0.009 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00505 (44232) covalent geometry : angle 0.67756 (59982) hydrogen bonds : bond 0.04047 ( 1975) hydrogen bonds : angle 5.15392 ( 5652) metal coordination : bond 0.01108 ( 16) metal coordination : angle 2.87886 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 287 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 THR cc_start: 0.9338 (OUTLIER) cc_final: 0.8928 (p) REVERT: B 211 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8887 (pm20) REVERT: B 351 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7023 (tmm) REVERT: B 410 MET cc_start: 0.8329 (ppp) cc_final: 0.7543 (ppp) REVERT: B 450 MET cc_start: 0.9011 (mtm) cc_final: 0.8596 (mtm) REVERT: B 653 MET cc_start: 0.9058 (tpp) cc_final: 0.8822 (tpp) REVERT: B 1044 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7653 (mm) REVERT: C 182 TRP cc_start: 0.7926 (OUTLIER) cc_final: 0.7541 (m100) REVERT: C 441 MET cc_start: 0.8120 (mmt) cc_final: 0.7235 (mmt) REVERT: C 481 LEU cc_start: 0.9225 (tt) cc_final: 0.8945 (mt) REVERT: C 931 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: C 1018 MET cc_start: 0.8427 (tpp) cc_final: 0.8044 (tpp) REVERT: C 1184 THR cc_start: 0.7781 (m) cc_final: 0.7404 (p) REVERT: E 1 MET cc_start: 0.7717 (mmt) cc_final: 0.6985 (mmt) REVERT: E 91 MET cc_start: 0.8800 (ppp) cc_final: 0.8476 (ppp) REVERT: E 274 MET cc_start: 0.8012 (mmm) cc_final: 0.7754 (mmm) REVERT: E 381 HIS cc_start: 0.7771 (OUTLIER) cc_final: 0.7228 (t-90) REVERT: E 417 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7311 (mmt) REVERT: E 554 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8823 (tp-100) REVERT: E 591 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6280 (tt) REVERT: E 669 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8279 (ptt90) REVERT: E 796 HIS cc_start: 0.7207 (OUTLIER) cc_final: 0.6692 (t-90) REVERT: E 988 GLN cc_start: 0.5891 (pt0) cc_final: 0.5282 (tm-30) REVERT: F 699 MET cc_start: 0.8234 (mpp) cc_final: 0.7890 (mpp) REVERT: D 439 CYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7210 (p) REVERT: D 458 PHE cc_start: 0.6933 (m-10) cc_final: 0.6585 (m-80) REVERT: D 492 GLN cc_start: 0.9133 (pt0) cc_final: 0.8822 (pp30) REVERT: D 568 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.6831 (m-80) REVERT: D 570 MET cc_start: 0.7277 (pmm) cc_final: 0.7043 (pmm) REVERT: D 575 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7374 (mp0) REVERT: D 611 MET cc_start: 0.8358 (mpp) cc_final: 0.7862 (mpp) REVERT: D 644 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8548 (t80) REVERT: D 827 MET cc_start: 0.7775 (ppp) cc_final: 0.7495 (ptm) REVERT: D 857 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7077 (m-10) REVERT: D 901 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6308 (mm) REVERT: D 1085 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: D 1253 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7905 (m-80) outliers start: 172 outliers final: 136 residues processed: 435 average time/residue: 0.2078 time to fit residues: 154.0757 Evaluate side-chains 431 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 276 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 533 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 687 PHE Chi-restraints excluded: chain B residue 746 LYS Chi-restraints excluded: chain B residue 903 HIS Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1044 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1055 PHE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1230 ARG Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 182 TRP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 760 TYR Chi-restraints excluded: chain C residue 902 ILE Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain C residue 931 GLU Chi-restraints excluded: chain C residue 1198 PHE Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 PHE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 349 GLN Chi-restraints excluded: chain E residue 381 HIS Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 436 ASP Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 548 ILE Chi-restraints excluded: chain E residue 554 GLN Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 669 ARG Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 916 VAL Chi-restraints excluded: chain E residue 927 CYS Chi-restraints excluded: chain E residue 974 LEU Chi-restraints excluded: chain E residue 990 HIS Chi-restraints excluded: chain E residue 1234 GLU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 361 PHE Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 788 ILE Chi-restraints excluded: chain F residue 797 GLU Chi-restraints excluded: chain F residue 814 ARG Chi-restraints excluded: chain F residue 828 THR Chi-restraints excluded: chain F residue 833 GLU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 339 TRP Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 568 TYR Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 644 PHE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain D residue 857 TYR Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 957 THR Chi-restraints excluded: chain D residue 994 ASN Chi-restraints excluded: chain D residue 1029 GLU Chi-restraints excluded: chain D residue 1085 GLU Chi-restraints excluded: chain D residue 1098 GLU Chi-restraints excluded: chain D residue 1189 LYS Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1228 ARG Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1317 LEU Chi-restraints excluded: chain D residue 1319 LEU Chi-restraints excluded: chain D residue 1327 GLU Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 ILE Chi-restraints excluded: chain D residue 1431 PHE Chi-restraints excluded: chain D residue 1439 HIS Chi-restraints excluded: chain D residue 1467 LEU Chi-restraints excluded: chain D residue 1473 THR Chi-restraints excluded: chain D residue 1521 THR Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1557 SER Chi-restraints excluded: chain D residue 1561 ASN Chi-restraints excluded: chain D residue 1593 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 551 random chunks: chunk 540 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.0040 chunk 258 optimal weight: 7.9990 chunk 349 optimal weight: 20.0000 chunk 430 optimal weight: 30.0000 chunk 395 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 426 optimal weight: 20.0000 chunk 528 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN D 422 GLN ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN D 848 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.099561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.076141 restraints weight = 186509.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.077201 restraints weight = 121896.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.077180 restraints weight = 81621.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.076916 restraints weight = 80591.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.077019 restraints weight = 70590.766| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 44248 Z= 0.121 Angle : 0.633 12.485 60006 Z= 0.313 Chirality : 0.043 0.302 6828 Planarity : 0.004 0.089 7739 Dihedral : 5.770 75.426 6112 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.14 % Allowed : 19.39 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.11), residues: 5485 helix: 0.34 (0.11), residues: 2159 sheet: -0.42 (0.16), residues: 1073 loop : -0.65 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 593 TYR 0.015 0.001 TYR D 733 PHE 0.036 0.001 PHE B 945 TRP 0.044 0.001 TRP B 353 HIS 0.013 0.001 HIS E 63 Details of bonding type rmsd covalent geometry : bond 0.00265 (44232) covalent geometry : angle 0.63107 (59982) hydrogen bonds : bond 0.03562 ( 1975) hydrogen bonds : angle 4.88286 ( 5652) metal coordination : bond 0.00494 ( 16) metal coordination : angle 2.22291 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 289 time to evaluate : 1.481 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: B 1 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.6154 (ppp) REVERT: B 72 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.8898 (p) REVERT: B 211 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8687 (pm20) REVERT: B 351 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7107 (tmm) REVERT: B 410 MET cc_start: 0.8201 (ppp) cc_final: 0.7405 (ppp) REVERT: B 450 MET cc_start: 0.8911 (mtm) cc_final: 0.8506 (mtm) REVERT: B 653 MET cc_start: 0.9044 (tpp) cc_final: 0.8812 (tpp) REVERT: C 182 TRP cc_start: 0.7993 (OUTLIER) cc_final: 0.7629 (m100) REVERT: C 266 TRP cc_start: 0.7378 (t-100) cc_final: 0.7068 (t-100) REVERT: C 441 MET cc_start: 0.8044 (mmt) cc_final: 0.7187 (mmt) REVERT: C 481 LEU cc_start: 0.9210 (tt) cc_final: 0.8936 (mt) REVERT: E 1 MET cc_start: 0.7633 (mmt) cc_final: 0.7143 (mmt) REVERT: E 91 MET cc_start: 0.8734 (ppp) cc_final: 0.8418 (ppp) REVERT: E 274 MET cc_start: 0.8067 (mmm) cc_final: 0.7819 (mmm) REVERT: E 381 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.7211 (t-90) REVERT: E 554 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8849 (tp-100) REVERT: E 591 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6197 (tt) REVERT: E 669 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8090 (ptt90) REVERT: E 796 HIS cc_start: 0.7070 (OUTLIER) cc_final: 0.6671 (t-90) REVERT: E 988 GLN cc_start: 0.5736 (pt0) cc_final: 0.5420 (tm-30) REVERT: F 699 MET cc_start: 0.8099 (mpp) cc_final: 0.7809 (mpp) REVERT: D 380 ARG cc_start: 0.9082 (mmt90) cc_final: 0.8876 (mtm-85) REVERT: D 439 CYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7185 (p) REVERT: D 458 PHE cc_start: 0.6804 (m-10) cc_final: 0.6438 (m-80) REVERT: D 492 GLN cc_start: 0.9078 (pt0) cc_final: 0.8836 (pp30) REVERT: D 568 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.6549 (m-80) REVERT: D 575 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7154 (mp0) REVERT: D 644 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8467 (t80) REVERT: D 733 TYR cc_start: 0.7307 (t80) cc_final: 0.6741 (m-80) REVERT: D 751 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7620 (pt0) REVERT: D 822 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8288 (pp30) REVERT: D 827 MET cc_start: 0.7687 (ppp) cc_final: 0.7387 (ptm) REVERT: D 857 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.6996 (m-10) REVERT: D 901 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6317 (mm) REVERT: D 1085 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7431 (tm-30) REVERT: D 1253 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7697 (m-80) REVERT: D 1354 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7311 (pt0) REVERT: D 1479 MET cc_start: 0.3180 (mmt) cc_final: 0.2835 (mmt) outliers start: 147 outliers final: 115 residues processed: 414 average time/residue: 0.1947 time to fit residues: 138.8325 Evaluate side-chains 415 residues out of total 4677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 280 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 746 LYS Chi-restraints excluded: chain B residue 903 HIS Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 999 PHE Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1055 PHE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1230 ARG Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 182 TRP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 760 TYR Chi-restraints excluded: chain C residue 902 ILE Chi-restraints excluded: chain C residue 908 TYR Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain C residue 1198 PHE Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 PHE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 381 HIS Chi-restraints excluded: chain E residue 436 ASP Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 554 GLN Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 669 ARG Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 916 VAL Chi-restraints excluded: chain E residue 927 CYS Chi-restraints excluded: chain E residue 974 LEU Chi-restraints excluded: chain E residue 1234 GLU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 361 PHE Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 674 ASN Chi-restraints excluded: chain F residue 788 ILE Chi-restraints excluded: chain F residue 797 GLU Chi-restraints excluded: chain F residue 814 ARG Chi-restraints excluded: chain F residue 828 THR Chi-restraints excluded: chain F residue 833 GLU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 339 TRP Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 568 TYR Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 644 PHE Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 751 GLU Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain D residue 857 TYR Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 957 THR Chi-restraints excluded: chain D residue 994 ASN Chi-restraints excluded: chain D residue 1029 GLU Chi-restraints excluded: chain D residue 1085 GLU Chi-restraints excluded: chain D residue 1098 GLU Chi-restraints excluded: chain D residue 1189 LYS Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1228 ARG Chi-restraints excluded: chain D residue 1243 THR Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1317 LEU Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 ILE Chi-restraints excluded: chain D residue 1431 PHE Chi-restraints excluded: chain D residue 1439 HIS Chi-restraints excluded: chain D residue 1467 LEU Chi-restraints excluded: chain D residue 1473 THR Chi-restraints excluded: chain D residue 1539 LEU Chi-restraints excluded: chain D residue 1593 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 551 random chunks: chunk 346 optimal weight: 0.9980 chunk 303 optimal weight: 4.9990 chunk 426 optimal weight: 2.9990 chunk 408 optimal weight: 5.9990 chunk 466 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 306 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 530 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 GLN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN D 822 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.098123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.074455 restraints weight = 180480.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.072557 restraints weight = 116569.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.073438 restraints weight = 81672.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.073678 restraints weight = 61836.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.073678 restraints weight = 53558.852| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 44248 Z= 0.174 Angle : 0.650 11.453 60006 Z= 0.326 Chirality : 0.043 0.295 6828 Planarity : 0.004 0.090 7739 Dihedral : 5.737 76.746 6108 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.36 % Allowed : 19.37 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.11), residues: 5485 helix: 0.29 (0.11), residues: 2157 sheet: -0.49 (0.16), residues: 1096 loop : -0.65 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG D 348 TYR 0.021 0.001 TYR F 809 PHE 0.026 0.001 PHE B 945 TRP 0.043 0.001 TRP B 353 HIS 0.007 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00378 (44232) covalent geometry : angle 0.64832 (59982) hydrogen bonds : bond 0.03673 ( 1975) hydrogen bonds : angle 4.95394 ( 5652) metal coordination : bond 0.00808 ( 16) metal coordination : angle 2.62571 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13739.45 seconds wall clock time: 234 minutes 58.83 seconds (14098.83 seconds total)