Starting phenix.real_space_refine on Wed Aug 27 00:01:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fgw_29073/08_2025/8fgw_29073.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fgw_29073/08_2025/8fgw_29073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fgw_29073/08_2025/8fgw_29073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fgw_29073/08_2025/8fgw_29073.map" model { file = "/net/cci-nas-00/data/ceres_data/8fgw_29073/08_2025/8fgw_29073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fgw_29073/08_2025/8fgw_29073.cif" } resolution = 3.7 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= 0.026 sd= 0.073 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 5 6.06 5 S 289 5.16 5 C 27710 2.51 5 N 7456 2.21 5 O 8067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43527 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8435 Classifications: {'peptide': 1081} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 32, 'TRANS': 1048} Chain breaks: 8 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 13, 'ARG:plan': 2, 'ASP:plan': 5, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 102 Chain: "B" Number of atoms: 8941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 8941 Classifications: {'peptide': 1152} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 39, 'TRANS': 1112} Chain breaks: 3 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 21, 'ASP:plan': 12, 'TYR:plan': 2, 'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 9, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 217 Chain: "C" Number of atoms: 10313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1342, 10313 Classifications: {'peptide': 1342} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1297} Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 421 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 7, 'GLU:plan': 11, 'PHE:plan': 5, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 2, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 223 Chain: "D" Number of atoms: 10502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1315, 10502 Classifications: {'peptide': 1315} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 38, 'TRANS': 1276} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 52 Chain: "E" Number of atoms: 4790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4790 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 587} Chain breaks: 11 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "F" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 69} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8245 SG CYS A1155 93.047 101.985 122.578 1.00 82.75 S ATOM 8264 SG CYS A1158 91.002 102.361 119.311 1.00 83.26 S ATOM 8379 SG CYS A1173 92.949 105.114 120.659 1.00 70.96 S ATOM 8400 SG CYS A1176 89.935 103.821 122.853 1.00 65.91 S ATOM 16332 SG CYS B1057 47.874 21.462 299.725 1.00 24.96 S ATOM 16361 SG CYS B1060 49.408 18.284 301.141 1.00 28.83 S ATOM 16462 SG CYS B1074 51.001 21.743 301.698 1.00 33.58 S ATOM 16484 SG CYS B1077 51.125 20.016 298.305 1.00 41.59 S ATOM 17147 SG CYS B1207 39.119 40.365 283.020 1.00 14.60 S ATOM 17166 SG CYS B1210 42.919 39.922 284.509 1.00 16.98 S ATOM 17318 SG CYS B1229 39.952 42.118 285.933 1.00 18.52 S ATOM 17343 SG CYS B1232 42.100 42.522 282.499 1.00 19.41 S ATOM 27303 SG CYS C1292 89.341 60.526 206.787 1.00 55.06 S ATOM 27326 SG CYS C1295 89.304 64.230 205.954 1.00 49.54 S ATOM 27476 SG CYS C1314 89.152 61.535 203.159 1.00 45.94 S ATOM 27497 SG CYS C1317 92.298 62.150 204.899 1.00 43.85 S ATOM 26997 SG CYS C1253 69.117 72.501 206.186 1.00 33.64 S ATOM 27021 SG CYS C1256 65.682 74.125 207.176 1.00 36.51 S ATOM 27110 SG CYS C1267 67.445 75.312 204.243 1.00 31.69 S ATOM 27127 SG CYS C1270 68.911 76.069 207.608 1.00 22.79 S Time building chain proxies: 9.00, per 1000 atoms: 0.21 Number of scatterers: 43527 At special positions: 0 Unit cell: (152.44, 192.4, 408.48, 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 5 29.99 S 289 16.00 O 8067 8.00 N 7456 7.00 C 27710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 327 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1155 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1173 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1158 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1176 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1074 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1057 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1060 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1077 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1232 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1207 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1210 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1229 " pdb=" ZN C1401 " pdb="ZN ZN C1401 " - pdb=" SG CYS C1317 " pdb="ZN ZN C1401 " - pdb=" SG CYS C1314 " pdb="ZN ZN C1401 " - pdb=" SG CYS C1292 " pdb="ZN ZN C1401 " - pdb=" SG CYS C1295 " pdb=" ZN C1402 " pdb="ZN ZN C1402 " - pdb=" SG CYS C1267 " pdb="ZN ZN C1402 " - pdb=" SG CYS C1270 " pdb="ZN ZN C1402 " - pdb=" SG CYS C1256 " pdb="ZN ZN C1402 " - pdb=" SG CYS C1253 " Number of angles added : 30 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10552 Finding SS restraints... Secondary structure from input PDB file: 218 helices and 58 sheets defined 51.6% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 removed outlier: 3.911A pdb=" N VAL A 15 " --> pdb=" O PRO A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 removed outlier: 4.218A pdb=" N LYS A 498 " --> pdb=" O ASP A 495 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 499 " --> pdb=" O TYR A 496 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 500 " --> pdb=" O SER A 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 500' Processing helix chain 'A' and resid 647 through 652 Processing helix chain 'A' and resid 659 through 661 No H-bonds generated for 'chain 'A' and resid 659 through 661' Processing helix chain 'A' and resid 668 through 681 Processing helix chain 'A' and resid 682 through 693 Processing helix chain 'A' and resid 695 through 710 Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 724 through 737 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 766 through 777 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 794 through 812 removed outlier: 3.581A pdb=" N LEU A 798 " --> pdb=" O ALA A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 840 removed outlier: 3.592A pdb=" N GLU A 834 " --> pdb=" O GLU A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 852 Processing helix chain 'A' and resid 858 through 870 Processing helix chain 'A' and resid 871 through 883 Processing helix chain 'A' and resid 884 through 895 removed outlier: 3.682A pdb=" N CYS A 892 " --> pdb=" O ALA A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 927 removed outlier: 3.964A pdb=" N LEU A 916 " --> pdb=" O GLU A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 940 Processing helix chain 'A' and resid 942 through 961 Processing helix chain 'A' and resid 963 through 986 Processing helix chain 'A' and resid 1020 through 1043 removed outlier: 3.760A pdb=" N ARG A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A1030 " --> pdb=" O GLY A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1056 Processing helix chain 'A' and resid 1057 through 1059 No H-bonds generated for 'chain 'A' and resid 1057 through 1059' Processing helix chain 'A' and resid 1063 through 1078 Processing helix chain 'A' and resid 1080 through 1094 removed outlier: 3.701A pdb=" N LYS A1090 " --> pdb=" O LYS A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1116 Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 188 through 193 removed outlier: 3.658A pdb=" N SER B 192 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 627 removed outlier: 3.540A pdb=" N ARG B 627 " --> pdb=" O GLN B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 638 Processing helix chain 'B' and resid 642 through 656 removed outlier: 3.560A pdb=" N TRP B 646 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 670 Processing helix chain 'B' and resid 671 through 688 Processing helix chain 'B' and resid 693 through 704 Processing helix chain 'B' and resid 707 through 716 Processing helix chain 'B' and resid 718 through 729 removed outlier: 3.875A pdb=" N ALA B 722 " --> pdb=" O HIS B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 736 Processing helix chain 'B' and resid 746 through 761 Processing helix chain 'B' and resid 763 through 773 Processing helix chain 'B' and resid 776 through 788 Processing helix chain 'B' and resid 789 through 800 Processing helix chain 'B' and resid 804 through 818 Processing helix chain 'B' and resid 820 through 832 Processing helix chain 'B' and resid 833 through 844 Processing helix chain 'B' and resid 846 through 857 Processing helix chain 'B' and resid 857 through 865 Processing helix chain 'B' and resid 865 through 875 Processing helix chain 'B' and resid 877 through 888 Processing helix chain 'B' and resid 892 through 908 removed outlier: 3.506A pdb=" N GLN B 896 " --> pdb=" O ARG B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 928 Processing helix chain 'B' and resid 929 through 934 Proline residue: B 932 - end of helix No H-bonds generated for 'chain 'B' and resid 929 through 934' Processing helix chain 'B' and resid 935 through 962 removed outlier: 4.066A pdb=" N GLY B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS B 941 " --> pdb=" O THR B 937 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA B 957 " --> pdb=" O HIS B 953 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 958 " --> pdb=" O GLY B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 985 Processing helix chain 'B' and resid 994 through 1010 removed outlier: 3.668A pdb=" N ILE B 998 " --> pdb=" O SER B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1023 Processing helix chain 'B' and resid 1031 through 1042 removed outlier: 4.238A pdb=" N LEU B1040 " --> pdb=" O GLU B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1045 No H-bonds generated for 'chain 'B' and resid 1043 through 1045' Processing helix chain 'B' and resid 1050 through 1054 Processing helix chain 'B' and resid 1103 through 1113 removed outlier: 3.627A pdb=" N LEU B1113 " --> pdb=" O SER B1109 " (cutoff:3.500A) Processing helix chain 'B' and resid 1169 through 1176 Processing helix chain 'B' and resid 1177 through 1179 No H-bonds generated for 'chain 'B' and resid 1177 through 1179' Processing helix chain 'B' and resid 1216 through 1227 Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.565A pdb=" N LYS C 320 " --> pdb=" O GLU C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 639 removed outlier: 3.755A pdb=" N LEU C 638 " --> pdb=" O HIS C 635 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER C 639 " --> pdb=" O GLY C 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 635 through 639' Processing helix chain 'C' and resid 645 through 659 Proline residue: C 651 - end of helix Processing helix chain 'C' and resid 661 through 673 Processing helix chain 'C' and resid 674 through 688 Processing helix chain 'C' and resid 690 through 702 Processing helix chain 'C' and resid 703 through 713 Processing helix chain 'C' and resid 718 through 730 Processing helix chain 'C' and resid 732 through 742 removed outlier: 3.641A pdb=" N ALA C 742 " --> pdb=" O ASP C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 756 removed outlier: 4.031A pdb=" N LEU C 750 " --> pdb=" O PRO C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 767 Processing helix chain 'C' and resid 770 through 772 No H-bonds generated for 'chain 'C' and resid 770 through 772' Processing helix chain 'C' and resid 773 through 788 Processing helix chain 'C' and resid 790 through 801 Processing helix chain 'C' and resid 806 through 824 Processing helix chain 'C' and resid 826 through 836 Processing helix chain 'C' and resid 839 through 854 removed outlier: 3.723A pdb=" N LYS C 843 " --> pdb=" O SER C 839 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 848 " --> pdb=" O ARG C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 866 removed outlier: 3.885A pdb=" N GLY C 866 " --> pdb=" O LEU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 880 Processing helix chain 'C' and resid 881 through 889 Processing helix chain 'C' and resid 894 through 909 removed outlier: 3.579A pdb=" N HIS C 898 " --> pdb=" O SER C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 921 Processing helix chain 'C' and resid 923 through 934 removed outlier: 3.705A pdb=" N ARG C 929 " --> pdb=" O GLN C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 949 Processing helix chain 'C' and resid 953 through 962 removed outlier: 3.862A pdb=" N ALA C 958 " --> pdb=" O ALA C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 974 Processing helix chain 'C' and resid 981 through 993 removed outlier: 5.436A pdb=" N ASN C 991 " --> pdb=" O ALA C 987 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1004 removed outlier: 3.990A pdb=" N ALA C 997 " --> pdb=" O MET C 993 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY C1001 " --> pdb=" O ALA C 997 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER C1002 " --> pdb=" O ASP C 998 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU C1003 " --> pdb=" O ILE C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1009 No H-bonds generated for 'chain 'C' and resid 1007 through 1009' Processing helix chain 'C' and resid 1010 through 1019 Processing helix chain 'C' and resid 1024 through 1031 removed outlier: 3.944A pdb=" N LYS C1028 " --> pdb=" O LEU C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1045 removed outlier: 4.438A pdb=" N ALA C1039 " --> pdb=" O GLN C1035 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS C1041 " --> pdb=" O SER C1037 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS C1042 " --> pdb=" O ARG C1038 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1064 Processing helix chain 'C' and resid 1068 through 1080 removed outlier: 3.996A pdb=" N ASN C1072 " --> pdb=" O GLU C1068 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1100 Processing helix chain 'C' and resid 1101 through 1120 removed outlier: 3.573A pdb=" N ALA C1105 " --> pdb=" O GLN C1101 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA C1106 " --> pdb=" O TYR C1102 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN C1107 " --> pdb=" O ARG C1103 " (cutoff:3.500A) Processing helix chain 'C' and resid 1121 through 1138 Processing helix chain 'C' and resid 1144 through 1166 removed outlier: 3.825A pdb=" N LYS C1161 " --> pdb=" O TYR C1157 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE C1162 " --> pdb=" O ILE C1158 " (cutoff:3.500A) Processing helix chain 'C' and resid 1168 through 1181 Processing helix chain 'C' and resid 1182 through 1188 Proline residue: C1187 - end of helix Processing helix chain 'C' and resid 1189 through 1204 Processing helix chain 'C' and resid 1206 through 1218 Processing helix chain 'C' and resid 1227 through 1240 removed outlier: 4.710A pdb=" N LYS C1232 " --> pdb=" O ALA C1228 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS C1233 " --> pdb=" O LYS C1229 " (cutoff:3.500A) Processing helix chain 'C' and resid 1285 through 1287 No H-bonds generated for 'chain 'C' and resid 1285 through 1287' Processing helix chain 'C' and resid 1301 through 1309 removed outlier: 3.642A pdb=" N ASN C1309 " --> pdb=" O LYS C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1322 through 1326 Processing helix chain 'D' and resid 2 through 16 Processing helix chain 'D' and resid 18 through 33 Processing helix chain 'D' and resid 36 through 51 removed outlier: 4.020A pdb=" N ARG D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 64 removed outlier: 3.809A pdb=" N ALA D 56 " --> pdb=" O LYS D 52 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG D 58 " --> pdb=" O GLN D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 84 removed outlier: 4.876A pdb=" N CYS D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 105 Processing helix chain 'D' and resid 107 through 122 Processing helix chain 'D' and resid 123 through 139 Processing helix chain 'D' and resid 141 through 155 Processing helix chain 'D' and resid 157 through 175 removed outlier: 3.593A pdb=" N LYS D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 191 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 211 through 225 removed outlier: 3.510A pdb=" N PHE D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 242 Processing helix chain 'D' and resid 245 through 259 Processing helix chain 'D' and resid 262 through 281 Processing helix chain 'D' and resid 284 through 299 removed outlier: 3.535A pdb=" N PHE D 288 " --> pdb=" O ASN D 284 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALA D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 320 Processing helix chain 'D' and resid 323 through 337 Processing helix chain 'D' and resid 339 through 354 Processing helix chain 'D' and resid 357 through 372 Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 389 through 391 No H-bonds generated for 'chain 'D' and resid 389 through 391' Processing helix chain 'D' and resid 394 through 409 Processing helix chain 'D' and resid 411 through 430 Processing helix chain 'D' and resid 436 through 444 removed outlier: 3.801A pdb=" N ASN D 444 " --> pdb=" O PHE D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 459 Processing helix chain 'D' and resid 471 through 488 Processing helix chain 'D' and resid 491 through 506 removed outlier: 3.917A pdb=" N VAL D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 522 Processing helix chain 'D' and resid 525 through 539 removed outlier: 3.634A pdb=" N HIS D 529 " --> pdb=" O TYR D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 556 Processing helix chain 'D' and resid 557 through 561 Processing helix chain 'D' and resid 562 through 576 removed outlier: 3.722A pdb=" N HIS D 566 " --> pdb=" O TYR D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 591 Processing helix chain 'D' and resid 612 through 630 Processing helix chain 'D' and resid 632 through 648 Processing helix chain 'D' and resid 652 through 668 Processing helix chain 'D' and resid 669 through 679 Processing helix chain 'D' and resid 686 through 701 Processing helix chain 'D' and resid 704 through 719 removed outlier: 3.809A pdb=" N PHE D 712 " --> pdb=" O TYR D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 735 Processing helix chain 'D' and resid 737 through 752 Processing helix chain 'D' and resid 756 through 769 removed outlier: 3.859A pdb=" N SER D 760 " --> pdb=" O GLY D 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 785 removed outlier: 3.965A pdb=" N THR D 785 " --> pdb=" O ALA D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 802 removed outlier: 4.173A pdb=" N CYS D 792 " --> pdb=" O LYS D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 817 Processing helix chain 'D' and resid 823 through 844 Processing helix chain 'D' and resid 846 through 872 removed outlier: 3.777A pdb=" N GLN D 869 " --> pdb=" O LEU D 865 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N MET D 870 " --> pdb=" O LYS D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 875 through 897 Processing helix chain 'D' and resid 899 through 914 Processing helix chain 'D' and resid 917 through 931 Processing helix chain 'D' and resid 933 through 948 Processing helix chain 'D' and resid 951 through 965 Processing helix chain 'D' and resid 967 through 982 Processing helix chain 'D' and resid 986 through 1000 Processing helix chain 'D' and resid 1001 through 1003 No H-bonds generated for 'chain 'D' and resid 1001 through 1003' Processing helix chain 'D' and resid 1004 through 1016 removed outlier: 4.060A pdb=" N PHE D1008 " --> pdb=" O ASP D1004 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE D1009 " --> pdb=" O VAL D1005 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET D1011 " --> pdb=" O ARG D1007 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN D1016 " --> pdb=" O ALA D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1018 through 1021 Processing helix chain 'D' and resid 1022 through 1037 Processing helix chain 'D' and resid 1038 through 1048 removed outlier: 3.747A pdb=" N LYS D1048 " --> pdb=" O ARG D1044 " (cutoff:3.500A) Processing helix chain 'D' and resid 1054 through 1069 removed outlier: 4.464A pdb=" N ASN D1058 " --> pdb=" O ASP D1054 " (cutoff:3.500A) Processing helix chain 'D' and resid 1081 through 1085 removed outlier: 3.903A pdb=" N GLY D1085 " --> pdb=" O ASN D1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 1086 through 1089 Processing helix chain 'D' and resid 1090 through 1111 removed outlier: 3.763A pdb=" N GLN D1094 " --> pdb=" O SER D1090 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D1109 " --> pdb=" O GLU D1105 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU D1110 " --> pdb=" O LYS D1106 " (cutoff:3.500A) Processing helix chain 'D' and resid 1115 through 1133 Processing helix chain 'D' and resid 1135 through 1153 Processing helix chain 'D' and resid 1156 through 1170 Processing helix chain 'D' and resid 1172 through 1186 removed outlier: 3.612A pdb=" N LYS D1185 " --> pdb=" O LYS D1181 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET D1186 " --> pdb=" O ARG D1182 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1210 Processing helix chain 'D' and resid 1212 through 1227 Processing helix chain 'D' and resid 1230 through 1244 Processing helix chain 'D' and resid 1246 through 1261 Processing helix chain 'D' and resid 1265 through 1279 Processing helix chain 'D' and resid 1281 through 1296 Processing helix chain 'D' and resid 1306 through 1313 Processing helix chain 'E' and resid 562 through 566 Processing helix chain 'E' and resid 769 through 786 Processing helix chain 'E' and resid 787 through 796 Processing helix chain 'E' and resid 800 through 814 Processing helix chain 'E' and resid 817 through 822 removed outlier: 3.774A pdb=" N VAL E 822 " --> pdb=" O ASP E 818 " (cutoff:3.500A) Processing helix chain 'E' and resid 829 through 840 Processing helix chain 'E' and resid 845 through 856 Processing helix chain 'E' and resid 858 through 870 Processing helix chain 'E' and resid 871 through 882 Processing helix chain 'E' and resid 886 through 895 Processing helix chain 'E' and resid 899 through 914 Processing helix chain 'E' and resid 916 through 927 removed outlier: 3.588A pdb=" N SER E 927 " --> pdb=" O TYR E 923 " (cutoff:3.500A) Processing helix chain 'E' and resid 929 through 938 Proline residue: E 935 - end of helix Processing helix chain 'E' and resid 941 through 953 Processing helix chain 'E' and resid 956 through 967 Processing helix chain 'E' and resid 970 through 982 Processing helix chain 'E' and resid 983 through 995 Processing helix chain 'E' and resid 996 through 1008 removed outlier: 3.952A pdb=" N ALA E1000 " --> pdb=" O ASN E 996 " (cutoff:3.500A) Processing helix chain 'E' and resid 1009 through 1023 Processing helix chain 'E' and resid 1026 through 1036 Processing helix chain 'E' and resid 1038 through 1050 Processing helix chain 'E' and resid 1051 through 1061 removed outlier: 3.823A pdb=" N ASN E1057 " --> pdb=" O ASP E1053 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU E1058 " --> pdb=" O GLN E1054 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU E1061 " --> pdb=" O ASN E1057 " (cutoff:3.500A) Processing helix chain 'E' and resid 1065 through 1078 removed outlier: 3.884A pdb=" N GLU E1069 " --> pdb=" O GLU E1065 " (cutoff:3.500A) Processing helix chain 'E' and resid 1080 through 1091 Processing helix chain 'E' and resid 1093 through 1105 removed outlier: 4.161A pdb=" N GLU E1099 " --> pdb=" O SER E1095 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU E1100 " --> pdb=" O LYS E1096 " (cutoff:3.500A) Processing helix chain 'E' and resid 1106 through 1116 Processing helix chain 'F' and resid 123 through 146 removed outlier: 3.819A pdb=" N ASP F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET F 140 " --> pdb=" O ASP F 136 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA F 144 " --> pdb=" O MET F 140 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 159 removed outlier: 3.620A pdb=" N LYS F 159 " --> pdb=" O LYS F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 168 Processing helix chain 'F' and resid 175 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 6.777A pdb=" N PHE A 328 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 308 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.910A pdb=" N CYS A 19 " --> pdb=" O GLY A 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 79 removed outlier: 6.696A pdb=" N SER A 89 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 77 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR A 87 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TRP A 79 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS A 85 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 90 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A 95 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE A 110 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 97 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 123 removed outlier: 4.337A pdb=" N TRP A 150 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N SER A 143 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ARG A 148 " --> pdb=" O SER A 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 159 through 164 removed outlier: 6.359A pdb=" N GLY A 174 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL A 162 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU A 172 " --> pdb=" O VAL A 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 removed outlier: 4.797A pdb=" N ILE A 182 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 210 through 212 Processing sheet with id=AA8, first strand: chain 'A' and resid 254 through 261 removed outlier: 4.895A pdb=" N TYR A 255 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N PHE A 273 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A 271 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE A 259 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 269 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE A 288 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 336 through 340 removed outlier: 4.705A pdb=" N LYS A 336 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 378 through 381 Processing sheet with id=AB2, first strand: chain 'A' and resid 433 through 437 Processing sheet with id=AB3, first strand: chain 'A' and resid 507 through 512 removed outlier: 6.600A pdb=" N SER A 530 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU A 536 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 546 through 551 Processing sheet with id=AB5, first strand: chain 'A' and resid 596 through 601 removed outlier: 3.916A pdb=" N ASP A 598 " --> pdb=" O MET A 612 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 634 through 639 removed outlier: 5.791A pdb=" N ILE A 635 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A 646 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1153 through 1154 Processing sheet with id=AB8, first strand: chain 'B' and resid 2 through 10 removed outlier: 6.715A pdb=" N PHE B 347 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG B 8 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE B 345 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR B 344 " --> pdb=" O CYS B 340 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 19 through 20 removed outlier: 5.735A pdb=" N LEU B 35 " --> pdb=" O PRO B 48 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 60 through 61 removed outlier: 6.581A pdb=" N THR B 81 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLY B 86 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N ALA B 221 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE B 87 " --> pdb=" O ALA B 221 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 96 through 101 removed outlier: 3.829A pdb=" N CYS B 98 " --> pdb=" O CYS B 111 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP B 115 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL B 126 " --> pdb=" O GLN B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 135 through 140 removed outlier: 6.562A pdb=" N GLY B 150 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N CYS B 138 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 148 " --> pdb=" O CYS B 138 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE B 155 " --> pdb=" O MET B 151 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 179 through 184 removed outlier: 4.185A pdb=" N LYS B 262 " --> pdb=" O ASP B 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 283 through 288 removed outlier: 6.685A pdb=" N GLY B 298 " --> pdb=" O CYS B 284 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE B 286 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 296 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR B 288 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR B 294 " --> pdb=" O TYR B 288 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY B 299 " --> pdb=" O GLN B 303 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLN B 303 " --> pdb=" O GLY B 299 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 304 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 315 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR B 308 " --> pdb=" O ARG B 313 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG B 313 " --> pdb=" O THR B 308 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 356 through 359 Processing sheet with id=AC7, first strand: chain 'B' and resid 393 through 397 removed outlier: 3.624A pdb=" N LYS B 393 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE B 409 " --> pdb=" O LYS B 429 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS B 429 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE B 411 " --> pdb=" O LYS B 427 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 438 through 442 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 478 removed outlier: 4.176A pdb=" N GLN B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 497 " --> pdb=" O LEU B 510 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 518 through 522 removed outlier: 4.777A pdb=" N CYS B 519 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL B 532 " --> pdb=" O CYS B 519 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N CYS B 538 " --> pdb=" O GLN B 551 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN B 551 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 540 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 557 through 560 Processing sheet with id=AD3, first strand: chain 'B' and resid 593 through 598 removed outlier: 6.603A pdb=" N PHE B 603 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR B 597 " --> pdb=" O LYS B 601 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS B 601 " --> pdb=" O TYR B 597 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1166 through 1167 removed outlier: 4.800A pdb=" N VAL B1166 " --> pdb=" O GLU B1095 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR B1194 " --> pdb=" O PHE B1096 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1204 through 1206 Processing sheet with id=AD6, first strand: chain 'C' and resid 2 through 8 removed outlier: 4.392A pdb=" N LYS C 2 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C 345 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER C 6 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU C 343 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER C 342 " --> pdb=" O THR C 338 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA C 335 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU C 325 " --> pdb=" O ALA C 335 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER C 337 " --> pdb=" O GLY C 323 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 18 through 21 removed outlier: 6.661A pdb=" N VAL C 38 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU C 50 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 40 " --> pdb=" O ARG C 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 68 through 71 Processing sheet with id=AD9, first strand: chain 'C' and resid 100 through 105 Processing sheet with id=AE1, first strand: chain 'C' and resid 142 through 147 removed outlier: 7.236A pdb=" N GLY C 156 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY C 145 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA C 154 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET C 161 " --> pdb=" O GLY C 157 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 181 through 185 removed outlier: 4.341A pdb=" N MET C 184 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER C 203 " --> pdb=" O MET C 184 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 234 through 240 removed outlier: 4.103A pdb=" N CYS C 236 " --> pdb=" O GLY C 248 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS C 253 " --> pdb=" O PHE C 249 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE C 254 " --> pdb=" O GLN C 270 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN C 270 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL C 256 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN C 266 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 280 through 284 Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 357 removed outlier: 5.326A pdb=" N ASN C 374 " --> pdb=" O LEU C 380 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU C 380 " --> pdb=" O ASN C 374 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 392 through 395 removed outlier: 3.846A pdb=" N LYS C 422 " --> pdb=" O PHE C 410 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL C 412 " --> pdb=" O LYS C 420 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LYS C 420 " --> pdb=" O VAL C 412 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 430 through 436 Processing sheet with id=AE8, first strand: chain 'C' and resid 478 through 483 removed outlier: 4.008A pdb=" N VAL C 496 " --> pdb=" O THR C 492 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN C 509 " --> pdb=" O TYR C 499 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR C 501 " --> pdb=" O PHE C 507 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE C 507 " --> pdb=" O TYR C 501 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 517 through 522 Processing sheet with id=AF1, first strand: chain 'C' and resid 560 through 563 removed outlier: 6.440A pdb=" N VAL C 581 " --> pdb=" O SER C 601 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER C 601 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR C 583 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 609 through 614 removed outlier: 6.594A pdb=" N THR C 619 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU C 613 " --> pdb=" O GLU C 617 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU C 617 " --> pdb=" O LEU C 613 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1250 through 1252 Processing sheet with id=AF4, first strand: chain 'C' and resid 1289 through 1291 Processing sheet with id=AF5, first strand: chain 'E' and resid 412 through 414 Processing sheet with id=AF6, first strand: chain 'E' and resid 448 through 451 Processing sheet with id=AF7, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AF8, first strand: chain 'E' and resid 496 through 498 Processing sheet with id=AF9, first strand: chain 'E' and resid 526 through 530 removed outlier: 6.587A pdb=" N PHE E 543 " --> pdb=" O SER E 558 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER E 558 " --> pdb=" O PHE E 543 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER E 545 " --> pdb=" O HIS E 556 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 583 through 584 Processing sheet with id=AG2, first strand: chain 'E' and resid 646 through 653 removed outlier: 5.928A pdb=" N VAL E 666 " --> pdb=" O PRO E 648 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN E 650 " --> pdb=" O GLU E 664 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL E 692 " --> pdb=" O PRO E 712 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE E 694 " --> pdb=" O SER E 710 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER E 710 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER E 696 " --> pdb=" O HIS E 708 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 717 through 724 removed outlier: 6.390A pdb=" N LEU E 720 " --> pdb=" O THR E 731 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR E 731 " --> pdb=" O LEU E 720 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 147 through 148 2464 hydrogen bonds defined for protein. 7095 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: 12.27 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 14317 1.35 - 1.47: 10386 1.47 - 1.59: 19270 1.59 - 1.71: 0 1.71 - 1.84: 436 Bond restraints: 44409 Sorted by residual: bond pdb=" CG1 ILE B 602 " pdb=" CD1 ILE B 602 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.43e+00 bond pdb=" CG LEU B1067 " pdb=" CD1 LEU B1067 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.40e+00 bond pdb=" CA MET C1085 " pdb=" CB MET C1085 " ideal model delta sigma weight residual 1.528 1.542 -0.013 1.17e-02 7.31e+03 1.28e+00 bond pdb=" CB MET D 956 " pdb=" CG MET D 956 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CA VAL B 222 " pdb=" CB VAL B 222 " ideal model delta sigma weight residual 1.538 1.527 0.011 1.13e-02 7.83e+03 1.02e+00 ... (remaining 44404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 59013 1.64 - 3.28: 941 3.28 - 4.93: 132 4.93 - 6.57: 31 6.57 - 8.21: 14 Bond angle restraints: 60131 Sorted by residual: angle pdb=" C LEU A 154 " pdb=" CA LEU A 154 " pdb=" CB LEU A 154 " ideal model delta sigma weight residual 116.54 110.95 5.59 1.15e+00 7.56e-01 2.36e+01 angle pdb=" C SER B1209 " pdb=" N CYS B1210 " pdb=" CA CYS B1210 " ideal model delta sigma weight residual 121.54 128.55 -7.01 1.91e+00 2.74e-01 1.35e+01 angle pdb=" C TRP A 816 " pdb=" N LEU A 817 " pdb=" CA LEU A 817 " ideal model delta sigma weight residual 121.54 128.35 -6.81 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C LYS D 82 " pdb=" N MET D 83 " pdb=" CA MET D 83 " ideal model delta sigma weight residual 121.58 115.26 6.32 1.95e+00 2.63e-01 1.05e+01 angle pdb=" N GLY E 825 " pdb=" CA GLY E 825 " pdb=" C GLY E 825 " ideal model delta sigma weight residual 113.18 106.02 7.16 2.37e+00 1.78e-01 9.14e+00 ... (remaining 60126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 24580 17.81 - 35.62: 1843 35.62 - 53.43: 226 53.43 - 71.24: 38 71.24 - 89.05: 14 Dihedral angle restraints: 26701 sinusoidal: 10382 harmonic: 16319 Sorted by residual: dihedral pdb=" CA MET B 770 " pdb=" C MET B 770 " pdb=" N TYR B 771 " pdb=" CA TYR B 771 " ideal model delta harmonic sigma weight residual 180.00 148.56 31.44 0 5.00e+00 4.00e-02 3.95e+01 dihedral pdb=" CA LEU D 802 " pdb=" C LEU D 802 " pdb=" N LYS D 803 " pdb=" CA LYS D 803 " ideal model delta harmonic sigma weight residual 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA TRP B 259 " pdb=" C TRP B 259 " pdb=" N GLY B 260 " pdb=" CA GLY B 260 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 26698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 4526 0.034 - 0.068: 1508 0.068 - 0.102: 492 0.102 - 0.136: 197 0.136 - 0.170: 12 Chirality restraints: 6735 Sorted by residual: chirality pdb=" CA ILE B 602 " pdb=" N ILE B 602 " pdb=" C ILE B 602 " pdb=" CB ILE B 602 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA MET B 770 " pdb=" N MET B 770 " pdb=" C MET B 770 " pdb=" CB MET B 770 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA ILE A 259 " pdb=" N ILE A 259 " pdb=" C ILE A 259 " pdb=" CB ILE A 259 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.66e-01 ... (remaining 6732 not shown) Planarity restraints: 7711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C1289 " -0.015 2.00e-02 2.50e+03 1.75e-02 7.68e+00 pdb=" CG TRP C1289 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C1289 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP C1289 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C1289 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C1289 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C1289 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1289 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1289 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C1289 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 645 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO C 646 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 646 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 646 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 597 " -0.017 2.00e-02 2.50e+03 1.32e-02 3.49e+00 pdb=" CG TYR B 597 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR B 597 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 597 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 597 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 597 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 597 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 597 " -0.001 2.00e-02 2.50e+03 ... (remaining 7708 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 485 2.64 - 3.21: 40254 3.21 - 3.77: 69327 3.77 - 4.34: 95300 4.34 - 4.90: 154964 Nonbonded interactions: 360330 Sorted by model distance: nonbonded pdb=" OH TYR C 733 " pdb=" O GLY E 828 " model vdw 2.078 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" OH TYR A 289 " model vdw 2.094 3.040 nonbonded pdb=" OG SER A 741 " pdb=" OE1 GLU C1340 " model vdw 2.102 3.040 nonbonded pdb=" O ARG D1007 " pdb=" OG SER D1010 " model vdw 2.157 3.040 nonbonded pdb=" OD1 ASP A 808 " pdb=" OH TYR A 823 " model vdw 2.175 3.040 ... (remaining 360325 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 45.370 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 44430 Z= 0.140 Angle : 0.556 16.062 60163 Z= 0.291 Chirality : 0.041 0.170 6735 Planarity : 0.003 0.053 7711 Dihedral : 12.359 89.048 16146 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.16 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: 0.55 (0.12), residues: 5508 helix: 1.61 (0.10), residues: 2723 sheet: -0.60 (0.17), residues: 891 loop : -0.95 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 168 TYR 0.032 0.001 TYR B 597 PHE 0.020 0.001 PHE D 41 TRP 0.045 0.001 TRP C1289 HIS 0.016 0.001 HIS B1017 Details of bonding type rmsd covalent geometry : bond 0.00307 (44409) covalent geometry : angle 0.53771 (60131) SS BOND : bond 0.00482 ( 1) SS BOND : angle 0.64640 ( 2) hydrogen bonds : bond 0.13357 ( 2464) hydrogen bonds : angle 5.51787 ( 7095) metal coordination : bond 0.00796 ( 20) metal coordination : angle 6.37103 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.587 Fit side-chains revert: symmetry clash REVERT: A 175 MET cc_start: 0.8555 (mmp) cc_final: 0.8352 (mmm) REVERT: A 871 MET cc_start: 0.8437 (mpp) cc_final: 0.7821 (mpp) REVERT: C 1237 MET cc_start: 0.7828 (mtt) cc_final: 0.7566 (mtm) REVERT: E 971 MET cc_start: 0.7662 (mmp) cc_final: 0.7306 (mmp) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2226 time to fit residues: 78.8500 Evaluate side-chains 185 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 394 optimal weight: 10.0000 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 20.0000 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 20.0000 chunk 223 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN A 896 ASN B 145 GLN B 444 ASN ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 757 GLN ** C1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 GLN D 879 GLN ** E 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 826 ASN E 855 GLN ** E 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.078978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.058636 restraints weight = 212000.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.058598 restraints weight = 147814.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.058368 restraints weight = 120129.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.058447 restraints weight = 123477.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.058463 restraints weight = 111848.105| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.122 44430 Z= 0.553 Angle : 0.876 18.828 60163 Z= 0.446 Chirality : 0.053 0.226 6735 Planarity : 0.005 0.049 7711 Dihedral : 5.357 26.187 6012 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.33 % Allowed : 7.60 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.11), residues: 5508 helix: 0.99 (0.10), residues: 2751 sheet: -0.93 (0.17), residues: 880 loop : -1.24 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 721 TYR 0.035 0.003 TYR B 288 PHE 0.040 0.003 PHE B 307 TRP 0.033 0.003 TRP C1289 HIS 0.015 0.002 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.01260 (44409) covalent geometry : angle 0.85238 (60131) SS BOND : bond 0.01309 ( 1) SS BOND : angle 3.25461 ( 2) hydrogen bonds : bond 0.05097 ( 2464) hydrogen bonds : angle 5.39909 ( 7095) metal coordination : bond 0.02929 ( 20) metal coordination : angle 9.14623 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 1.799 Fit side-chains REVERT: A 320 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8584 (pp) REVERT: B 792 MET cc_start: 0.7570 (ptp) cc_final: 0.7285 (ptp) REVERT: C 100 MET cc_start: 0.1593 (tpt) cc_final: -0.0087 (ptm) REVERT: C 708 MET cc_start: 0.8516 (mtp) cc_final: 0.8261 (mtp) REVERT: C 853 MET cc_start: 0.8168 (mpp) cc_final: 0.7928 (mpp) REVERT: D 406 MET cc_start: 0.8470 (tmm) cc_final: 0.7704 (tmm) REVERT: D 461 MET cc_start: 0.4688 (mpp) cc_final: 0.3892 (ptp) REVERT: D 694 MET cc_start: 0.9012 (tpp) cc_final: 0.8603 (tpp) REVERT: D 844 MET cc_start: 0.7975 (ppp) cc_final: 0.7686 (ppp) REVERT: D 958 MET cc_start: 0.8653 (ppp) cc_final: 0.8425 (ppp) REVERT: D 987 MET cc_start: 0.8085 (tpp) cc_final: 0.7611 (tpp) REVERT: D 1237 MET cc_start: 0.8261 (tpp) cc_final: 0.8040 (tpp) REVERT: E 1067 MET cc_start: 0.6833 (pmm) cc_final: 0.6609 (pmm) outliers start: 15 outliers final: 9 residues processed: 201 average time/residue: 0.2395 time to fit residues: 84.4091 Evaluate side-chains 199 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 1085 MET Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 719 MET Chi-restraints excluded: chain E residue 932 PHE Chi-restraints excluded: chain F residue 145 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 231 optimal weight: 20.0000 chunk 48 optimal weight: 0.4980 chunk 453 optimal weight: 1.9990 chunk 398 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 446 optimal weight: 0.8980 chunk 359 optimal weight: 4.9990 chunk 341 optimal weight: 0.6980 chunk 527 optimal weight: 0.7980 chunk 430 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 HIS A 527 GLN B 513 GLN ** C 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 ASN ** E 991 HIS ** 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 = 0.3709 r_free = 0.3709 target = 0.083698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.066281 restraints weight = 201809.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.065863 restraints weight = 162142.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.066091 restraints weight = 137633.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.066156 restraints weight = 119953.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.066209 restraints weight = 107935.519| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 44430 Z= 0.138 Angle : 0.549 14.561 60163 Z= 0.282 Chirality : 0.041 0.155 6735 Planarity : 0.003 0.045 7711 Dihedral : 4.746 24.919 6012 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.13 % Rotamer: Outliers : 0.66 % Allowed : 8.96 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.12), residues: 5508 helix: 1.54 (0.10), residues: 2769 sheet: -0.73 (0.17), residues: 885 loop : -1.03 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 647 TYR 0.015 0.001 TYR C 490 PHE 0.016 0.001 PHE E 762 TRP 0.015 0.001 TRP B 80 HIS 0.009 0.001 HIS B1017 Details of bonding type rmsd covalent geometry : bond 0.00304 (44409) covalent geometry : angle 0.52793 (60131) SS BOND : bond 0.00599 ( 1) SS BOND : angle 2.10915 ( 2) hydrogen bonds : bond 0.03651 ( 2464) hydrogen bonds : angle 4.64342 ( 7095) metal coordination : bond 0.00945 ( 20) metal coordination : angle 6.82316 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: B 792 MET cc_start: 0.7605 (ptp) cc_final: 0.7312 (ptp) REVERT: C 1 MET cc_start: 0.5499 (tmm) cc_final: 0.3759 (tmm) REVERT: C 100 MET cc_start: 0.0143 (tpt) cc_final: -0.1100 (ptm) REVERT: C 708 MET cc_start: 0.8364 (mtp) cc_final: 0.8069 (mtp) REVERT: C 853 MET cc_start: 0.8129 (mpp) cc_final: 0.7726 (mpp) REVERT: C 1132 MET cc_start: 0.8117 (mtt) cc_final: 0.7878 (mtt) REVERT: D 406 MET cc_start: 0.8125 (tmm) cc_final: 0.7313 (tmm) REVERT: D 461 MET cc_start: 0.4434 (mpp) cc_final: 0.3690 (ptt) REVERT: D 694 MET cc_start: 0.8867 (tpp) cc_final: 0.8576 (tpp) REVERT: D 767 ILE cc_start: 0.9523 (OUTLIER) cc_final: 0.9267 (tp) REVERT: D 844 MET cc_start: 0.7894 (ppp) cc_final: 0.7518 (ppp) REVERT: D 958 MET cc_start: 0.8485 (ppp) cc_final: 0.8205 (ppp) REVERT: D 987 MET cc_start: 0.7994 (tpp) cc_final: 0.7748 (tpp) REVERT: D 1237 MET cc_start: 0.8510 (tpp) cc_final: 0.8210 (tpp) REVERT: E 608 THR cc_start: 0.1422 (OUTLIER) cc_final: 0.1220 (p) REVERT: E 1067 MET cc_start: 0.7189 (pmm) cc_final: 0.6932 (pmm) REVERT: F 168 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7736 (mmm160) outliers start: 30 outliers final: 11 residues processed: 212 average time/residue: 0.2436 time to fit residues: 90.8033 Evaluate side-chains 199 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 767 ILE Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 812 VAL Chi-restraints excluded: chain E residue 975 LEU Chi-restraints excluded: chain F residue 145 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 119 optimal weight: 4.9990 chunk 235 optimal weight: 50.0000 chunk 236 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 250 optimal weight: 30.0000 chunk 148 optimal weight: 0.7980 chunk 439 optimal weight: 2.9990 chunk 399 optimal weight: 0.9980 chunk 271 optimal weight: 0.8980 chunk 330 optimal weight: 6.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 809 HIS C1139 GLN ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.078468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.059534 restraints weight = 215109.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.059279 restraints weight = 157238.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.059302 restraints weight = 123191.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.059477 restraints weight = 116132.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.059489 restraints weight = 104535.814| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 44430 Z= 0.200 Angle : 0.573 13.958 60163 Z= 0.291 Chirality : 0.042 0.160 6735 Planarity : 0.003 0.046 7711 Dihedral : 4.696 25.029 6012 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.03 % Allowed : 10.45 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.12), residues: 5508 helix: 1.59 (0.10), residues: 2771 sheet: -0.72 (0.17), residues: 886 loop : -1.02 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 647 TYR 0.017 0.001 TYR B 90 PHE 0.016 0.001 PHE B 307 TRP 0.015 0.001 TRP D1258 HIS 0.009 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00454 (44409) covalent geometry : angle 0.55169 (60131) SS BOND : bond 0.00723 ( 1) SS BOND : angle 2.34814 ( 2) hydrogen bonds : bond 0.03625 ( 2464) hydrogen bonds : angle 4.59620 ( 7095) metal coordination : bond 0.01259 ( 20) metal coordination : angle 6.86376 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 1.602 Fit side-chains revert: symmetry clash REVERT: A 99 MET cc_start: 0.6855 (ptt) cc_final: 0.6631 (ptt) REVERT: C 1 MET cc_start: 0.5957 (tmm) cc_final: 0.4410 (tmm) REVERT: C 100 MET cc_start: 0.0548 (tpt) cc_final: -0.1034 (ptm) REVERT: C 189 MET cc_start: 0.1053 (mmt) cc_final: 0.0742 (mmt) REVERT: C 708 MET cc_start: 0.8446 (mtp) cc_final: 0.8087 (mtp) REVERT: C 853 MET cc_start: 0.8174 (mpp) cc_final: 0.7534 (mpp) REVERT: D 406 MET cc_start: 0.8215 (tmm) cc_final: 0.7375 (tmm) REVERT: D 461 MET cc_start: 0.4641 (mpp) cc_final: 0.3813 (ptt) REVERT: D 694 MET cc_start: 0.8933 (tpp) cc_final: 0.8614 (tpp) REVERT: D 767 ILE cc_start: 0.9542 (OUTLIER) cc_final: 0.9288 (tp) REVERT: D 844 MET cc_start: 0.7967 (ppp) cc_final: 0.7506 (ppp) REVERT: D 987 MET cc_start: 0.7858 (tpp) cc_final: 0.7617 (tpp) REVERT: D 1237 MET cc_start: 0.8146 (tpp) cc_final: 0.7898 (tpp) REVERT: E 810 MET cc_start: 0.7853 (tmm) cc_final: 0.7605 (tmm) REVERT: E 1067 MET cc_start: 0.7223 (pmm) cc_final: 0.6769 (pmm) REVERT: E 1086 MET cc_start: 0.7435 (mmm) cc_final: 0.6835 (tpp) outliers start: 47 outliers final: 26 residues processed: 229 average time/residue: 0.2343 time to fit residues: 94.6396 Evaluate side-chains 215 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 767 ILE Chi-restraints excluded: chain D residue 956 MET Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain E residue 807 MET Chi-restraints excluded: chain E residue 812 VAL Chi-restraints excluded: chain E residue 932 PHE Chi-restraints excluded: chain E residue 975 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 376 optimal weight: 0.5980 chunk 383 optimal weight: 5.9990 chunk 214 optimal weight: 0.9990 chunk 545 optimal weight: 10.0000 chunk 342 optimal weight: 3.9990 chunk 405 optimal weight: 4.9990 chunk 344 optimal weight: 0.2980 chunk 59 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 450 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 HIS ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 855 GLN D1062 ASN E 855 GLN ** E 991 HIS ** 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 = 0.3723 r_free = 0.3723 target = 0.084615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.067708 restraints weight = 203412.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.066594 restraints weight = 213274.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.066895 restraints weight = 188673.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.067087 restraints weight = 140765.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.067189 restraints weight = 132515.160| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 44430 Z= 0.113 Angle : 0.508 12.496 60163 Z= 0.261 Chirality : 0.040 0.152 6735 Planarity : 0.003 0.044 7711 Dihedral : 4.435 23.457 6012 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.14 % Allowed : 11.07 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.12), residues: 5508 helix: 1.77 (0.10), residues: 2774 sheet: -0.63 (0.17), residues: 898 loop : -0.91 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 919 TYR 0.012 0.001 TYR B 90 PHE 0.013 0.001 PHE C1017 TRP 0.015 0.001 TRP D1258 HIS 0.007 0.001 HIS A 923 Details of bonding type rmsd covalent geometry : bond 0.00245 (44409) covalent geometry : angle 0.49175 (60131) SS BOND : bond 0.00557 ( 1) SS BOND : angle 2.14541 ( 2) hydrogen bonds : bond 0.03203 ( 2464) hydrogen bonds : angle 4.34575 ( 7095) metal coordination : bond 0.00729 ( 20) metal coordination : angle 5.63165 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 2.087 Fit side-chains REVERT: A 3 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8903 (p90) REVERT: A 99 MET cc_start: 0.6772 (ptt) cc_final: 0.6562 (ptt) REVERT: B 702 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.6974 (t80) REVERT: B 865 TYR cc_start: 0.6798 (t80) cc_final: 0.6155 (t80) REVERT: B 1073 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8739 (t) REVERT: C 1 MET cc_start: 0.5920 (tmm) cc_final: 0.5138 (tmm) REVERT: C 100 MET cc_start: -0.0674 (tpt) cc_final: -0.1178 (ptm) REVERT: C 189 MET cc_start: 0.1013 (mmt) cc_final: 0.0731 (mmt) REVERT: C 708 MET cc_start: 0.8443 (mtp) cc_final: 0.8086 (mtp) REVERT: C 853 MET cc_start: 0.8298 (mpp) cc_final: 0.7688 (mpp) REVERT: C 1132 MET cc_start: 0.8202 (mtt) cc_final: 0.7969 (mtt) REVERT: D 406 MET cc_start: 0.8042 (tmm) cc_final: 0.7139 (tmm) REVERT: D 461 MET cc_start: 0.4415 (mpp) cc_final: 0.3649 (ptp) REVERT: D 694 MET cc_start: 0.8739 (tpp) cc_final: 0.8445 (tpp) REVERT: D 767 ILE cc_start: 0.9518 (OUTLIER) cc_final: 0.9260 (tp) REVERT: D 844 MET cc_start: 0.7995 (ppp) cc_final: 0.7525 (ppp) REVERT: D 962 MET cc_start: 0.8582 (ptt) cc_final: 0.8134 (ppp) REVERT: D 1237 MET cc_start: 0.8388 (tpp) cc_final: 0.8092 (tpp) REVERT: E 810 MET cc_start: 0.7846 (tmm) cc_final: 0.7580 (tmm) REVERT: E 1067 MET cc_start: 0.6751 (pmm) cc_final: 0.6342 (pmm) REVERT: E 1086 MET cc_start: 0.7350 (mmm) cc_final: 0.7055 (tpp) REVERT: F 168 ARG cc_start: 0.7987 (mmm160) cc_final: 0.7666 (tpp80) outliers start: 52 outliers final: 22 residues processed: 233 average time/residue: 0.2356 time to fit residues: 96.6879 Evaluate side-chains 210 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1229 CYS Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 1313 THR Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 767 ILE Chi-restraints excluded: chain D residue 956 MET Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain E residue 807 MET Chi-restraints excluded: chain E residue 975 LEU Chi-restraints excluded: chain E residue 1020 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 534 optimal weight: 2.9990 chunk 527 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 510 optimal weight: 40.0000 chunk 91 optimal weight: 1.9990 chunk 229 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 533 optimal weight: 2.9990 chunk 452 optimal weight: 0.8980 chunk 247 optimal weight: 8.9990 chunk 428 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN A 923 HIS ** B1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 931 GLN D 951 ASN D 976 GLN ** E 991 HIS ** 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 = 0.3681 r_free = 0.3681 target = 0.078346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.057040 restraints weight = 213078.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.057775 restraints weight = 145920.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.057935 restraints weight = 107535.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.058247 restraints weight = 87669.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.058238 restraints weight = 81819.447| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 44430 Z= 0.270 Angle : 0.615 15.199 60163 Z= 0.311 Chirality : 0.043 0.173 6735 Planarity : 0.004 0.045 7711 Dihedral : 4.680 24.861 6012 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.45 % Allowed : 11.51 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.12), residues: 5508 helix: 1.65 (0.10), residues: 2776 sheet: -0.69 (0.17), residues: 877 loop : -0.98 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 721 TYR 0.028 0.002 TYR E 495 PHE 0.023 0.002 PHE B 307 TRP 0.017 0.002 TRP A 105 HIS 0.009 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00614 (44409) covalent geometry : angle 0.59539 (60131) SS BOND : bond 0.00773 ( 1) SS BOND : angle 2.54918 ( 2) hydrogen bonds : bond 0.03685 ( 2464) hydrogen bonds : angle 4.59337 ( 7095) metal coordination : bond 0.01608 ( 20) metal coordination : angle 6.88157 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 189 time to evaluate : 1.967 Fit side-chains revert: symmetry clash REVERT: A 3 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8937 (p90) REVERT: A 99 MET cc_start: 0.6866 (ptt) cc_final: 0.6614 (ptt) REVERT: B 702 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7073 (t80) REVERT: B 1073 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8861 (t) REVERT: C 1 MET cc_start: 0.6338 (tmm) cc_final: 0.4896 (tmm) REVERT: C 100 MET cc_start: 0.1086 (tpt) cc_final: -0.0409 (ptm) REVERT: C 189 MET cc_start: 0.0907 (mmt) cc_final: 0.0590 (mmt) REVERT: C 853 MET cc_start: 0.8315 (mpp) cc_final: 0.7599 (mpp) REVERT: C 1237 MET cc_start: 0.8371 (mtt) cc_final: 0.8131 (mtm) REVERT: D 219 MET cc_start: 0.8872 (ttm) cc_final: 0.8620 (ttp) REVERT: D 406 MET cc_start: 0.8280 (tmm) cc_final: 0.7385 (tmm) REVERT: D 461 MET cc_start: 0.5008 (mpp) cc_final: 0.3686 (ptt) REVERT: D 767 ILE cc_start: 0.9599 (OUTLIER) cc_final: 0.9334 (tp) REVERT: D 844 MET cc_start: 0.8072 (ppp) cc_final: 0.7530 (ppp) REVERT: D 957 MET cc_start: 0.7774 (tpp) cc_final: 0.7123 (tpp) REVERT: D 987 MET cc_start: 0.7623 (tpp) cc_final: 0.7007 (tpp) REVERT: D 1237 MET cc_start: 0.8187 (tpp) cc_final: 0.7899 (tpp) REVERT: E 810 MET cc_start: 0.8073 (tmm) cc_final: 0.7775 (tmm) REVERT: F 168 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7702 (tpp80) outliers start: 66 outliers final: 39 residues processed: 244 average time/residue: 0.2471 time to fit residues: 105.8621 Evaluate side-chains 230 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1229 CYS Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain C residue 1313 THR Chi-restraints excluded: chain C residue 1338 THR Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 719 MET Chi-restraints excluded: chain D residue 767 ILE Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain E residue 807 MET Chi-restraints excluded: chain E residue 932 PHE Chi-restraints excluded: chain E residue 975 LEU Chi-restraints excluded: chain E residue 1020 TYR Chi-restraints excluded: chain F residue 145 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 94 optimal weight: 0.5980 chunk 252 optimal weight: 40.0000 chunk 226 optimal weight: 8.9990 chunk 343 optimal weight: 7.9990 chunk 472 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 203 optimal weight: 0.9980 chunk 393 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 245 optimal weight: 7.9990 chunk 475 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 GLN ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 855 GLN ** E 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.078701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.057997 restraints weight = 212758.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.058396 restraints weight = 163802.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.058628 restraints weight = 117776.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.058627 restraints weight = 105186.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.058745 restraints weight = 98774.889| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 44430 Z= 0.168 Angle : 0.554 13.386 60163 Z= 0.281 Chirality : 0.041 0.156 6735 Planarity : 0.003 0.045 7711 Dihedral : 4.579 24.455 6012 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.18 % Allowed : 12.21 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.12), residues: 5508 helix: 1.72 (0.10), residues: 2772 sheet: -0.67 (0.17), residues: 891 loop : -0.92 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 235 TYR 0.023 0.001 TYR E 495 PHE 0.016 0.001 PHE C 507 TRP 0.015 0.001 TRP A 105 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00381 (44409) covalent geometry : angle 0.53636 (60131) SS BOND : bond 0.00577 ( 1) SS BOND : angle 2.25216 ( 2) hydrogen bonds : bond 0.03379 ( 2464) hydrogen bonds : angle 4.45063 ( 7095) metal coordination : bond 0.01108 ( 20) metal coordination : angle 6.27553 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 1.771 Fit side-chains revert: symmetry clash REVERT: A 3 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8921 (p90) REVERT: B 442 CYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7177 (m) REVERT: B 702 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.7156 (t80) REVERT: B 1073 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8780 (t) REVERT: C 1 MET cc_start: 0.6289 (tmm) cc_final: 0.5213 (tmm) REVERT: C 100 MET cc_start: 0.0356 (tpt) cc_final: -0.0771 (ptm) REVERT: C 189 MET cc_start: 0.1054 (mmt) cc_final: 0.0734 (mmt) REVERT: C 708 MET cc_start: 0.8552 (mtp) cc_final: 0.8287 (mtp) REVERT: C 853 MET cc_start: 0.8330 (mpp) cc_final: 0.7606 (mpp) REVERT: C 1132 MET cc_start: 0.8117 (mtt) cc_final: 0.7798 (mtt) REVERT: D 406 MET cc_start: 0.8231 (tmm) cc_final: 0.7337 (tmm) REVERT: D 461 MET cc_start: 0.4993 (mpp) cc_final: 0.3688 (ptt) REVERT: D 694 MET cc_start: 0.8898 (tpp) cc_final: 0.8552 (tpp) REVERT: D 767 ILE cc_start: 0.9572 (OUTLIER) cc_final: 0.9299 (tp) REVERT: D 844 MET cc_start: 0.8079 (ppp) cc_final: 0.7499 (ppp) REVERT: D 962 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7711 (ppp) REVERT: D 1237 MET cc_start: 0.8188 (tpp) cc_final: 0.7924 (tpp) REVERT: E 810 MET cc_start: 0.8070 (tmm) cc_final: 0.7748 (tmm) REVERT: E 1067 MET cc_start: 0.5511 (pmm) cc_final: 0.4854 (pmm) REVERT: E 1086 MET cc_start: 0.7545 (mmm) cc_final: 0.7159 (tpp) REVERT: F 168 ARG cc_start: 0.8177 (mmm160) cc_final: 0.7897 (tpp80) REVERT: F 178 HIS cc_start: 0.8268 (OUTLIER) cc_final: 0.7660 (p90) outliers start: 54 outliers final: 34 residues processed: 232 average time/residue: 0.2445 time to fit residues: 99.9418 Evaluate side-chains 228 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1229 CYS Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 957 VAL Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain C residue 1313 THR Chi-restraints excluded: chain C residue 1338 THR Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 719 MET Chi-restraints excluded: chain D residue 767 ILE Chi-restraints excluded: chain D residue 962 MET Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain E residue 807 MET Chi-restraints excluded: chain E residue 975 LEU Chi-restraints excluded: chain E residue 1020 TYR Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 178 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 119 optimal weight: 0.6980 chunk 494 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 308 optimal weight: 8.9990 chunk 233 optimal weight: 20.0000 chunk 60 optimal weight: 0.5980 chunk 213 optimal weight: 0.2980 chunk 63 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 419 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 GLN ** E 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.079906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.060276 restraints weight = 214455.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.060317 restraints weight = 162013.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.060193 restraints weight = 134588.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.060271 restraints weight = 122268.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.060322 restraints weight = 112176.096| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 44430 Z= 0.171 Angle : 0.555 12.945 60163 Z= 0.281 Chirality : 0.041 0.158 6735 Planarity : 0.003 0.044 7711 Dihedral : 4.549 24.214 6012 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.23 % Allowed : 12.58 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.12), residues: 5508 helix: 1.76 (0.10), residues: 2771 sheet: -0.68 (0.17), residues: 896 loop : -0.91 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 148 TYR 0.020 0.001 TYR E 495 PHE 0.014 0.001 PHE B 307 TRP 0.014 0.001 TRP A 105 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00389 (44409) covalent geometry : angle 0.53818 (60131) SS BOND : bond 0.00598 ( 1) SS BOND : angle 2.21333 ( 2) hydrogen bonds : bond 0.03360 ( 2464) hydrogen bonds : angle 4.41622 ( 7095) metal coordination : bond 0.01130 ( 20) metal coordination : angle 6.14655 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 1.791 Fit side-chains revert: symmetry clash REVERT: A 3 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8919 (p90) REVERT: B 442 CYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7422 (m) REVERT: B 702 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7178 (t80) REVERT: B 1073 VAL cc_start: 0.9085 (OUTLIER) cc_final: 0.8789 (t) REVERT: C 1 MET cc_start: 0.6286 (tmm) cc_final: 0.5190 (tmm) REVERT: C 100 MET cc_start: 0.0681 (tpt) cc_final: 0.0043 (ptm) REVERT: C 189 MET cc_start: 0.1091 (mmt) cc_final: 0.0678 (mmt) REVERT: C 708 MET cc_start: 0.8568 (mtp) cc_final: 0.8283 (mtp) REVERT: C 822 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8355 (mm) REVERT: C 853 MET cc_start: 0.8333 (mpp) cc_final: 0.7667 (mpp) REVERT: D 406 MET cc_start: 0.8203 (tmm) cc_final: 0.7312 (tmm) REVERT: D 461 MET cc_start: 0.4981 (mpp) cc_final: 0.3675 (ptt) REVERT: D 694 MET cc_start: 0.8876 (tpp) cc_final: 0.8505 (tpp) REVERT: D 767 ILE cc_start: 0.9546 (OUTLIER) cc_final: 0.9289 (tp) REVERT: D 844 MET cc_start: 0.8089 (ppp) cc_final: 0.7510 (ppp) REVERT: D 958 MET cc_start: 0.8476 (ppp) cc_final: 0.8224 (ppp) REVERT: D 962 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7459 (ppp) REVERT: D 1163 MET cc_start: 0.6514 (ppp) cc_final: 0.6215 (ppp) REVERT: D 1237 MET cc_start: 0.8217 (tpp) cc_final: 0.7900 (tpp) REVERT: E 810 MET cc_start: 0.8104 (tmm) cc_final: 0.7767 (tmm) REVERT: E 1067 MET cc_start: 0.5554 (pmm) cc_final: 0.4867 (pmm) REVERT: E 1086 MET cc_start: 0.7736 (mmm) cc_final: 0.7234 (tpp) REVERT: F 168 ARG cc_start: 0.8211 (mmm160) cc_final: 0.7916 (tpp80) outliers start: 56 outliers final: 43 residues processed: 232 average time/residue: 0.2405 time to fit residues: 98.6731 Evaluate side-chains 237 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1229 CYS Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 822 ILE Chi-restraints excluded: chain C residue 957 VAL Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain C residue 1313 THR Chi-restraints excluded: chain C residue 1338 THR Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 719 MET Chi-restraints excluded: chain D residue 767 ILE Chi-restraints excluded: chain D residue 962 MET Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain E residue 807 MET Chi-restraints excluded: chain E residue 975 LEU Chi-restraints excluded: chain E residue 1020 TYR Chi-restraints excluded: chain F residue 145 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 69 optimal weight: 1.9990 chunk 448 optimal weight: 0.0870 chunk 303 optimal weight: 10.0000 chunk 305 optimal weight: 0.9980 chunk 297 optimal weight: 0.0010 chunk 140 optimal weight: 0.5980 chunk 419 optimal weight: 7.9990 chunk 346 optimal weight: 5.9990 chunk 406 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 234 optimal weight: 7.9990 overall best weight: 0.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 GLN C 481 HIS ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.083856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.066709 restraints weight = 202417.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.065941 restraints weight = 174827.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.066285 restraints weight = 150987.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.066386 restraints weight = 121945.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.066443 restraints weight = 113908.968| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 44430 Z= 0.112 Angle : 0.521 11.927 60163 Z= 0.266 Chirality : 0.040 0.166 6735 Planarity : 0.003 0.044 7711 Dihedral : 4.390 24.797 6012 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.03 % Allowed : 13.00 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.12), residues: 5508 helix: 1.83 (0.10), residues: 2778 sheet: -0.59 (0.17), residues: 892 loop : -0.87 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 868 TYR 0.015 0.001 TYR E 495 PHE 0.022 0.001 PHE B 851 TRP 0.014 0.001 TRP A 98 HIS 0.007 0.001 HIS B1092 Details of bonding type rmsd covalent geometry : bond 0.00247 (44409) covalent geometry : angle 0.50791 (60131) SS BOND : bond 0.00496 ( 1) SS BOND : angle 2.08522 ( 2) hydrogen bonds : bond 0.03135 ( 2464) hydrogen bonds : angle 4.26898 ( 7095) metal coordination : bond 0.00725 ( 20) metal coordination : angle 5.26918 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 1.779 Fit side-chains revert: symmetry clash REVERT: A 3 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8866 (p90) REVERT: B 442 CYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7261 (m) REVERT: B 702 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.7068 (t80) REVERT: B 1073 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8757 (t) REVERT: C 1 MET cc_start: 0.5367 (tmm) cc_final: 0.3995 (tmm) REVERT: C 189 MET cc_start: 0.1243 (mmt) cc_final: 0.0951 (mmt) REVERT: C 708 MET cc_start: 0.8428 (mtp) cc_final: 0.8193 (mtp) REVERT: C 822 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8356 (mm) REVERT: C 824 MET cc_start: 0.8756 (mmp) cc_final: 0.8501 (mmt) REVERT: C 853 MET cc_start: 0.8378 (mpp) cc_final: 0.7862 (mpp) REVERT: D 406 MET cc_start: 0.7929 (tmm) cc_final: 0.7122 (tmm) REVERT: D 461 MET cc_start: 0.4629 (mpp) cc_final: 0.3492 (ptt) REVERT: D 767 ILE cc_start: 0.9499 (OUTLIER) cc_final: 0.9243 (tp) REVERT: D 844 MET cc_start: 0.8012 (ppp) cc_final: 0.7474 (ppp) REVERT: D 958 MET cc_start: 0.8491 (ppp) cc_final: 0.8245 (ppp) REVERT: D 962 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7656 (ppp) REVERT: D 1163 MET cc_start: 0.6476 (ppp) cc_final: 0.6174 (ppp) REVERT: D 1237 MET cc_start: 0.8400 (tpp) cc_final: 0.8068 (tpp) REVERT: E 810 MET cc_start: 0.7889 (tmm) cc_final: 0.7584 (tmm) REVERT: E 1067 MET cc_start: 0.5551 (pmm) cc_final: 0.4875 (pmm) REVERT: E 1086 MET cc_start: 0.7853 (mmm) cc_final: 0.7290 (tpp) REVERT: F 168 ARG cc_start: 0.8180 (mmm160) cc_final: 0.7897 (tpp80) REVERT: F 178 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.7381 (p90) outliers start: 47 outliers final: 32 residues processed: 224 average time/residue: 0.2423 time to fit residues: 95.7758 Evaluate side-chains 225 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1229 CYS Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 822 ILE Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain C residue 1338 THR Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 719 MET Chi-restraints excluded: chain D residue 767 ILE Chi-restraints excluded: chain D residue 962 MET Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain E residue 807 MET Chi-restraints excluded: chain E residue 975 LEU Chi-restraints excluded: chain E residue 1020 TYR Chi-restraints excluded: chain F residue 178 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 521 optimal weight: 6.9990 chunk 283 optimal weight: 1.9990 chunk 326 optimal weight: 1.9990 chunk 369 optimal weight: 1.9990 chunk 290 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 518 optimal weight: 0.9990 chunk 390 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 923 HIS C 481 HIS ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.084803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.066861 restraints weight = 195262.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.066092 restraints weight = 193241.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.066451 restraints weight = 163189.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.066505 restraints weight = 129427.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.066628 restraints weight = 122768.637| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 44430 Z= 0.164 Angle : 0.548 12.121 60163 Z= 0.278 Chirality : 0.041 0.163 6735 Planarity : 0.003 0.044 7711 Dihedral : 4.437 23.969 6012 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.05 % Allowed : 12.95 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.12), residues: 5508 helix: 1.83 (0.10), residues: 2782 sheet: -0.55 (0.17), residues: 884 loop : -0.87 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 919 TYR 0.017 0.001 TYR E 495 PHE 0.018 0.001 PHE B 851 TRP 0.015 0.001 TRP A 105 HIS 0.010 0.001 HIS B1092 Details of bonding type rmsd covalent geometry : bond 0.00372 (44409) covalent geometry : angle 0.53315 (60131) SS BOND : bond 0.00542 ( 1) SS BOND : angle 2.20945 ( 2) hydrogen bonds : bond 0.03266 ( 2464) hydrogen bonds : angle 4.32339 ( 7095) metal coordination : bond 0.01030 ( 20) metal coordination : angle 5.60497 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11016 Ramachandran restraints generated. 5508 Oldfield, 0 Emsley, 5508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 1.765 Fit side-chains revert: symmetry clash REVERT: A 3 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8908 (p90) REVERT: B 442 CYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7330 (m) REVERT: B 702 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7200 (t80) REVERT: B 1073 VAL cc_start: 0.9076 (OUTLIER) cc_final: 0.8802 (t) REVERT: C 1 MET cc_start: 0.5474 (tmm) cc_final: 0.4416 (tmm) REVERT: C 189 MET cc_start: 0.0715 (mmt) cc_final: 0.0351 (mmt) REVERT: C 708 MET cc_start: 0.8475 (mtp) cc_final: 0.8222 (mtp) REVERT: C 822 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8386 (mm) REVERT: C 824 MET cc_start: 0.8719 (mmp) cc_final: 0.8473 (mmt) REVERT: C 853 MET cc_start: 0.8395 (mpp) cc_final: 0.7899 (mpp) REVERT: D 406 MET cc_start: 0.8026 (tmm) cc_final: 0.7575 (tmm) REVERT: D 461 MET cc_start: 0.4405 (mpp) cc_final: 0.3324 (ptt) REVERT: D 767 ILE cc_start: 0.9517 (OUTLIER) cc_final: 0.9250 (tp) REVERT: D 844 MET cc_start: 0.7992 (ppp) cc_final: 0.7461 (ppp) REVERT: D 958 MET cc_start: 0.8637 (ppp) cc_final: 0.8389 (ppp) REVERT: D 962 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7548 (ppp) REVERT: D 1163 MET cc_start: 0.6429 (ppp) cc_final: 0.6189 (ppp) REVERT: D 1237 MET cc_start: 0.8544 (tpp) cc_final: 0.8189 (tpp) REVERT: E 810 MET cc_start: 0.7914 (tmm) cc_final: 0.7602 (tmm) REVERT: E 1067 MET cc_start: 0.5603 (pmm) cc_final: 0.4889 (pmm) REVERT: F 168 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7875 (tpp80) REVERT: F 178 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7347 (p90) outliers start: 48 outliers final: 36 residues processed: 223 average time/residue: 0.2489 time to fit residues: 97.9011 Evaluate side-chains 229 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1229 CYS Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 822 ILE Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 1043 PHE Chi-restraints excluded: chain C residue 1338 THR Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 719 MET Chi-restraints excluded: chain D residue 767 ILE Chi-restraints excluded: chain D residue 962 MET Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain E residue 807 MET Chi-restraints excluded: chain E residue 975 LEU Chi-restraints excluded: chain E residue 1020 TYR Chi-restraints excluded: chain F residue 178 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 524 optimal weight: 2.9990 chunk 299 optimal weight: 5.9990 chunk 351 optimal weight: 2.9990 chunk 490 optimal weight: 3.9990 chunk 521 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 chunk 518 optimal weight: 2.9990 chunk 357 optimal weight: 9.9990 chunk 247 optimal weight: 0.0270 chunk 285 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN B 841 HIS C 238 ASN ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.082360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.065625 restraints weight = 211066.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.064253 restraints weight = 215032.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.064856 restraints weight = 224925.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.064786 restraints weight = 171996.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.065074 restraints weight = 145209.346| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 44430 Z= 0.227 Angle : 0.597 13.024 60163 Z= 0.302 Chirality : 0.043 0.165 6735 Planarity : 0.003 0.044 7711 Dihedral : 4.603 25.268 6012 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.10 % Allowed : 13.06 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.12), residues: 5508 helix: 1.77 (0.10), residues: 2775 sheet: -0.61 (0.17), residues: 887 loop : -0.91 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 148 TYR 0.030 0.002 TYR B 865 PHE 0.019 0.002 PHE B 307 TRP 0.016 0.002 TRP A 105 HIS 0.012 0.001 HIS B1092 Details of bonding type rmsd covalent geometry : bond 0.00516 (44409) covalent geometry : angle 0.57968 (60131) SS BOND : bond 0.00765 ( 1) SS BOND : angle 2.43316 ( 2) hydrogen bonds : bond 0.03500 ( 2464) hydrogen bonds : angle 4.46635 ( 7095) metal coordination : bond 0.01422 ( 20) metal coordination : angle 6.36981 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7210.59 seconds wall clock time: 126 minutes 21.66 seconds (7581.66 seconds total)