Starting phenix.real_space_refine on Thu Dec 26 07:10:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fgw_29073/12_2024/8fgw_29073.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fgw_29073/12_2024/8fgw_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_29073/12_2024/8fgw_29073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fgw_29073/12_2024/8fgw_29073.map" model { file = "/net/cci-nas-00/data/ceres_data/8fgw_29073/12_2024/8fgw_29073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fgw_29073/12_2024/8fgw_29073.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.026 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 13, 'ARG:plan': 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 9} 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: {'GLN:plan1': 7, 'ASP:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 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, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 4, 'ASP:plan': 2} 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, 'GLU:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4} 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: 23.07, per 1000 atoms: 0.53 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: 10.70 Conformation dependent library (CDL) restraints added in 6.0 seconds 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: 6.14 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: 21.58 Time building geometry restraints manager: 12.56 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: 10.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.590 Check model and map are aligned: 0.340 Set scattering table: 0.380 Process input model: 104.870 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.150 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.850 ------------------------------------------------------------------------------- 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 44409 Z= 0.199 Angle : 0.538 8.212 60131 Z= 0.290 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 : 10.57 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (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 TRP 0.045 0.001 TRP C1289 HIS 0.016 0.001 HIS B1017 PHE 0.020 0.001 PHE D 41 TYR 0.032 0.001 TYR B 597 ARG 0.004 0.000 ARG F 168 *********************** 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 : 5.202 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: 0.5309 time to fit residues: 188.7366 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 : 5.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 468 optimal weight: 3.9990 chunk 420 optimal weight: 4.9990 chunk 233 optimal weight: 20.0000 chunk 143 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 chunk 224 optimal weight: 8.9990 chunk 435 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 264 optimal weight: 0.7980 chunk 323 optimal weight: 0.6980 chunk 504 optimal weight: 20.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 HIS A 527 GLN A 923 HIS ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 GLN D 879 GLN E 428 ASN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 44409 Z= 0.359 Angle : 0.598 10.828 60131 Z= 0.314 Chirality : 0.044 0.166 6735 Planarity : 0.004 0.045 7711 Dihedral : 4.736 27.172 6012 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.20 % Allowed : 5.24 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.12), residues: 5508 helix: 1.57 (0.10), residues: 2767 sheet: -0.69 (0.17), residues: 885 loop : -0.95 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C1289 HIS 0.013 0.001 HIS B1017 PHE 0.019 0.002 PHE B 307 TYR 0.020 0.002 TYR B 597 ARG 0.007 0.000 ARG A 919 *********************** 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 199 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 5.364 Fit side-chains revert: symmetry clash REVERT: A 871 MET cc_start: 0.8492 (mpp) cc_final: 0.8261 (mpp) REVERT: C 1 MET cc_start: 0.4900 (tmm) cc_final: 0.3635 (tmm) REVERT: C 100 MET cc_start: -0.0645 (tpt) cc_final: -0.1573 (ptm) REVERT: C 1218 MET cc_start: 0.6862 (mtt) cc_final: 0.6557 (mtt) REVERT: D 406 MET cc_start: 0.7668 (tmm) cc_final: 0.7154 (tmm) REVERT: D 461 MET cc_start: 0.3921 (mpp) cc_final: 0.3319 (ptp) REVERT: D 694 MET cc_start: 0.8928 (tpp) cc_final: 0.8615 (tpp) REVERT: D 987 MET cc_start: 0.7505 (tpp) cc_final: 0.7236 (tpp) REVERT: D 1237 MET cc_start: 0.7954 (tpp) cc_final: 0.7704 (tpp) outliers start: 9 outliers final: 2 residues processed: 192 average time/residue: 0.5411 time to fit residues: 182.5833 Evaluate side-chains 189 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 4.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain D residue 160 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 280 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 419 optimal weight: 7.9990 chunk 343 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 504 optimal weight: 20.0000 chunk 545 optimal weight: 10.0000 chunk 449 optimal weight: 7.9990 chunk 500 optimal weight: 30.0000 chunk 172 optimal weight: 1.9990 chunk 405 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 896 ASN B 513 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 968 GLN ** E 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 44409 Z= 0.504 Angle : 0.663 11.741 60131 Z= 0.347 Chirality : 0.046 0.186 6735 Planarity : 0.004 0.048 7711 Dihedral : 4.993 25.736 6012 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.61 % Allowed : 8.50 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.11), residues: 5508 helix: 1.38 (0.10), residues: 2758 sheet: -0.77 (0.17), residues: 877 loop : -1.07 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 105 HIS 0.013 0.002 HIS A 214 PHE 0.027 0.002 PHE B 307 TYR 0.026 0.002 TYR D 79 ARG 0.008 0.001 ARG A 148 *********************** 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 224 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 5.130 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.4975 (tmm) cc_final: 0.3385 (tmm) REVERT: C 100 MET cc_start: -0.0431 (tpt) cc_final: -0.1392 (ptm) REVERT: C 1218 MET cc_start: 0.6993 (mtt) cc_final: 0.6787 (mtt) REVERT: D 406 MET cc_start: 0.7687 (tmm) cc_final: 0.7135 (tmm) REVERT: D 461 MET cc_start: 0.4242 (mpp) cc_final: 0.3673 (ptt) REVERT: D 694 MET cc_start: 0.8820 (tpp) cc_final: 0.8579 (tpp) REVERT: D 987 MET cc_start: 0.7743 (tpp) cc_final: 0.7535 (tpp) REVERT: E 1067 MET cc_start: 0.6600 (pmm) cc_final: 0.6054 (pmm) outliers start: 28 outliers final: 10 residues processed: 216 average time/residue: 0.5476 time to fit residues: 208.3092 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 : 5.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 257 VAL 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 D residue 160 TYR Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain E residue 812 VAL Chi-restraints excluded: chain E residue 932 PHE 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 498 optimal weight: 2.9990 chunk 379 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 240 optimal weight: 7.9990 chunk 339 optimal weight: 3.9990 chunk 506 optimal weight: 20.0000 chunk 536 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 chunk 480 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 923 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 44409 Z= 0.286 Angle : 0.553 9.189 60131 Z= 0.291 Chirality : 0.042 0.184 6735 Planarity : 0.003 0.046 7711 Dihedral : 4.762 24.883 6012 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.83 % Allowed : 10.10 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.12), residues: 5508 helix: 1.55 (0.10), residues: 2764 sheet: -0.72 (0.17), residues: 890 loop : -0.99 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 105 HIS 0.009 0.001 HIS A 241 PHE 0.016 0.001 PHE B 307 TYR 0.017 0.001 TYR B 90 ARG 0.003 0.000 ARG B 647 *********************** 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 230 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 5.089 Fit side-chains revert: symmetry clash REVERT: B 702 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7390 (t80) REVERT: C 1 MET cc_start: 0.5523 (tmm) cc_final: 0.3827 (tmm) REVERT: C 100 MET cc_start: -0.0695 (tpt) cc_final: -0.1471 (ptm) REVERT: C 1218 MET cc_start: 0.6969 (mtt) cc_final: 0.6725 (mtt) REVERT: D 406 MET cc_start: 0.7650 (tmm) cc_final: 0.7080 (tmm) REVERT: D 461 MET cc_start: 0.4455 (mpp) cc_final: 0.3305 (ptp) REVERT: D 694 MET cc_start: 0.8774 (tpp) cc_final: 0.8519 (tpp) REVERT: D 767 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9166 (tp) REVERT: D 987 MET cc_start: 0.7659 (tpp) cc_final: 0.7450 (tpp) REVERT: E 1067 MET cc_start: 0.7003 (pmm) cc_final: 0.6527 (pmm) outliers start: 38 outliers final: 18 residues processed: 219 average time/residue: 0.5335 time to fit residues: 204.6334 Evaluate side-chains 209 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 5.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 LEU 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 702 TYR 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 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 Chi-restraints excluded: chain F residue 145 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 446 optimal weight: 1.9990 chunk 304 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 399 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 457 optimal weight: 0.0020 chunk 370 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 273 optimal weight: 0.7980 chunk 481 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 923 HIS ** B1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 809 HIS C1139 GLN ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 855 GLN D1062 ASN ** E 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 44409 Z= 0.288 Angle : 0.551 10.661 60131 Z= 0.289 Chirality : 0.042 0.179 6735 Planarity : 0.003 0.045 7711 Dihedral : 4.690 24.961 6012 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.31 % Allowed : 10.74 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.12), residues: 5508 helix: 1.62 (0.10), residues: 2764 sheet: -0.70 (0.17), residues: 894 loop : -0.96 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 105 HIS 0.008 0.001 HIS A 241 PHE 0.016 0.001 PHE D 41 TYR 0.026 0.001 TYR D 79 ARG 0.003 0.000 ARG B 647 *********************** 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 251 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 191 time to evaluate : 4.490 Fit side-chains revert: symmetry clash REVERT: A 3 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8826 (p90) REVERT: B 702 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7297 (t80) REVERT: C 1 MET cc_start: 0.5468 (tmm) cc_final: 0.3711 (tmm) REVERT: C 100 MET cc_start: -0.1045 (tpt) cc_final: -0.1329 (ptm) REVERT: D 406 MET cc_start: 0.7637 (tmm) cc_final: 0.7066 (tmm) REVERT: D 461 MET cc_start: 0.4388 (mpp) cc_final: 0.3331 (ptp) REVERT: D 694 MET cc_start: 0.8740 (tpp) cc_final: 0.8478 (tpp) REVERT: D 767 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9176 (tp) REVERT: E 1086 MET cc_start: 0.7680 (mmm) cc_final: 0.7351 (tpp) outliers start: 60 outliers final: 27 residues processed: 240 average time/residue: 0.5558 time to fit residues: 235.9624 Evaluate side-chains 218 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 5.005 ------------------------------------------------------------------------------- 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 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 917 LEU 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 641 VAL Chi-restraints excluded: chain B residue 702 TYR 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 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 534 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 180 optimal weight: 4.9990 chunk 483 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 314 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 536 optimal weight: 3.9990 chunk 445 optimal weight: 4.9990 chunk 248 optimal weight: 50.0000 chunk 44 optimal weight: 7.9990 chunk 177 optimal weight: 0.5980 chunk 281 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 931 GLN D 976 GLN E 905 HIS ** E 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 44409 Z= 0.319 Angle : 0.569 11.933 60131 Z= 0.297 Chirality : 0.042 0.228 6735 Planarity : 0.004 0.046 7711 Dihedral : 4.701 25.209 6012 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.36 % Allowed : 11.31 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.12), residues: 5508 helix: 1.61 (0.10), residues: 2770 sheet: -0.68 (0.17), residues: 882 loop : -0.97 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 105 HIS 0.008 0.001 HIS A 241 PHE 0.018 0.002 PHE B 307 TYR 0.024 0.001 TYR D 79 ARG 0.008 0.000 ARG A 919 *********************** 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: 62 poor density : 193 time to evaluate : 4.834 Fit side-chains revert: symmetry clash REVERT: A 3 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8906 (p90) REVERT: B 702 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7384 (t80) REVERT: C 1 MET cc_start: 0.5565 (tmm) cc_final: 0.3794 (tmm) REVERT: C 189 MET cc_start: 0.1000 (OUTLIER) cc_final: 0.0528 (mmt) REVERT: C 1218 MET cc_start: 0.7036 (mtt) cc_final: 0.6656 (mtt) REVERT: C 1237 MET cc_start: 0.7952 (mtt) cc_final: 0.7738 (mtm) REVERT: D 406 MET cc_start: 0.7582 (tmm) cc_final: 0.6999 (tmm) REVERT: D 461 MET cc_start: 0.4386 (mpp) cc_final: 0.3359 (ptt) REVERT: D 694 MET cc_start: 0.8758 (tpp) cc_final: 0.8453 (tpp) REVERT: D 987 MET cc_start: 0.7297 (tpp) cc_final: 0.7086 (tpp) REVERT: D 1237 MET cc_start: 0.7883 (tpp) cc_final: 0.7610 (tpp) REVERT: F 178 HIS cc_start: 0.7579 (OUTLIER) cc_final: 0.7182 (p90) outliers start: 62 outliers final: 35 residues processed: 242 average time/residue: 0.5106 time to fit residues: 217.3681 Evaluate side-chains 228 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 5.237 ------------------------------------------------------------------------------- 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 67 LEU 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 447 GLU 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 548 LEU Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 1092 HIS Chi-restraints excluded: chain B residue 1229 CYS Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 568 MET 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 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 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 Chi-restraints excluded: chain F residue 178 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 517 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 305 optimal weight: 9.9990 chunk 392 optimal weight: 0.6980 chunk 303 optimal weight: 0.1980 chunk 452 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 chunk 534 optimal weight: 2.9990 chunk 334 optimal weight: 2.9990 chunk 326 optimal weight: 8.9990 chunk 246 optimal weight: 40.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 HIS ** C 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 44409 Z= 0.333 Angle : 0.578 11.178 60131 Z= 0.301 Chirality : 0.043 0.212 6735 Planarity : 0.004 0.046 7711 Dihedral : 4.718 25.233 6012 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.38 % Allowed : 11.83 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.12), residues: 5508 helix: 1.59 (0.10), residues: 2770 sheet: -0.72 (0.17), residues: 889 loop : -0.97 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 105 HIS 0.008 0.001 HIS A 241 PHE 0.019 0.002 PHE B 307 TYR 0.025 0.002 TYR D 79 ARG 0.004 0.000 ARG A 919 *********************** 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 255 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 192 time to evaluate : 5.192 Fit side-chains REVERT: A 3 PHE cc_start: 0.9223 (OUTLIER) cc_final: 0.8902 (p90) REVERT: A 148 ARG cc_start: 0.5888 (ttp80) cc_final: 0.5495 (ttp80) REVERT: B 702 TYR cc_start: 0.8210 (OUTLIER) cc_final: 0.7353 (t80) REVERT: C 1 MET cc_start: 0.5568 (tmm) cc_final: 0.3797 (tmm) REVERT: C 1218 MET cc_start: 0.7076 (mtt) cc_final: 0.6820 (mtt) REVERT: D 406 MET cc_start: 0.7588 (tmm) cc_final: 0.7014 (tmm) REVERT: D 461 MET cc_start: 0.4262 (mpp) cc_final: 0.3282 (ptt) REVERT: D 694 MET cc_start: 0.8750 (tpp) cc_final: 0.8439 (tpp) REVERT: D 987 MET cc_start: 0.7372 (tpp) cc_final: 0.6777 (tpp) REVERT: D 1237 MET cc_start: 0.7889 (tpp) cc_final: 0.7610 (tpp) REVERT: E 1067 MET cc_start: 0.6274 (pmm) cc_final: 0.5501 (pmm) REVERT: F 178 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.7190 (p90) outliers start: 63 outliers final: 44 residues processed: 240 average time/residue: 0.5477 time to fit residues: 232.6537 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 : 5.006 ------------------------------------------------------------------------------- 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 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 175 MET 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 349 THR Chi-restraints excluded: chain A residue 447 GLU 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 585 VAL Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 702 TYR 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 400 LEU Chi-restraints excluded: chain C residue 502 ILE 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 1205 ASP Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 514 LEU 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 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 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 330 optimal weight: 5.9990 chunk 213 optimal weight: 0.7980 chunk 319 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 103 optimal weight: 10.0000 chunk 340 optimal weight: 0.9990 chunk 364 optimal weight: 10.0000 chunk 264 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 420 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** C 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 GLN E 855 GLN E 905 HIS ** E 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 44409 Z= 0.185 Angle : 0.527 18.197 60131 Z= 0.274 Chirality : 0.041 0.190 6735 Planarity : 0.003 0.044 7711 Dihedral : 4.502 24.059 6012 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.94 % Allowed : 12.56 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.12), residues: 5508 helix: 1.75 (0.10), residues: 2772 sheet: -0.60 (0.17), residues: 891 loop : -0.88 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 105 HIS 0.006 0.001 HIS A 241 PHE 0.014 0.001 PHE C 187 TYR 0.020 0.001 TYR B 865 ARG 0.004 0.000 ARG A 919 *********************** 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 234 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 5.141 Fit side-chains REVERT: A 3 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8882 (p90) REVERT: B 702 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7277 (t80) REVERT: C 1 MET cc_start: 0.5729 (tmm) cc_final: 0.4668 (tmm) REVERT: C 1218 MET cc_start: 0.7056 (mtt) cc_final: 0.6747 (mtt) REVERT: C 1237 MET cc_start: 0.7930 (mtt) cc_final: 0.7670 (mtm) REVERT: D 83 MET cc_start: 0.5177 (pmm) cc_final: 0.4355 (mmp) REVERT: D 406 MET cc_start: 0.7507 (tmm) cc_final: 0.6909 (tmm) REVERT: D 461 MET cc_start: 0.4306 (mpp) cc_final: 0.3282 (ptt) REVERT: D 694 MET cc_start: 0.8633 (tpp) cc_final: 0.8382 (tpp) REVERT: D 1237 MET cc_start: 0.7818 (tpp) cc_final: 0.7539 (tpp) REVERT: E 606 MET cc_start: 0.4845 (tmm) cc_final: 0.4512 (tmm) REVERT: E 855 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7617 (mp-120) REVERT: E 1067 MET cc_start: 0.5753 (pmm) cc_final: 0.5123 (pmm) REVERT: F 178 HIS cc_start: 0.7515 (OUTLIER) cc_final: 0.7069 (p90) outliers start: 43 outliers final: 32 residues processed: 225 average time/residue: 0.5250 time to fit residues: 211.8224 Evaluate side-chains 221 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 5.600 ------------------------------------------------------------------------------- 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 175 MET 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 320 LEU Chi-restraints excluded: chain A residue 917 LEU 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 641 VAL Chi-restraints excluded: chain B residue 702 TYR 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 400 LEU Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 975 VAL 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 1205 ASP Chi-restraints excluded: chain D residue 1277 LEU 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 855 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 486 optimal weight: 2.9990 chunk 512 optimal weight: 20.0000 chunk 467 optimal weight: 1.9990 chunk 498 optimal weight: 0.0770 chunk 300 optimal weight: 0.6980 chunk 217 optimal weight: 0.7980 chunk 391 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 450 optimal weight: 0.6980 chunk 471 optimal weight: 7.9990 chunk 496 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 923 HIS ** C 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 44409 Z= 0.171 Angle : 0.523 13.899 60131 Z= 0.271 Chirality : 0.041 0.216 6735 Planarity : 0.003 0.042 7711 Dihedral : 4.418 23.566 6012 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.94 % Allowed : 12.80 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.12), residues: 5508 helix: 1.79 (0.10), residues: 2779 sheet: -0.57 (0.17), residues: 897 loop : -0.85 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 105 HIS 0.009 0.001 HIS A 923 PHE 0.013 0.001 PHE D 41 TYR 0.023 0.001 TYR E 495 ARG 0.004 0.000 ARG A 919 *********************** 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 230 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 5.528 Fit side-chains REVERT: A 3 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8872 (p90) REVERT: B 702 TYR cc_start: 0.8178 (OUTLIER) cc_final: 0.7233 (t80) REVERT: C 1 MET cc_start: 0.5731 (tmm) cc_final: 0.4961 (tmm) REVERT: C 100 MET cc_start: 0.1009 (ppp) cc_final: 0.0788 (ppp) REVERT: C 824 MET cc_start: 0.8190 (mmp) cc_final: 0.7942 (mmt) REVERT: C 1218 MET cc_start: 0.7095 (mtt) cc_final: 0.6815 (mtt) REVERT: C 1237 MET cc_start: 0.7907 (mtt) cc_final: 0.7644 (mtm) REVERT: D 83 MET cc_start: 0.4532 (pmm) cc_final: 0.3573 (mmp) REVERT: D 406 MET cc_start: 0.7481 (tmm) cc_final: 0.6884 (tmm) REVERT: D 461 MET cc_start: 0.4199 (mpp) cc_final: 0.3201 (ptt) REVERT: D 1237 MET cc_start: 0.7799 (tpp) cc_final: 0.7524 (tpp) REVERT: E 1067 MET cc_start: 0.5740 (pmm) cc_final: 0.5080 (pmm) REVERT: F 178 HIS cc_start: 0.7519 (OUTLIER) cc_final: 0.7061 (p90) outliers start: 43 outliers final: 33 residues processed: 220 average time/residue: 0.5154 time to fit residues: 203.8139 Evaluate side-chains 220 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 5.085 ------------------------------------------------------------------------------- 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 175 MET Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 198 LEU 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 917 LEU 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 641 VAL Chi-restraints excluded: chain B residue 702 TYR 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 400 LEU 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 1338 THR Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 719 MET Chi-restraints excluded: chain D residue 1205 ASP Chi-restraints excluded: chain D residue 1277 LEU 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 327 optimal weight: 4.9990 chunk 527 optimal weight: 3.9990 chunk 321 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 366 optimal weight: 10.0000 chunk 552 optimal weight: 0.9990 chunk 508 optimal weight: 8.9990 chunk 440 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 340 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 ASN ** E 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 44409 Z= 0.333 Angle : 0.584 11.728 60131 Z= 0.301 Chirality : 0.043 0.166 6735 Planarity : 0.003 0.044 7711 Dihedral : 4.588 24.755 6012 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.99 % Allowed : 12.78 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.12), residues: 5508 helix: 1.73 (0.10), residues: 2776 sheet: -0.61 (0.17), residues: 891 loop : -0.90 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D1258 HIS 0.010 0.001 HIS B1092 PHE 0.019 0.002 PHE B 307 TYR 0.026 0.002 TYR E 495 ARG 0.005 0.000 ARG C 929 ********************** 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 233 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 5.288 Fit side-chains REVERT: A 3 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8886 (p90) REVERT: B 702 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7298 (t80) REVERT: C 1 MET cc_start: 0.5832 (tmm) cc_final: 0.4767 (tmm) REVERT: C 189 MET cc_start: 0.0616 (mmt) cc_final: -0.0129 (mmt) REVERT: C 246 MET cc_start: 0.6270 (ttp) cc_final: 0.5819 (ppp) REVERT: C 824 MET cc_start: 0.8253 (mmp) cc_final: 0.8018 (mmt) REVERT: C 1218 MET cc_start: 0.7098 (mtt) cc_final: 0.6789 (mtt) REVERT: C 1237 MET cc_start: 0.7955 (mtt) cc_final: 0.7683 (mtm) REVERT: D 83 MET cc_start: 0.4681 (pmm) cc_final: 0.3587 (mmp) REVERT: D 406 MET cc_start: 0.7525 (tmm) cc_final: 0.7238 (tmm) REVERT: D 461 MET cc_start: 0.4250 (mpp) cc_final: 0.3232 (ptt) REVERT: D 1237 MET cc_start: 0.7902 (tpp) cc_final: 0.7593 (tpp) REVERT: E 1067 MET cc_start: 0.5798 (pmm) cc_final: 0.5166 (pmm) REVERT: F 178 HIS cc_start: 0.7590 (OUTLIER) cc_final: 0.7144 (p90) outliers start: 45 outliers final: 34 residues processed: 222 average time/residue: 0.5376 time to fit residues: 211.9662 Evaluate side-chains 223 residues out of total 4821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 5.336 ------------------------------------------------------------------------------- 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 175 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 349 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 917 LEU 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 641 VAL Chi-restraints excluded: chain B residue 702 TYR 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 400 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 568 MET 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 1205 ASP Chi-restraints excluded: chain D residue 1277 LEU 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 349 optimal weight: 0.0050 chunk 469 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 405 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 440 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 452 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 923 HIS C 238 ASN ** C 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3716 r_free = 0.3716 target = 0.083494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.066857 restraints weight = 204805.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.065458 restraints weight = 190035.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.065783 restraints weight = 177821.488| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 44409 Z= 0.178 Angle : 0.526 11.058 60131 Z= 0.273 Chirality : 0.041 0.162 6735 Planarity : 0.003 0.043 7711 Dihedral : 4.443 23.846 6012 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.88 % Allowed : 12.91 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.12), residues: 5508 helix: 1.79 (0.10), residues: 2785 sheet: -0.55 (0.17), residues: 897 loop : -0.85 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 105 HIS 0.010 0.001 HIS A 923 PHE 0.012 0.001 PHE B 878 TYR 0.019 0.001 TYR E 495 ARG 0.004 0.000 ARG A 919 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6824.67 seconds wall clock time: 130 minutes 31.84 seconds (7831.84 seconds total)