Starting phenix.real_space_refine on Wed Sep 25 21:48:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdt_33152/09_2024/7xdt_33152_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdt_33152/09_2024/7xdt_33152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdt_33152/09_2024/7xdt_33152.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdt_33152/09_2024/7xdt_33152.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdt_33152/09_2024/7xdt_33152_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdt_33152/09_2024/7xdt_33152_neut.cif" } resolution = 3.31 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= 0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 18700 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 200 5.16 5 C 26780 2.51 5 N 7230 2.21 5 O 7780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 41990 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4199 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 513} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 9.65, per 1000 atoms: 0.23 Number of scatterers: 41990 At special positions: 0 Unit cell: (157.29, 149.8, 210.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 200 16.00 O 7780 8.00 N 7230 7.00 C 26780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.72 Conformation dependent library (CDL) restraints added in 4.0 seconds 10420 Ramachandran restraints generated. 5210 Oldfield, 0 Emsley, 5210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10180 Finding SS restraints... Secondary structure from input PDB file: 340 helices and 0 sheets defined 84.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 859 through 875 Processing helix chain 'A' and resid 885 through 890 removed outlier: 4.108A pdb=" N GLU A 889 " --> pdb=" O ALA A 885 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG A 890 " --> pdb=" O ASP A 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 885 through 890' Processing helix chain 'A' and resid 891 through 896 Processing helix chain 'A' and resid 898 through 913 removed outlier: 3.708A pdb=" N LEU A 902 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 903 " --> pdb=" O ARG A 899 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG A 904 " --> pdb=" O ALA A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 930 removed outlier: 3.989A pdb=" N MET A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 927 " --> pdb=" O HIS A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 942 removed outlier: 3.657A pdb=" N ALA A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 942 " --> pdb=" O THR A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 952 removed outlier: 3.860A pdb=" N MET A 952 " --> pdb=" O ASN A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 957 removed outlier: 4.340A pdb=" N ALA A 956 " --> pdb=" O MET A 952 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY A 957 " --> pdb=" O ALA A 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 952 through 957' Processing helix chain 'A' and resid 957 through 975 removed outlier: 3.676A pdb=" N LYS A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 988 removed outlier: 3.595A pdb=" N ILE A 988 " --> pdb=" O HIS A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1001 removed outlier: 3.693A pdb=" N GLU A 996 " --> pdb=" O TYR A 992 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 997 " --> pdb=" O GLU A 993 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 998 " --> pdb=" O ALA A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1015 removed outlier: 3.704A pdb=" N ALA A1007 " --> pdb=" O PHE A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1037 removed outlier: 4.586A pdb=" N LYS A1023 " --> pdb=" O ASP A1019 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP A1024 " --> pdb=" O PRO A1020 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU A1025 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG A1035 " --> pdb=" O THR A1031 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A1036 " --> pdb=" O VAL A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1052 through 1061 removed outlier: 3.789A pdb=" N ALA A1056 " --> pdb=" O ALA A1052 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS A1057 " --> pdb=" O TYR A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1078 Processing helix chain 'A' and resid 1080 through 1096 removed outlier: 3.918A pdb=" N GLN A1093 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A1094 " --> pdb=" O ARG A1090 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A1096 " --> pdb=" O ALA A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1108 Processing helix chain 'A' and resid 1114 through 1130 Processing helix chain 'A' and resid 1156 through 1169 removed outlier: 4.045A pdb=" N THR A1161 " --> pdb=" O VAL A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1182 removed outlier: 3.795A pdb=" N GLN A1177 " --> pdb=" O PRO A1173 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU A1178 " --> pdb=" O GLU A1174 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A1180 " --> pdb=" O TYR A1176 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A1182 " --> pdb=" O GLU A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1218 removed outlier: 3.834A pdb=" N LEU A1200 " --> pdb=" O PRO A1196 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLN A1216 " --> pdb=" O VAL A1212 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N MET A1217 " --> pdb=" O LEU A1213 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA A1218 " --> pdb=" O SER A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1237 removed outlier: 4.397A pdb=" N ALA A1223 " --> pdb=" O SER A1219 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A1237 " --> pdb=" O ARG A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1251 removed outlier: 3.581A pdb=" N TYR A1247 " --> pdb=" O MET A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1261 removed outlier: 3.520A pdb=" N ASP A1260 " --> pdb=" O ASP A1256 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS A1261 " --> pdb=" O HIS A1257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1256 through 1261' Processing helix chain 'A' and resid 1269 through 1293 removed outlier: 3.902A pdb=" N PHE A1273 " --> pdb=" O ALA A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1354 Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 4.041A pdb=" N GLU A1358 " --> pdb=" O THR A1355 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A1360 " --> pdb=" O LYS A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1391 removed outlier: 3.819A pdb=" N SER A1366 " --> pdb=" O GLU A1362 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU A1367 " --> pdb=" O LYS A1363 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A1368 " --> pdb=" O HIS A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1448 removed outlier: 3.587A pdb=" N GLN A1443 " --> pdb=" O THR A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1455 removed outlier: 3.592A pdb=" N LYS A1453 " --> pdb=" O PRO A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1459 through 1473 Processing helix chain 'A' and resid 1480 through 1493 removed outlier: 4.168A pdb=" N GLN A1484 " --> pdb=" O GLN A1480 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 859 through 875 Processing helix chain 'B' and resid 885 through 890 removed outlier: 4.108A pdb=" N GLU B 889 " --> pdb=" O ALA B 885 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG B 890 " --> pdb=" O ASP B 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 885 through 890' Processing helix chain 'B' and resid 891 through 896 Processing helix chain 'B' and resid 898 through 913 removed outlier: 3.709A pdb=" N LEU B 902 " --> pdb=" O ASP B 898 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR B 903 " --> pdb=" O ARG B 899 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG B 904 " --> pdb=" O ALA B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 930 removed outlier: 3.989A pdb=" N MET B 926 " --> pdb=" O PHE B 922 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 927 " --> pdb=" O HIS B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 942 removed outlier: 3.658A pdb=" N ALA B 940 " --> pdb=" O LEU B 936 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 941 " --> pdb=" O GLN B 937 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 942 " --> pdb=" O THR B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 952 removed outlier: 3.860A pdb=" N MET B 952 " --> pdb=" O ASN B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 957 removed outlier: 4.339A pdb=" N ALA B 956 " --> pdb=" O MET B 952 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 952 through 957' Processing helix chain 'B' and resid 957 through 975 removed outlier: 3.675A pdb=" N LYS B 970 " --> pdb=" O GLU B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 988 removed outlier: 3.595A pdb=" N ILE B 988 " --> pdb=" O HIS B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1001 removed outlier: 3.693A pdb=" N GLU B 996 " --> pdb=" O TYR B 992 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 997 " --> pdb=" O GLU B 993 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU B 998 " --> pdb=" O ALA B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1015 removed outlier: 3.704A pdb=" N ALA B1007 " --> pdb=" O PHE B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1037 removed outlier: 4.586A pdb=" N LYS B1023 " --> pdb=" O ASP B1019 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP B1024 " --> pdb=" O PRO B1020 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU B1025 " --> pdb=" O VAL B1021 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG B1035 " --> pdb=" O THR B1031 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP B1036 " --> pdb=" O VAL B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1049 Processing helix chain 'B' and resid 1052 through 1061 removed outlier: 3.789A pdb=" N ALA B1056 " --> pdb=" O ALA B1052 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS B1057 " --> pdb=" O TYR B1053 " (cutoff:3.500A) Processing helix chain 'B' and resid 1064 through 1078 Processing helix chain 'B' and resid 1080 through 1096 removed outlier: 3.919A pdb=" N GLN B1093 " --> pdb=" O LEU B1089 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B1094 " --> pdb=" O ARG B1090 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B1096 " --> pdb=" O ALA B1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 1101 through 1108 Processing helix chain 'B' and resid 1114 through 1130 Processing helix chain 'B' and resid 1156 through 1169 removed outlier: 4.044A pdb=" N THR B1161 " --> pdb=" O VAL B1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 1172 through 1182 removed outlier: 3.796A pdb=" N GLN B1177 " --> pdb=" O PRO B1173 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU B1178 " --> pdb=" O GLU B1174 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B1180 " --> pdb=" O TYR B1176 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B1182 " --> pdb=" O GLU B1178 " (cutoff:3.500A) Processing helix chain 'B' and resid 1196 through 1218 removed outlier: 3.835A pdb=" N LEU B1200 " --> pdb=" O PRO B1196 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLN B1216 " --> pdb=" O VAL B1212 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N MET B1217 " --> pdb=" O LEU B1213 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B1218 " --> pdb=" O SER B1214 " (cutoff:3.500A) Processing helix chain 'B' and resid 1219 through 1237 removed outlier: 4.398A pdb=" N ALA B1223 " --> pdb=" O SER B1219 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B1237 " --> pdb=" O ARG B1233 " (cutoff:3.500A) Processing helix chain 'B' and resid 1242 through 1251 removed outlier: 3.582A pdb=" N TYR B1247 " --> pdb=" O MET B1243 " (cutoff:3.500A) Processing helix chain 'B' and resid 1256 through 1261 removed outlier: 3.520A pdb=" N ASP B1260 " --> pdb=" O ASP B1256 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS B1261 " --> pdb=" O HIS B1257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1256 through 1261' Processing helix chain 'B' and resid 1269 through 1293 removed outlier: 3.903A pdb=" N PHE B1273 " --> pdb=" O ALA B1269 " (cutoff:3.500A) Processing helix chain 'B' and resid 1349 through 1354 Processing helix chain 'B' and resid 1355 through 1360 removed outlier: 4.042A pdb=" N GLU B1358 " --> pdb=" O THR B1355 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B1360 " --> pdb=" O LYS B1357 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1391 removed outlier: 3.819A pdb=" N SER B1366 " --> pdb=" O GLU B1362 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU B1367 " --> pdb=" O LYS B1363 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN B1368 " --> pdb=" O HIS B1364 " (cutoff:3.500A) Processing helix chain 'B' and resid 1431 through 1448 removed outlier: 3.587A pdb=" N GLN B1443 " --> pdb=" O THR B1439 " (cutoff:3.500A) Processing helix chain 'B' and resid 1449 through 1455 removed outlier: 3.592A pdb=" N LYS B1453 " --> pdb=" O PRO B1449 " (cutoff:3.500A) Processing helix chain 'B' and resid 1459 through 1473 Processing helix chain 'B' and resid 1480 through 1493 removed outlier: 4.169A pdb=" N GLN B1484 " --> pdb=" O GLN B1480 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 859 through 875 Processing helix chain 'C' and resid 885 through 890 removed outlier: 4.107A pdb=" N GLU C 889 " --> pdb=" O ALA C 885 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG C 890 " --> pdb=" O ASP C 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 885 through 890' Processing helix chain 'C' and resid 891 through 896 Processing helix chain 'C' and resid 898 through 913 removed outlier: 3.708A pdb=" N LEU C 902 " --> pdb=" O ASP C 898 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR C 903 " --> pdb=" O ARG C 899 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG C 904 " --> pdb=" O ALA C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 930 removed outlier: 3.989A pdb=" N MET C 926 " --> pdb=" O PHE C 922 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU C 927 " --> pdb=" O HIS C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 942 removed outlier: 3.657A pdb=" N ALA C 940 " --> pdb=" O LEU C 936 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU C 941 " --> pdb=" O GLN C 937 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 942 " --> pdb=" O THR C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 952 removed outlier: 3.860A pdb=" N MET C 952 " --> pdb=" O ASN C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 952 through 957 removed outlier: 4.340A pdb=" N ALA C 956 " --> pdb=" O MET C 952 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY C 957 " --> pdb=" O ALA C 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 952 through 957' Processing helix chain 'C' and resid 957 through 975 removed outlier: 3.675A pdb=" N LYS C 970 " --> pdb=" O GLU C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 988 removed outlier: 3.594A pdb=" N ILE C 988 " --> pdb=" O HIS C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1001 removed outlier: 3.693A pdb=" N GLU C 996 " --> pdb=" O TYR C 992 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 997 " --> pdb=" O GLU C 993 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU C 998 " --> pdb=" O ALA C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1015 removed outlier: 3.704A pdb=" N ALA C1007 " --> pdb=" O PHE C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1037 removed outlier: 4.586A pdb=" N LYS C1023 " --> pdb=" O ASP C1019 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP C1024 " --> pdb=" O PRO C1020 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU C1025 " --> pdb=" O VAL C1021 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG C1035 " --> pdb=" O THR C1031 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP C1036 " --> pdb=" O VAL C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1049 Processing helix chain 'C' and resid 1052 through 1061 removed outlier: 3.788A pdb=" N ALA C1056 " --> pdb=" O ALA C1052 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS C1057 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing helix chain 'C' and resid 1064 through 1078 Processing helix chain 'C' and resid 1080 through 1096 removed outlier: 3.918A pdb=" N GLN C1093 " --> pdb=" O LEU C1089 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C1094 " --> pdb=" O ARG C1090 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C1096 " --> pdb=" O ALA C1092 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1108 Processing helix chain 'C' and resid 1114 through 1130 Processing helix chain 'C' and resid 1156 through 1169 removed outlier: 4.045A pdb=" N THR C1161 " --> pdb=" O VAL C1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 1172 through 1182 removed outlier: 3.795A pdb=" N GLN C1177 " --> pdb=" O PRO C1173 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU C1178 " --> pdb=" O GLU C1174 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE C1180 " --> pdb=" O TYR C1176 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS C1182 " --> pdb=" O GLU C1178 " (cutoff:3.500A) Processing helix chain 'C' and resid 1196 through 1218 removed outlier: 3.834A pdb=" N LEU C1200 " --> pdb=" O PRO C1196 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN C1216 " --> pdb=" O VAL C1212 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N MET C1217 " --> pdb=" O LEU C1213 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA C1218 " --> pdb=" O SER C1214 " (cutoff:3.500A) Processing helix chain 'C' and resid 1219 through 1237 removed outlier: 4.398A pdb=" N ALA C1223 " --> pdb=" O SER C1219 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER C1237 " --> pdb=" O ARG C1233 " (cutoff:3.500A) Processing helix chain 'C' and resid 1242 through 1251 removed outlier: 3.582A pdb=" N TYR C1247 " --> pdb=" O MET C1243 " (cutoff:3.500A) Processing helix chain 'C' and resid 1256 through 1261 removed outlier: 3.521A pdb=" N ASP C1260 " --> pdb=" O ASP C1256 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS C1261 " --> pdb=" O HIS C1257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1256 through 1261' Processing helix chain 'C' and resid 1269 through 1293 removed outlier: 3.902A pdb=" N PHE C1273 " --> pdb=" O ALA C1269 " (cutoff:3.500A) Processing helix chain 'C' and resid 1349 through 1354 Processing helix chain 'C' and resid 1355 through 1360 removed outlier: 4.041A pdb=" N GLU C1358 " --> pdb=" O THR C1355 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE C1360 " --> pdb=" O LYS C1357 " (cutoff:3.500A) Processing helix chain 'C' and resid 1361 through 1391 removed outlier: 3.819A pdb=" N SER C1366 " --> pdb=" O GLU C1362 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU C1367 " --> pdb=" O LYS C1363 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN C1368 " --> pdb=" O HIS C1364 " (cutoff:3.500A) Processing helix chain 'C' and resid 1431 through 1448 removed outlier: 3.587A pdb=" N GLN C1443 " --> pdb=" O THR C1439 " (cutoff:3.500A) Processing helix chain 'C' and resid 1449 through 1455 removed outlier: 3.592A pdb=" N LYS C1453 " --> pdb=" O PRO C1449 " (cutoff:3.500A) Processing helix chain 'C' and resid 1459 through 1473 Processing helix chain 'C' and resid 1480 through 1493 removed outlier: 4.168A pdb=" N GLN C1484 " --> pdb=" O GLN C1480 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 855 Processing helix chain 'D' and resid 859 through 875 Processing helix chain 'D' and resid 885 through 890 removed outlier: 4.107A pdb=" N GLU D 889 " --> pdb=" O ALA D 885 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG D 890 " --> pdb=" O ASP D 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 885 through 890' Processing helix chain 'D' and resid 891 through 896 Processing helix chain 'D' and resid 898 through 913 removed outlier: 3.708A pdb=" N LEU D 902 " --> pdb=" O ASP D 898 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR D 903 " --> pdb=" O ARG D 899 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG D 904 " --> pdb=" O ALA D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 930 removed outlier: 3.990A pdb=" N MET D 926 " --> pdb=" O PHE D 922 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU D 927 " --> pdb=" O HIS D 923 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 942 removed outlier: 3.659A pdb=" N ALA D 940 " --> pdb=" O LEU D 936 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU D 941 " --> pdb=" O GLN D 937 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG D 942 " --> pdb=" O THR D 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 952 removed outlier: 3.859A pdb=" N MET D 952 " --> pdb=" O ASN D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 952 through 957 removed outlier: 4.340A pdb=" N ALA D 956 " --> pdb=" O MET D 952 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY D 957 " --> pdb=" O ALA D 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 952 through 957' Processing helix chain 'D' and resid 957 through 975 removed outlier: 3.675A pdb=" N LYS D 970 " --> pdb=" O GLU D 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 977 through 988 removed outlier: 3.594A pdb=" N ILE D 988 " --> pdb=" O HIS D 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 1001 removed outlier: 3.693A pdb=" N GLU D 996 " --> pdb=" O TYR D 992 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 997 " --> pdb=" O GLU D 993 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1003 through 1015 removed outlier: 3.704A pdb=" N ALA D1007 " --> pdb=" O PHE D1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1037 removed outlier: 4.586A pdb=" N LYS D1023 " --> pdb=" O ASP D1019 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP D1024 " --> pdb=" O PRO D1020 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU D1025 " --> pdb=" O VAL D1021 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG D1035 " --> pdb=" O THR D1031 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP D1036 " --> pdb=" O VAL D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1049 Processing helix chain 'D' and resid 1052 through 1061 removed outlier: 3.789A pdb=" N ALA D1056 " --> pdb=" O ALA D1052 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS D1057 " --> pdb=" O TYR D1053 " (cutoff:3.500A) Processing helix chain 'D' and resid 1064 through 1078 Processing helix chain 'D' and resid 1080 through 1096 removed outlier: 3.918A pdb=" N GLN D1093 " --> pdb=" O LEU D1089 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU D1094 " --> pdb=" O ARG D1090 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D1096 " --> pdb=" O ALA D1092 " (cutoff:3.500A) Processing helix chain 'D' and resid 1101 through 1108 Processing helix chain 'D' and resid 1114 through 1130 Processing helix chain 'D' and resid 1156 through 1169 removed outlier: 4.044A pdb=" N THR D1161 " --> pdb=" O VAL D1157 " (cutoff:3.500A) Processing helix chain 'D' and resid 1172 through 1182 removed outlier: 3.795A pdb=" N GLN D1177 " --> pdb=" O PRO D1173 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU D1178 " --> pdb=" O GLU D1174 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE D1180 " --> pdb=" O TYR D1176 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS D1182 " --> pdb=" O GLU D1178 " (cutoff:3.500A) Processing helix chain 'D' and resid 1196 through 1218 removed outlier: 3.835A pdb=" N LEU D1200 " --> pdb=" O PRO D1196 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLN D1216 " --> pdb=" O VAL D1212 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N MET D1217 " --> pdb=" O LEU D1213 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA D1218 " --> pdb=" O SER D1214 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1237 removed outlier: 4.397A pdb=" N ALA D1223 " --> pdb=" O SER D1219 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER D1237 " --> pdb=" O ARG D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1242 through 1251 removed outlier: 3.582A pdb=" N TYR D1247 " --> pdb=" O MET D1243 " (cutoff:3.500A) Processing helix chain 'D' and resid 1256 through 1261 removed outlier: 3.520A pdb=" N ASP D1260 " --> pdb=" O ASP D1256 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS D1261 " --> pdb=" O HIS D1257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1256 through 1261' Processing helix chain 'D' and resid 1269 through 1293 removed outlier: 3.903A pdb=" N PHE D1273 " --> pdb=" O ALA D1269 " (cutoff:3.500A) Processing helix chain 'D' and resid 1349 through 1354 Processing helix chain 'D' and resid 1355 through 1360 removed outlier: 4.042A pdb=" N GLU D1358 " --> pdb=" O THR D1355 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE D1360 " --> pdb=" O LYS D1357 " (cutoff:3.500A) Processing helix chain 'D' and resid 1361 through 1391 removed outlier: 3.819A pdb=" N SER D1366 " --> pdb=" O GLU D1362 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU D1367 " --> pdb=" O LYS D1363 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN D1368 " --> pdb=" O HIS D1364 " (cutoff:3.500A) Processing helix chain 'D' and resid 1431 through 1448 removed outlier: 3.588A pdb=" N GLN D1443 " --> pdb=" O THR D1439 " (cutoff:3.500A) Processing helix chain 'D' and resid 1449 through 1455 removed outlier: 3.591A pdb=" N LYS D1453 " --> pdb=" O PRO D1449 " (cutoff:3.500A) Processing helix chain 'D' and resid 1459 through 1473 Processing helix chain 'D' and resid 1480 through 1493 removed outlier: 4.169A pdb=" N GLN D1484 " --> pdb=" O GLN D1480 " (cutoff:3.500A) Processing helix chain 'E' and resid 849 through 855 Processing helix chain 'E' and resid 859 through 875 Processing helix chain 'E' and resid 885 through 890 removed outlier: 4.108A pdb=" N GLU E 889 " --> pdb=" O ALA E 885 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG E 890 " --> pdb=" O ASP E 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 885 through 890' Processing helix chain 'E' and resid 891 through 896 Processing helix chain 'E' and resid 898 through 913 removed outlier: 3.708A pdb=" N LEU E 902 " --> pdb=" O ASP E 898 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR E 903 " --> pdb=" O ARG E 899 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG E 904 " --> pdb=" O ALA E 900 " (cutoff:3.500A) Processing helix chain 'E' and resid 918 through 930 removed outlier: 3.989A pdb=" N MET E 926 " --> pdb=" O PHE E 922 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU E 927 " --> pdb=" O HIS E 923 " (cutoff:3.500A) Processing helix chain 'E' and resid 931 through 942 removed outlier: 3.657A pdb=" N ALA E 940 " --> pdb=" O LEU E 936 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU E 941 " --> pdb=" O GLN E 937 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG E 942 " --> pdb=" O THR E 938 " (cutoff:3.500A) Processing helix chain 'E' and resid 946 through 952 removed outlier: 3.861A pdb=" N MET E 952 " --> pdb=" O ASN E 948 " (cutoff:3.500A) Processing helix chain 'E' and resid 952 through 957 removed outlier: 4.340A pdb=" N ALA E 956 " --> pdb=" O MET E 952 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY E 957 " --> pdb=" O ALA E 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 952 through 957' Processing helix chain 'E' and resid 957 through 975 removed outlier: 3.676A pdb=" N LYS E 970 " --> pdb=" O GLU E 966 " (cutoff:3.500A) Processing helix chain 'E' and resid 977 through 988 removed outlier: 3.595A pdb=" N ILE E 988 " --> pdb=" O HIS E 984 " (cutoff:3.500A) Processing helix chain 'E' and resid 992 through 1001 removed outlier: 3.693A pdb=" N GLU E 996 " --> pdb=" O TYR E 992 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU E 997 " --> pdb=" O GLU E 993 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU E 998 " --> pdb=" O ALA E 994 " (cutoff:3.500A) Processing helix chain 'E' and resid 1003 through 1015 removed outlier: 3.704A pdb=" N ALA E1007 " --> pdb=" O PHE E1003 " (cutoff:3.500A) Processing helix chain 'E' and resid 1019 through 1037 removed outlier: 4.587A pdb=" N LYS E1023 " --> pdb=" O ASP E1019 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP E1024 " --> pdb=" O PRO E1020 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU E1025 " --> pdb=" O VAL E1021 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG E1035 " --> pdb=" O THR E1031 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP E1036 " --> pdb=" O VAL E1032 " (cutoff:3.500A) Processing helix chain 'E' and resid 1038 through 1049 Processing helix chain 'E' and resid 1052 through 1061 removed outlier: 3.788A pdb=" N ALA E1056 " --> pdb=" O ALA E1052 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS E1057 " --> pdb=" O TYR E1053 " (cutoff:3.500A) Processing helix chain 'E' and resid 1064 through 1078 Processing helix chain 'E' and resid 1080 through 1096 removed outlier: 3.919A pdb=" N GLN E1093 " --> pdb=" O LEU E1089 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU E1094 " --> pdb=" O ARG E1090 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E1096 " --> pdb=" O ALA E1092 " (cutoff:3.500A) Processing helix chain 'E' and resid 1101 through 1108 Processing helix chain 'E' and resid 1114 through 1130 Processing helix chain 'E' and resid 1156 through 1169 removed outlier: 4.045A pdb=" N THR E1161 " --> pdb=" O VAL E1157 " (cutoff:3.500A) Processing helix chain 'E' and resid 1172 through 1182 removed outlier: 3.795A pdb=" N GLN E1177 " --> pdb=" O PRO E1173 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU E1178 " --> pdb=" O GLU E1174 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE E1180 " --> pdb=" O TYR E1176 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS E1182 " --> pdb=" O GLU E1178 " (cutoff:3.500A) Processing helix chain 'E' and resid 1196 through 1218 removed outlier: 3.834A pdb=" N LEU E1200 " --> pdb=" O PRO E1196 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLN E1216 " --> pdb=" O VAL E1212 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N MET E1217 " --> pdb=" O LEU E1213 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA E1218 " --> pdb=" O SER E1214 " (cutoff:3.500A) Processing helix chain 'E' and resid 1219 through 1237 removed outlier: 4.397A pdb=" N ALA E1223 " --> pdb=" O SER E1219 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER E1237 " --> pdb=" O ARG E1233 " (cutoff:3.500A) Processing helix chain 'E' and resid 1242 through 1251 removed outlier: 3.581A pdb=" N TYR E1247 " --> pdb=" O MET E1243 " (cutoff:3.500A) Processing helix chain 'E' and resid 1256 through 1261 removed outlier: 3.520A pdb=" N ASP E1260 " --> pdb=" O ASP E1256 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS E1261 " --> pdb=" O HIS E1257 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1256 through 1261' Processing helix chain 'E' and resid 1269 through 1293 removed outlier: 3.902A pdb=" N PHE E1273 " --> pdb=" O ALA E1269 " (cutoff:3.500A) Processing helix chain 'E' and resid 1349 through 1354 Processing helix chain 'E' and resid 1355 through 1360 removed outlier: 4.041A pdb=" N GLU E1358 " --> pdb=" O THR E1355 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE E1360 " --> pdb=" O LYS E1357 " (cutoff:3.500A) Processing helix chain 'E' and resid 1361 through 1391 removed outlier: 3.818A pdb=" N SER E1366 " --> pdb=" O GLU E1362 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU E1367 " --> pdb=" O LYS E1363 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN E1368 " --> pdb=" O HIS E1364 " (cutoff:3.500A) Processing helix chain 'E' and resid 1431 through 1448 removed outlier: 3.588A pdb=" N GLN E1443 " --> pdb=" O THR E1439 " (cutoff:3.500A) Processing helix chain 'E' and resid 1449 through 1455 removed outlier: 3.592A pdb=" N LYS E1453 " --> pdb=" O PRO E1449 " (cutoff:3.500A) Processing helix chain 'E' and resid 1459 through 1473 Processing helix chain 'E' and resid 1480 through 1493 removed outlier: 4.169A pdb=" N GLN E1484 " --> pdb=" O GLN E1480 " (cutoff:3.500A) Processing helix chain 'F' and resid 849 through 855 Processing helix chain 'F' and resid 859 through 875 Processing helix chain 'F' and resid 885 through 890 removed outlier: 4.108A pdb=" N GLU F 889 " --> pdb=" O ALA F 885 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG F 890 " --> pdb=" O ASP F 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 885 through 890' Processing helix chain 'F' and resid 891 through 896 Processing helix chain 'F' and resid 898 through 913 removed outlier: 3.709A pdb=" N LEU F 902 " --> pdb=" O ASP F 898 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR F 903 " --> pdb=" O ARG F 899 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG F 904 " --> pdb=" O ALA F 900 " (cutoff:3.500A) Processing helix chain 'F' and resid 918 through 930 removed outlier: 3.989A pdb=" N MET F 926 " --> pdb=" O PHE F 922 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU F 927 " --> pdb=" O HIS F 923 " (cutoff:3.500A) Processing helix chain 'F' and resid 931 through 942 removed outlier: 3.658A pdb=" N ALA F 940 " --> pdb=" O LEU F 936 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU F 941 " --> pdb=" O GLN F 937 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG F 942 " --> pdb=" O THR F 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 946 through 952 removed outlier: 3.860A pdb=" N MET F 952 " --> pdb=" O ASN F 948 " (cutoff:3.500A) Processing helix chain 'F' and resid 952 through 957 removed outlier: 4.339A pdb=" N ALA F 956 " --> pdb=" O MET F 952 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY F 957 " --> pdb=" O ALA F 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 952 through 957' Processing helix chain 'F' and resid 957 through 975 removed outlier: 3.675A pdb=" N LYS F 970 " --> pdb=" O GLU F 966 " (cutoff:3.500A) Processing helix chain 'F' and resid 977 through 988 removed outlier: 3.595A pdb=" N ILE F 988 " --> pdb=" O HIS F 984 " (cutoff:3.500A) Processing helix chain 'F' and resid 992 through 1001 removed outlier: 3.693A pdb=" N GLU F 996 " --> pdb=" O TYR F 992 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 997 " --> pdb=" O GLU F 993 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU F 998 " --> pdb=" O ALA F 994 " (cutoff:3.500A) Processing helix chain 'F' and resid 1003 through 1015 removed outlier: 3.704A pdb=" N ALA F1007 " --> pdb=" O PHE F1003 " (cutoff:3.500A) Processing helix chain 'F' and resid 1019 through 1037 removed outlier: 4.586A pdb=" N LYS F1023 " --> pdb=" O ASP F1019 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP F1024 " --> pdb=" O PRO F1020 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU F1025 " --> pdb=" O VAL F1021 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG F1035 " --> pdb=" O THR F1031 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP F1036 " --> pdb=" O VAL F1032 " (cutoff:3.500A) Processing helix chain 'F' and resid 1038 through 1049 Processing helix chain 'F' and resid 1052 through 1061 removed outlier: 3.789A pdb=" N ALA F1056 " --> pdb=" O ALA F1052 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS F1057 " --> pdb=" O TYR F1053 " (cutoff:3.500A) Processing helix chain 'F' and resid 1064 through 1078 Processing helix chain 'F' and resid 1080 through 1096 removed outlier: 3.918A pdb=" N GLN F1093 " --> pdb=" O LEU F1089 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU F1094 " --> pdb=" O ARG F1090 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU F1096 " --> pdb=" O ALA F1092 " (cutoff:3.500A) Processing helix chain 'F' and resid 1101 through 1108 Processing helix chain 'F' and resid 1114 through 1130 Processing helix chain 'F' and resid 1156 through 1169 removed outlier: 4.044A pdb=" N THR F1161 " --> pdb=" O VAL F1157 " (cutoff:3.500A) Processing helix chain 'F' and resid 1172 through 1182 removed outlier: 3.796A pdb=" N GLN F1177 " --> pdb=" O PRO F1173 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU F1178 " --> pdb=" O GLU F1174 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE F1180 " --> pdb=" O TYR F1176 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS F1182 " --> pdb=" O GLU F1178 " (cutoff:3.500A) Processing helix chain 'F' and resid 1196 through 1218 removed outlier: 3.835A pdb=" N LEU F1200 " --> pdb=" O PRO F1196 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLN F1216 " --> pdb=" O VAL F1212 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N MET F1217 " --> pdb=" O LEU F1213 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA F1218 " --> pdb=" O SER F1214 " (cutoff:3.500A) Processing helix chain 'F' and resid 1219 through 1237 removed outlier: 4.398A pdb=" N ALA F1223 " --> pdb=" O SER F1219 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER F1237 " --> pdb=" O ARG F1233 " (cutoff:3.500A) Processing helix chain 'F' and resid 1242 through 1251 removed outlier: 3.582A pdb=" N TYR F1247 " --> pdb=" O MET F1243 " (cutoff:3.500A) Processing helix chain 'F' and resid 1256 through 1261 removed outlier: 3.521A pdb=" N ASP F1260 " --> pdb=" O ASP F1256 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS F1261 " --> pdb=" O HIS F1257 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1256 through 1261' Processing helix chain 'F' and resid 1269 through 1293 removed outlier: 3.903A pdb=" N PHE F1273 " --> pdb=" O ALA F1269 " (cutoff:3.500A) Processing helix chain 'F' and resid 1349 through 1354 Processing helix chain 'F' and resid 1355 through 1360 removed outlier: 4.042A pdb=" N GLU F1358 " --> pdb=" O THR F1355 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE F1360 " --> pdb=" O LYS F1357 " (cutoff:3.500A) Processing helix chain 'F' and resid 1361 through 1391 removed outlier: 3.819A pdb=" N SER F1366 " --> pdb=" O GLU F1362 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU F1367 " --> pdb=" O LYS F1363 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN F1368 " --> pdb=" O HIS F1364 " (cutoff:3.500A) Processing helix chain 'F' and resid 1431 through 1448 removed outlier: 3.587A pdb=" N GLN F1443 " --> pdb=" O THR F1439 " (cutoff:3.500A) Processing helix chain 'F' and resid 1449 through 1455 removed outlier: 3.592A pdb=" N LYS F1453 " --> pdb=" O PRO F1449 " (cutoff:3.500A) Processing helix chain 'F' and resid 1459 through 1473 Processing helix chain 'F' and resid 1480 through 1493 removed outlier: 4.169A pdb=" N GLN F1484 " --> pdb=" O GLN F1480 " (cutoff:3.500A) Processing helix chain 'G' and resid 849 through 855 Processing helix chain 'G' and resid 859 through 875 Processing helix chain 'G' and resid 885 through 890 removed outlier: 4.108A pdb=" N GLU G 889 " --> pdb=" O ALA G 885 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG G 890 " --> pdb=" O ASP G 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 885 through 890' Processing helix chain 'G' and resid 891 through 896 Processing helix chain 'G' and resid 898 through 913 removed outlier: 3.709A pdb=" N LEU G 902 " --> pdb=" O ASP G 898 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR G 903 " --> pdb=" O ARG G 899 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG G 904 " --> pdb=" O ALA G 900 " (cutoff:3.500A) Processing helix chain 'G' and resid 918 through 930 removed outlier: 3.989A pdb=" N MET G 926 " --> pdb=" O PHE G 922 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU G 927 " --> pdb=" O HIS G 923 " (cutoff:3.500A) Processing helix chain 'G' and resid 931 through 942 removed outlier: 3.657A pdb=" N ALA G 940 " --> pdb=" O LEU G 936 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU G 941 " --> pdb=" O GLN G 937 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG G 942 " --> pdb=" O THR G 938 " (cutoff:3.500A) Processing helix chain 'G' and resid 946 through 952 removed outlier: 3.859A pdb=" N MET G 952 " --> pdb=" O ASN G 948 " (cutoff:3.500A) Processing helix chain 'G' and resid 952 through 957 removed outlier: 4.340A pdb=" N ALA G 956 " --> pdb=" O MET G 952 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY G 957 " --> pdb=" O ALA G 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 952 through 957' Processing helix chain 'G' and resid 957 through 975 removed outlier: 3.676A pdb=" N LYS G 970 " --> pdb=" O GLU G 966 " (cutoff:3.500A) Processing helix chain 'G' and resid 977 through 988 removed outlier: 3.595A pdb=" N ILE G 988 " --> pdb=" O HIS G 984 " (cutoff:3.500A) Processing helix chain 'G' and resid 992 through 1001 removed outlier: 3.694A pdb=" N GLU G 996 " --> pdb=" O TYR G 992 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU G 997 " --> pdb=" O GLU G 993 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU G 998 " --> pdb=" O ALA G 994 " (cutoff:3.500A) Processing helix chain 'G' and resid 1003 through 1015 removed outlier: 3.704A pdb=" N ALA G1007 " --> pdb=" O PHE G1003 " (cutoff:3.500A) Processing helix chain 'G' and resid 1019 through 1037 removed outlier: 4.586A pdb=" N LYS G1023 " --> pdb=" O ASP G1019 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP G1024 " --> pdb=" O PRO G1020 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU G1025 " --> pdb=" O VAL G1021 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG G1035 " --> pdb=" O THR G1031 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP G1036 " --> pdb=" O VAL G1032 " (cutoff:3.500A) Processing helix chain 'G' and resid 1038 through 1049 Processing helix chain 'G' and resid 1052 through 1061 removed outlier: 3.788A pdb=" N ALA G1056 " --> pdb=" O ALA G1052 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS G1057 " --> pdb=" O TYR G1053 " (cutoff:3.500A) Processing helix chain 'G' and resid 1064 through 1078 Processing helix chain 'G' and resid 1080 through 1096 removed outlier: 3.918A pdb=" N GLN G1093 " --> pdb=" O LEU G1089 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU G1094 " --> pdb=" O ARG G1090 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU G1096 " --> pdb=" O ALA G1092 " (cutoff:3.500A) Processing helix chain 'G' and resid 1101 through 1108 Processing helix chain 'G' and resid 1114 through 1130 Processing helix chain 'G' and resid 1156 through 1169 removed outlier: 4.045A pdb=" N THR G1161 " --> pdb=" O VAL G1157 " (cutoff:3.500A) Processing helix chain 'G' and resid 1172 through 1182 removed outlier: 3.795A pdb=" N GLN G1177 " --> pdb=" O PRO G1173 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU G1178 " --> pdb=" O GLU G1174 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE G1180 " --> pdb=" O TYR G1176 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS G1182 " --> pdb=" O GLU G1178 " (cutoff:3.500A) Processing helix chain 'G' and resid 1196 through 1218 removed outlier: 3.835A pdb=" N LEU G1200 " --> pdb=" O PRO G1196 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLN G1216 " --> pdb=" O VAL G1212 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N MET G1217 " --> pdb=" O LEU G1213 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA G1218 " --> pdb=" O SER G1214 " (cutoff:3.500A) Processing helix chain 'G' and resid 1219 through 1237 removed outlier: 4.398A pdb=" N ALA G1223 " --> pdb=" O SER G1219 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER G1237 " --> pdb=" O ARG G1233 " (cutoff:3.500A) Processing helix chain 'G' and resid 1242 through 1251 removed outlier: 3.582A pdb=" N TYR G1247 " --> pdb=" O MET G1243 " (cutoff:3.500A) Processing helix chain 'G' and resid 1256 through 1261 removed outlier: 3.521A pdb=" N ASP G1260 " --> pdb=" O ASP G1256 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS G1261 " --> pdb=" O HIS G1257 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1256 through 1261' Processing helix chain 'G' and resid 1269 through 1293 removed outlier: 3.903A pdb=" N PHE G1273 " --> pdb=" O ALA G1269 " (cutoff:3.500A) Processing helix chain 'G' and resid 1349 through 1354 Processing helix chain 'G' and resid 1355 through 1360 removed outlier: 4.041A pdb=" N GLU G1358 " --> pdb=" O THR G1355 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE G1360 " --> pdb=" O LYS G1357 " (cutoff:3.500A) Processing helix chain 'G' and resid 1361 through 1391 removed outlier: 3.818A pdb=" N SER G1366 " --> pdb=" O GLU G1362 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU G1367 " --> pdb=" O LYS G1363 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN G1368 " --> pdb=" O HIS G1364 " (cutoff:3.500A) Processing helix chain 'G' and resid 1431 through 1448 removed outlier: 3.588A pdb=" N GLN G1443 " --> pdb=" O THR G1439 " (cutoff:3.500A) Processing helix chain 'G' and resid 1449 through 1455 removed outlier: 3.592A pdb=" N LYS G1453 " --> pdb=" O PRO G1449 " (cutoff:3.500A) Processing helix chain 'G' and resid 1459 through 1473 Processing helix chain 'G' and resid 1480 through 1493 removed outlier: 4.168A pdb=" N GLN G1484 " --> pdb=" O GLN G1480 " (cutoff:3.500A) Processing helix chain 'H' and resid 849 through 855 Processing helix chain 'H' and resid 859 through 875 Processing helix chain 'H' and resid 885 through 890 removed outlier: 4.108A pdb=" N GLU H 889 " --> pdb=" O ALA H 885 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG H 890 " --> pdb=" O ASP H 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 885 through 890' Processing helix chain 'H' and resid 891 through 896 Processing helix chain 'H' and resid 898 through 913 removed outlier: 3.709A pdb=" N LEU H 902 " --> pdb=" O ASP H 898 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR H 903 " --> pdb=" O ARG H 899 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG H 904 " --> pdb=" O ALA H 900 " (cutoff:3.500A) Processing helix chain 'H' and resid 918 through 930 removed outlier: 3.988A pdb=" N MET H 926 " --> pdb=" O PHE H 922 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU H 927 " --> pdb=" O HIS H 923 " (cutoff:3.500A) Processing helix chain 'H' and resid 931 through 942 removed outlier: 3.658A pdb=" N ALA H 940 " --> pdb=" O LEU H 936 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU H 941 " --> pdb=" O GLN H 937 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG H 942 " --> pdb=" O THR H 938 " (cutoff:3.500A) Processing helix chain 'H' and resid 946 through 952 removed outlier: 3.860A pdb=" N MET H 952 " --> pdb=" O ASN H 948 " (cutoff:3.500A) Processing helix chain 'H' and resid 952 through 957 removed outlier: 4.339A pdb=" N ALA H 956 " --> pdb=" O MET H 952 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY H 957 " --> pdb=" O ALA H 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 952 through 957' Processing helix chain 'H' and resid 957 through 975 removed outlier: 3.676A pdb=" N LYS H 970 " --> pdb=" O GLU H 966 " (cutoff:3.500A) Processing helix chain 'H' and resid 977 through 988 removed outlier: 3.596A pdb=" N ILE H 988 " --> pdb=" O HIS H 984 " (cutoff:3.500A) Processing helix chain 'H' and resid 992 through 1001 removed outlier: 3.693A pdb=" N GLU H 996 " --> pdb=" O TYR H 992 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU H 997 " --> pdb=" O GLU H 993 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU H 998 " --> pdb=" O ALA H 994 " (cutoff:3.500A) Processing helix chain 'H' and resid 1003 through 1015 removed outlier: 3.704A pdb=" N ALA H1007 " --> pdb=" O PHE H1003 " (cutoff:3.500A) Processing helix chain 'H' and resid 1019 through 1037 removed outlier: 4.586A pdb=" N LYS H1023 " --> pdb=" O ASP H1019 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP H1024 " --> pdb=" O PRO H1020 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU H1025 " --> pdb=" O VAL H1021 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG H1035 " --> pdb=" O THR H1031 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP H1036 " --> pdb=" O VAL H1032 " (cutoff:3.500A) Processing helix chain 'H' and resid 1038 through 1049 Processing helix chain 'H' and resid 1052 through 1061 removed outlier: 3.789A pdb=" N ALA H1056 " --> pdb=" O ALA H1052 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS H1057 " --> pdb=" O TYR H1053 " (cutoff:3.500A) Processing helix chain 'H' and resid 1064 through 1078 Processing helix chain 'H' and resid 1080 through 1096 removed outlier: 3.919A pdb=" N GLN H1093 " --> pdb=" O LEU H1089 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU H1094 " --> pdb=" O ARG H1090 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU H1096 " --> pdb=" O ALA H1092 " (cutoff:3.500A) Processing helix chain 'H' and resid 1101 through 1108 Processing helix chain 'H' and resid 1114 through 1130 Processing helix chain 'H' and resid 1156 through 1169 removed outlier: 4.043A pdb=" N THR H1161 " --> pdb=" O VAL H1157 " (cutoff:3.500A) Processing helix chain 'H' and resid 1172 through 1182 removed outlier: 3.795A pdb=" N GLN H1177 " --> pdb=" O PRO H1173 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU H1178 " --> pdb=" O GLU H1174 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE H1180 " --> pdb=" O TYR H1176 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS H1182 " --> pdb=" O GLU H1178 " (cutoff:3.500A) Processing helix chain 'H' and resid 1196 through 1218 removed outlier: 3.835A pdb=" N LEU H1200 " --> pdb=" O PRO H1196 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN H1216 " --> pdb=" O VAL H1212 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N MET H1217 " --> pdb=" O LEU H1213 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA H1218 " --> pdb=" O SER H1214 " (cutoff:3.500A) Processing helix chain 'H' and resid 1219 through 1237 removed outlier: 4.397A pdb=" N ALA H1223 " --> pdb=" O SER H1219 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER H1237 " --> pdb=" O ARG H1233 " (cutoff:3.500A) Processing helix chain 'H' and resid 1242 through 1251 removed outlier: 3.582A pdb=" N TYR H1247 " --> pdb=" O MET H1243 " (cutoff:3.500A) Processing helix chain 'H' and resid 1256 through 1261 removed outlier: 3.521A pdb=" N ASP H1260 " --> pdb=" O ASP H1256 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS H1261 " --> pdb=" O HIS H1257 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1256 through 1261' Processing helix chain 'H' and resid 1269 through 1293 removed outlier: 3.903A pdb=" N PHE H1273 " --> pdb=" O ALA H1269 " (cutoff:3.500A) Processing helix chain 'H' and resid 1349 through 1354 Processing helix chain 'H' and resid 1355 through 1360 removed outlier: 4.041A pdb=" N GLU H1358 " --> pdb=" O THR H1355 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE H1360 " --> pdb=" O LYS H1357 " (cutoff:3.500A) Processing helix chain 'H' and resid 1361 through 1391 removed outlier: 3.819A pdb=" N SER H1366 " --> pdb=" O GLU H1362 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU H1367 " --> pdb=" O LYS H1363 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN H1368 " --> pdb=" O HIS H1364 " (cutoff:3.500A) Processing helix chain 'H' and resid 1431 through 1448 removed outlier: 3.587A pdb=" N GLN H1443 " --> pdb=" O THR H1439 " (cutoff:3.500A) Processing helix chain 'H' and resid 1449 through 1455 removed outlier: 3.591A pdb=" N LYS H1453 " --> pdb=" O PRO H1449 " (cutoff:3.500A) Processing helix chain 'H' and resid 1459 through 1473 Processing helix chain 'H' and resid 1480 through 1493 removed outlier: 4.168A pdb=" N GLN H1484 " --> pdb=" O GLN H1480 " (cutoff:3.500A) Processing helix chain 'I' and resid 849 through 855 Processing helix chain 'I' and resid 859 through 875 Processing helix chain 'I' and resid 885 through 890 removed outlier: 4.108A pdb=" N GLU I 889 " --> pdb=" O ALA I 885 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG I 890 " --> pdb=" O ASP I 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 885 through 890' Processing helix chain 'I' and resid 891 through 896 Processing helix chain 'I' and resid 898 through 913 removed outlier: 3.708A pdb=" N LEU I 902 " --> pdb=" O ASP I 898 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR I 903 " --> pdb=" O ARG I 899 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG I 904 " --> pdb=" O ALA I 900 " (cutoff:3.500A) Processing helix chain 'I' and resid 918 through 930 removed outlier: 3.989A pdb=" N MET I 926 " --> pdb=" O PHE I 922 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU I 927 " --> pdb=" O HIS I 923 " (cutoff:3.500A) Processing helix chain 'I' and resid 931 through 942 removed outlier: 3.657A pdb=" N ALA I 940 " --> pdb=" O LEU I 936 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU I 941 " --> pdb=" O GLN I 937 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG I 942 " --> pdb=" O THR I 938 " (cutoff:3.500A) Processing helix chain 'I' and resid 946 through 952 removed outlier: 3.860A pdb=" N MET I 952 " --> pdb=" O ASN I 948 " (cutoff:3.500A) Processing helix chain 'I' and resid 952 through 957 removed outlier: 4.340A pdb=" N ALA I 956 " --> pdb=" O MET I 952 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY I 957 " --> pdb=" O ALA I 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 952 through 957' Processing helix chain 'I' and resid 957 through 975 removed outlier: 3.676A pdb=" N LYS I 970 " --> pdb=" O GLU I 966 " (cutoff:3.500A) Processing helix chain 'I' and resid 977 through 988 removed outlier: 3.595A pdb=" N ILE I 988 " --> pdb=" O HIS I 984 " (cutoff:3.500A) Processing helix chain 'I' and resid 992 through 1001 removed outlier: 3.693A pdb=" N GLU I 996 " --> pdb=" O TYR I 992 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU I 997 " --> pdb=" O GLU I 993 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU I 998 " --> pdb=" O ALA I 994 " (cutoff:3.500A) Processing helix chain 'I' and resid 1003 through 1015 removed outlier: 3.703A pdb=" N ALA I1007 " --> pdb=" O PHE I1003 " (cutoff:3.500A) Processing helix chain 'I' and resid 1019 through 1037 removed outlier: 4.586A pdb=" N LYS I1023 " --> pdb=" O ASP I1019 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP I1024 " --> pdb=" O PRO I1020 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU I1025 " --> pdb=" O VAL I1021 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG I1035 " --> pdb=" O THR I1031 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP I1036 " --> pdb=" O VAL I1032 " (cutoff:3.500A) Processing helix chain 'I' and resid 1038 through 1049 Processing helix chain 'I' and resid 1052 through 1061 removed outlier: 3.788A pdb=" N ALA I1056 " --> pdb=" O ALA I1052 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS I1057 " --> pdb=" O TYR I1053 " (cutoff:3.500A) Processing helix chain 'I' and resid 1064 through 1078 Processing helix chain 'I' and resid 1080 through 1096 removed outlier: 3.918A pdb=" N GLN I1093 " --> pdb=" O LEU I1089 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU I1094 " --> pdb=" O ARG I1090 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU I1096 " --> pdb=" O ALA I1092 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1108 Processing helix chain 'I' and resid 1114 through 1130 Processing helix chain 'I' and resid 1156 through 1169 removed outlier: 4.045A pdb=" N THR I1161 " --> pdb=" O VAL I1157 " (cutoff:3.500A) Processing helix chain 'I' and resid 1172 through 1182 removed outlier: 3.795A pdb=" N GLN I1177 " --> pdb=" O PRO I1173 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU I1178 " --> pdb=" O GLU I1174 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE I1180 " --> pdb=" O TYR I1176 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS I1182 " --> pdb=" O GLU I1178 " (cutoff:3.500A) Processing helix chain 'I' and resid 1196 through 1218 removed outlier: 3.835A pdb=" N LEU I1200 " --> pdb=" O PRO I1196 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLN I1216 " --> pdb=" O VAL I1212 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N MET I1217 " --> pdb=" O LEU I1213 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA I1218 " --> pdb=" O SER I1214 " (cutoff:3.500A) Processing helix chain 'I' and resid 1219 through 1237 removed outlier: 4.398A pdb=" N ALA I1223 " --> pdb=" O SER I1219 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER I1237 " --> pdb=" O ARG I1233 " (cutoff:3.500A) Processing helix chain 'I' and resid 1242 through 1251 removed outlier: 3.581A pdb=" N TYR I1247 " --> pdb=" O MET I1243 " (cutoff:3.500A) Processing helix chain 'I' and resid 1256 through 1261 removed outlier: 3.520A pdb=" N ASP I1260 " --> pdb=" O ASP I1256 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS I1261 " --> pdb=" O HIS I1257 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1256 through 1261' Processing helix chain 'I' and resid 1269 through 1293 removed outlier: 3.902A pdb=" N PHE I1273 " --> pdb=" O ALA I1269 " (cutoff:3.500A) Processing helix chain 'I' and resid 1349 through 1354 Processing helix chain 'I' and resid 1355 through 1360 removed outlier: 4.041A pdb=" N GLU I1358 " --> pdb=" O THR I1355 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE I1360 " --> pdb=" O LYS I1357 " (cutoff:3.500A) Processing helix chain 'I' and resid 1361 through 1391 removed outlier: 3.819A pdb=" N SER I1366 " --> pdb=" O GLU I1362 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU I1367 " --> pdb=" O LYS I1363 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN I1368 " --> pdb=" O HIS I1364 " (cutoff:3.500A) Processing helix chain 'I' and resid 1431 through 1448 removed outlier: 3.588A pdb=" N GLN I1443 " --> pdb=" O THR I1439 " (cutoff:3.500A) Processing helix chain 'I' and resid 1449 through 1455 removed outlier: 3.592A pdb=" N LYS I1453 " --> pdb=" O PRO I1449 " (cutoff:3.500A) Processing helix chain 'I' and resid 1459 through 1473 Processing helix chain 'I' and resid 1480 through 1493 removed outlier: 4.168A pdb=" N GLN I1484 " --> pdb=" O GLN I1480 " (cutoff:3.500A) Processing helix chain 'J' and resid 849 through 855 Processing helix chain 'J' and resid 859 through 875 Processing helix chain 'J' and resid 885 through 890 removed outlier: 4.107A pdb=" N GLU J 889 " --> pdb=" O ALA J 885 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG J 890 " --> pdb=" O ASP J 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 885 through 890' Processing helix chain 'J' and resid 891 through 896 Processing helix chain 'J' and resid 898 through 913 removed outlier: 3.708A pdb=" N LEU J 902 " --> pdb=" O ASP J 898 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR J 903 " --> pdb=" O ARG J 899 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG J 904 " --> pdb=" O ALA J 900 " (cutoff:3.500A) Processing helix chain 'J' and resid 918 through 930 removed outlier: 3.989A pdb=" N MET J 926 " --> pdb=" O PHE J 922 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU J 927 " --> pdb=" O HIS J 923 " (cutoff:3.500A) Processing helix chain 'J' and resid 931 through 942 removed outlier: 3.658A pdb=" N ALA J 940 " --> pdb=" O LEU J 936 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU J 941 " --> pdb=" O GLN J 937 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG J 942 " --> pdb=" O THR J 938 " (cutoff:3.500A) Processing helix chain 'J' and resid 946 through 952 removed outlier: 3.860A pdb=" N MET J 952 " --> pdb=" O ASN J 948 " (cutoff:3.500A) Processing helix chain 'J' and resid 952 through 957 removed outlier: 4.340A pdb=" N ALA J 956 " --> pdb=" O MET J 952 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY J 957 " --> pdb=" O ALA J 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 952 through 957' Processing helix chain 'J' and resid 957 through 975 removed outlier: 3.675A pdb=" N LYS J 970 " --> pdb=" O GLU J 966 " (cutoff:3.500A) Processing helix chain 'J' and resid 977 through 988 removed outlier: 3.595A pdb=" N ILE J 988 " --> pdb=" O HIS J 984 " (cutoff:3.500A) Processing helix chain 'J' and resid 992 through 1001 removed outlier: 3.693A pdb=" N GLU J 996 " --> pdb=" O TYR J 992 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU J 997 " --> pdb=" O GLU J 993 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU J 998 " --> pdb=" O ALA J 994 " (cutoff:3.500A) Processing helix chain 'J' and resid 1003 through 1015 removed outlier: 3.704A pdb=" N ALA J1007 " --> pdb=" O PHE J1003 " (cutoff:3.500A) Processing helix chain 'J' and resid 1019 through 1037 removed outlier: 4.586A pdb=" N LYS J1023 " --> pdb=" O ASP J1019 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP J1024 " --> pdb=" O PRO J1020 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU J1025 " --> pdb=" O VAL J1021 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG J1035 " --> pdb=" O THR J1031 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP J1036 " --> pdb=" O VAL J1032 " (cutoff:3.500A) Processing helix chain 'J' and resid 1038 through 1049 Processing helix chain 'J' and resid 1052 through 1061 removed outlier: 3.790A pdb=" N ALA J1056 " --> pdb=" O ALA J1052 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS J1057 " --> pdb=" O TYR J1053 " (cutoff:3.500A) Processing helix chain 'J' and resid 1064 through 1078 Processing helix chain 'J' and resid 1080 through 1096 removed outlier: 3.918A pdb=" N GLN J1093 " --> pdb=" O LEU J1089 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU J1094 " --> pdb=" O ARG J1090 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU J1096 " --> pdb=" O ALA J1092 " (cutoff:3.500A) Processing helix chain 'J' and resid 1101 through 1108 Processing helix chain 'J' and resid 1114 through 1130 Processing helix chain 'J' and resid 1156 through 1169 removed outlier: 4.044A pdb=" N THR J1161 " --> pdb=" O VAL J1157 " (cutoff:3.500A) Processing helix chain 'J' and resid 1172 through 1182 removed outlier: 3.796A pdb=" N GLN J1177 " --> pdb=" O PRO J1173 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLU J1178 " --> pdb=" O GLU J1174 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE J1180 " --> pdb=" O TYR J1176 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS J1182 " --> pdb=" O GLU J1178 " (cutoff:3.500A) Processing helix chain 'J' and resid 1196 through 1218 removed outlier: 3.835A pdb=" N LEU J1200 " --> pdb=" O PRO J1196 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLN J1216 " --> pdb=" O VAL J1212 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N MET J1217 " --> pdb=" O LEU J1213 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA J1218 " --> pdb=" O SER J1214 " (cutoff:3.500A) Processing helix chain 'J' and resid 1219 through 1237 removed outlier: 4.398A pdb=" N ALA J1223 " --> pdb=" O SER J1219 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER J1237 " --> pdb=" O ARG J1233 " (cutoff:3.500A) Processing helix chain 'J' and resid 1242 through 1251 removed outlier: 3.581A pdb=" N TYR J1247 " --> pdb=" O MET J1243 " (cutoff:3.500A) Processing helix chain 'J' and resid 1256 through 1261 removed outlier: 3.520A pdb=" N ASP J1260 " --> pdb=" O ASP J1256 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS J1261 " --> pdb=" O HIS J1257 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1256 through 1261' Processing helix chain 'J' and resid 1269 through 1293 removed outlier: 3.903A pdb=" N PHE J1273 " --> pdb=" O ALA J1269 " (cutoff:3.500A) Processing helix chain 'J' and resid 1349 through 1354 Processing helix chain 'J' and resid 1355 through 1360 removed outlier: 4.041A pdb=" N GLU J1358 " --> pdb=" O THR J1355 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE J1360 " --> pdb=" O LYS J1357 " (cutoff:3.500A) Processing helix chain 'J' and resid 1361 through 1391 removed outlier: 3.819A pdb=" N SER J1366 " --> pdb=" O GLU J1362 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU J1367 " --> pdb=" O LYS J1363 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN J1368 " --> pdb=" O HIS J1364 " (cutoff:3.500A) Processing helix chain 'J' and resid 1431 through 1448 removed outlier: 3.588A pdb=" N GLN J1443 " --> pdb=" O THR J1439 " (cutoff:3.500A) Processing helix chain 'J' and resid 1449 through 1455 removed outlier: 3.592A pdb=" N LYS J1453 " --> pdb=" O PRO J1449 " (cutoff:3.500A) Processing helix chain 'J' and resid 1459 through 1473 Processing helix chain 'J' and resid 1480 through 1493 removed outlier: 4.169A pdb=" N GLN J1484 " --> pdb=" O GLN J1480 " (cutoff:3.500A) 2610 hydrogen bonds defined for protein. 7710 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.96 Time building geometry restraints manager: 9.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13830 1.34 - 1.46: 9006 1.46 - 1.58: 19754 1.58 - 1.69: 10 1.69 - 1.81: 290 Bond restraints: 42890 Sorted by residual: bond pdb=" N TRP A1455 " pdb=" CA TRP A1455 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.69e-02 3.50e+03 4.53e+00 bond pdb=" N TRP F1455 " pdb=" CA TRP F1455 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.69e-02 3.50e+03 4.41e+00 bond pdb=" N TRP J1455 " pdb=" CA TRP J1455 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.69e-02 3.50e+03 4.30e+00 bond pdb=" N TRP E1455 " pdb=" CA TRP E1455 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.69e-02 3.50e+03 4.28e+00 bond pdb=" N TRP B1455 " pdb=" CA TRP B1455 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.69e-02 3.50e+03 4.10e+00 ... (remaining 42885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 57184 2.02 - 4.03: 717 4.03 - 6.05: 145 6.05 - 8.06: 34 8.06 - 10.08: 10 Bond angle restraints: 58090 Sorted by residual: angle pdb=" CA PRO D1173 " pdb=" N PRO D1173 " pdb=" CD PRO D1173 " ideal model delta sigma weight residual 112.00 106.40 5.60 1.40e+00 5.10e-01 1.60e+01 angle pdb=" CA PRO F1173 " pdb=" N PRO F1173 " pdb=" CD PRO F1173 " ideal model delta sigma weight residual 112.00 106.42 5.58 1.40e+00 5.10e-01 1.59e+01 angle pdb=" CA PRO G1173 " pdb=" N PRO G1173 " pdb=" CD PRO G1173 " ideal model delta sigma weight residual 112.00 106.43 5.57 1.40e+00 5.10e-01 1.58e+01 angle pdb=" CA PRO C1173 " pdb=" N PRO C1173 " pdb=" CD PRO C1173 " ideal model delta sigma weight residual 112.00 106.44 5.56 1.40e+00 5.10e-01 1.58e+01 angle pdb=" CA PRO B1173 " pdb=" N PRO B1173 " pdb=" CD PRO B1173 " ideal model delta sigma weight residual 112.00 106.44 5.56 1.40e+00 5.10e-01 1.58e+01 ... (remaining 58085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 21664 17.10 - 34.19: 2836 34.19 - 51.29: 970 51.29 - 68.38: 143 68.38 - 85.48: 97 Dihedral angle restraints: 25710 sinusoidal: 10110 harmonic: 15600 Sorted by residual: dihedral pdb=" CA ASP I1019 " pdb=" CB ASP I1019 " pdb=" CG ASP I1019 " pdb=" OD1 ASP I1019 " ideal model delta sinusoidal sigma weight residual -30.00 -84.70 54.70 1 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CA ASP A1019 " pdb=" CB ASP A1019 " pdb=" CG ASP A1019 " pdb=" OD1 ASP A1019 " ideal model delta sinusoidal sigma weight residual -30.00 -84.67 54.67 1 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CA ASP G1019 " pdb=" CB ASP G1019 " pdb=" CG ASP G1019 " pdb=" OD1 ASP G1019 " ideal model delta sinusoidal sigma weight residual -30.00 -84.66 54.66 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 25707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 4081 0.029 - 0.058: 1795 0.058 - 0.087: 477 0.087 - 0.116: 152 0.116 - 0.145: 25 Chirality restraints: 6530 Sorted by residual: chirality pdb=" CA THR I1270 " pdb=" N THR I1270 " pdb=" C THR I1270 " pdb=" CB THR I1270 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA THR F1270 " pdb=" N THR F1270 " pdb=" C THR F1270 " pdb=" CB THR F1270 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA THR D1270 " pdb=" N THR D1270 " pdb=" C THR D1270 " pdb=" CB THR D1270 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 6527 not shown) Planarity restraints: 7410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D1172 " 0.080 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO D1173 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO D1173 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO D1173 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J1172 " 0.080 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO J1173 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO J1173 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO J1173 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F1172 " -0.080 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO F1173 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO F1173 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO F1173 " -0.063 5.00e-02 4.00e+02 ... (remaining 7407 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 461 2.64 - 3.21: 40017 3.21 - 3.77: 67959 3.77 - 4.34: 87787 4.34 - 4.90: 143688 Nonbonded interactions: 339912 Sorted by model distance: nonbonded pdb=" NH2 ARG A1014 " pdb=" O LEU B 927 " model vdw 2.081 3.120 nonbonded pdb=" NH2 ARG G1014 " pdb=" O LEU H 927 " model vdw 2.081 3.120 nonbonded pdb=" NH2 ARG I1014 " pdb=" O LEU J 927 " model vdw 2.081 3.120 nonbonded pdb=" NH2 ARG E1014 " pdb=" O LEU F 927 " model vdw 2.081 3.120 nonbonded pdb=" NH2 ARG C1014 " pdb=" O LEU D 927 " model vdw 2.081 3.120 ... (remaining 339907 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 individual isotropic 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.070 Extract box with map and model: 1.230 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 63.450 Find NCS groups from input model: 1.230 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 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 0.099 42890 Z= 0.191 Angle : 0.611 10.078 58090 Z= 0.317 Chirality : 0.036 0.145 6530 Planarity : 0.006 0.119 7410 Dihedral : 17.780 85.479 15530 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.23 % Allowed : 24.75 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.12), residues: 5210 helix: 0.49 (0.09), residues: 3900 sheet: None (None), residues: 0 loop : -1.35 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1455 HIS 0.005 0.001 HIS J1203 PHE 0.009 0.001 PHE D1457 TYR 0.009 0.001 TYR E1282 ARG 0.009 0.000 ARG H1035 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10420 Ramachandran restraints generated. 5210 Oldfield, 0 Emsley, 5210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10420 Ramachandran restraints generated. 5210 Oldfield, 0 Emsley, 5210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 437 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1243 MET cc_start: 0.7575 (ttt) cc_final: 0.7160 (ttt) REVERT: I 1243 MET cc_start: 0.7554 (ttt) cc_final: 0.7182 (ttt) outliers start: 10 outliers final: 0 residues processed: 447 average time/residue: 0.4602 time to fit residues: 330.5904 Evaluate side-chains 347 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 3.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 447 optimal weight: 0.9990 chunk 401 optimal weight: 0.4980 chunk 222 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 270 optimal weight: 0.9980 chunk 214 optimal weight: 0.9990 chunk 415 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 252 optimal weight: 3.9990 chunk 309 optimal weight: 1.9990 chunk 481 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 857 HIS A1257 HIS A1371 GLN B 857 HIS B1257 HIS B1371 GLN C 857 HIS C1257 HIS C1371 GLN D 857 HIS D1257 HIS D1371 GLN E 857 HIS E1257 HIS E1371 GLN F 857 HIS F1257 HIS F1371 GLN G 857 HIS G1257 HIS G1371 GLN H 857 HIS H1257 HIS H1371 GLN I 857 HIS I1099 ASN I1257 HIS I1371 GLN J 857 HIS J1257 HIS J1371 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42890 Z= 0.189 Angle : 0.565 8.176 58090 Z= 0.276 Chirality : 0.036 0.146 6530 Planarity : 0.005 0.077 7410 Dihedral : 3.962 15.169 5660 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.50 % Allowed : 23.80 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.12), residues: 5210 helix: 0.69 (0.08), residues: 3960 sheet: None (None), residues: 0 loop : -1.48 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 928 HIS 0.003 0.001 HIS G1203 PHE 0.025 0.002 PHE A 974 TYR 0.014 0.001 TYR C1282 ARG 0.004 0.000 ARG A1035 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10420 Ramachandran restraints generated. 5210 Oldfield, 0 Emsley, 5210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10420 Ramachandran restraints generated. 5210 Oldfield, 0 Emsley, 5210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 394 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1178 GLU cc_start: 0.6889 (tp30) cc_final: 0.6633 (tp30) REVERT: A 1286 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.6343 (m-80) REVERT: C 1186 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.5731 (pt) REVERT: D 1471 ARG cc_start: 0.6172 (OUTLIER) cc_final: 0.5954 (tmm-80) REVERT: F 1178 GLU cc_start: 0.6786 (tp30) cc_final: 0.6535 (tp30) REVERT: F 1286 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6487 (m-80) REVERT: H 1471 ARG cc_start: 0.6198 (OUTLIER) cc_final: 0.5976 (tmm-80) outliers start: 199 outliers final: 99 residues processed: 557 average time/residue: 0.4557 time to fit residues: 408.4207 Evaluate side-chains 471 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 367 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 857 HIS Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1005 ARG Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1286 TYR Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1005 ARG Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1094 GLU Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1186 ILE Chi-restraints excluded: chain B residue 1286 TYR Chi-restraints excluded: chain B residue 1471 ARG Chi-restraints excluded: chain C residue 857 HIS Chi-restraints excluded: chain C residue 893 LEU Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 988 ILE Chi-restraints excluded: chain C residue 1005 ARG Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1186 ILE Chi-restraints excluded: chain C residue 1286 TYR Chi-restraints excluded: chain C residue 1364 HIS Chi-restraints excluded: chain C residue 1387 GLN Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 979 VAL Chi-restraints excluded: chain D residue 988 ILE Chi-restraints excluded: chain D residue 1005 ARG Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1094 GLU Chi-restraints excluded: chain D residue 1119 LEU Chi-restraints excluded: chain D residue 1186 ILE Chi-restraints excluded: chain D residue 1286 TYR Chi-restraints excluded: chain D residue 1364 HIS Chi-restraints excluded: chain D residue 1471 ARG Chi-restraints excluded: chain E residue 857 HIS Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 988 ILE Chi-restraints excluded: chain E residue 1005 ARG Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1094 GLU Chi-restraints excluded: chain E residue 1119 LEU Chi-restraints excluded: chain E residue 1186 ILE Chi-restraints excluded: chain E residue 1471 ARG Chi-restraints excluded: chain F residue 853 THR Chi-restraints excluded: chain F residue 893 LEU Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 988 ILE Chi-restraints excluded: chain F residue 1005 ARG Chi-restraints excluded: chain F residue 1094 GLU Chi-restraints excluded: chain F residue 1119 LEU Chi-restraints excluded: chain F residue 1186 ILE Chi-restraints excluded: chain F residue 1286 TYR Chi-restraints excluded: chain F residue 1471 ARG Chi-restraints excluded: chain G residue 857 HIS Chi-restraints excluded: chain G residue 893 LEU Chi-restraints excluded: chain G residue 952 MET Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 988 ILE Chi-restraints excluded: chain G residue 1005 ARG Chi-restraints excluded: chain G residue 1087 LEU Chi-restraints excluded: chain G residue 1094 GLU Chi-restraints excluded: chain G residue 1119 LEU Chi-restraints excluded: chain G residue 1186 ILE Chi-restraints excluded: chain G residue 1286 TYR Chi-restraints excluded: chain G residue 1364 HIS Chi-restraints excluded: chain G residue 1387 GLN Chi-restraints excluded: chain G residue 1461 LEU Chi-restraints excluded: chain H residue 893 LEU Chi-restraints excluded: chain H residue 979 VAL Chi-restraints excluded: chain H residue 988 ILE Chi-restraints excluded: chain H residue 1005 ARG Chi-restraints excluded: chain H residue 1094 GLU Chi-restraints excluded: chain H residue 1119 LEU Chi-restraints excluded: chain H residue 1186 ILE Chi-restraints excluded: chain H residue 1286 TYR Chi-restraints excluded: chain H residue 1471 ARG Chi-restraints excluded: chain I residue 857 HIS Chi-restraints excluded: chain I residue 893 LEU Chi-restraints excluded: chain I residue 979 VAL Chi-restraints excluded: chain I residue 988 ILE Chi-restraints excluded: chain I residue 1005 ARG Chi-restraints excluded: chain I residue 1094 GLU Chi-restraints excluded: chain I residue 1119 LEU Chi-restraints excluded: chain I residue 1186 ILE Chi-restraints excluded: chain I residue 1286 TYR Chi-restraints excluded: chain J residue 979 VAL Chi-restraints excluded: chain J residue 988 ILE Chi-restraints excluded: chain J residue 1005 ARG Chi-restraints excluded: chain J residue 1087 LEU Chi-restraints excluded: chain J residue 1094 GLU Chi-restraints excluded: chain J residue 1119 LEU Chi-restraints excluded: chain J residue 1186 ILE Chi-restraints excluded: chain J residue 1286 TYR Chi-restraints excluded: chain J residue 1387 GLN Chi-restraints excluded: chain J residue 1461 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 267 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 400 optimal weight: 4.9990 chunk 327 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 482 optimal weight: 9.9990 chunk 520 optimal weight: 6.9990 chunk 429 optimal weight: 9.9990 chunk 478 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 chunk 386 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 977 GLN ** A1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 977 GLN ** B1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 977 GLN ** C1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1485 GLN ** D1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 977 GLN ** E1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 977 GLN ** F1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 977 GLN ** G1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1485 GLN H 977 GLN ** H1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1485 GLN I 977 GLN I1099 ASN ** I1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1485 GLN J 977 GLN ** J1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1485 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 42890 Z= 0.402 Angle : 0.723 11.166 58090 Z= 0.362 Chirality : 0.042 0.153 6530 Planarity : 0.005 0.062 7410 Dihedral : 4.561 18.536 5660 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 5.79 % Allowed : 25.41 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.11), residues: 5210 helix: -0.04 (0.08), residues: 3900 sheet: None (None), residues: 0 loop : -1.82 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D1220 HIS 0.012 0.001 HIS A 857 PHE 0.032 0.003 PHE D 974 TYR 0.018 0.002 TYR B1176 ARG 0.006 0.001 ARG C1471 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10420 Ramachandran restraints generated. 5210 Oldfield, 0 Emsley, 5210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10420 Ramachandran restraints generated. 5210 Oldfield, 0 Emsley, 5210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 363 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 998 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.6031 (tp) REVERT: A 1176 TYR cc_start: 0.4764 (OUTLIER) cc_final: 0.4284 (t80) REVERT: A 1178 GLU cc_start: 0.7040 (tp30) cc_final: 0.6720 (tp30) REVERT: A 1368 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: A 1431 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.6197 (mp) REVERT: B 1025 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5509 (mm) REVERT: B 1176 TYR cc_start: 0.4782 (OUTLIER) cc_final: 0.3812 (t80) REVERT: C 997 LEU cc_start: 0.4747 (OUTLIER) cc_final: 0.4487 (pp) REVERT: C 1176 TYR cc_start: 0.4960 (OUTLIER) cc_final: 0.4603 (t80) REVERT: C 1368 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7293 (mt0) REVERT: D 997 LEU cc_start: 0.4768 (OUTLIER) cc_final: 0.4480 (pp) REVERT: D 1176 TYR cc_start: 0.5044 (OUTLIER) cc_final: 0.3802 (t80) REVERT: D 1368 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7237 (mt0) REVERT: E 998 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.5979 (tp) REVERT: E 1176 TYR cc_start: 0.5096 (OUTLIER) cc_final: 0.4557 (t80) REVERT: F 998 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5664 (tp) REVERT: F 1176 TYR cc_start: 0.5123 (OUTLIER) cc_final: 0.4771 (t80) REVERT: F 1178 GLU cc_start: 0.7130 (tp30) cc_final: 0.6780 (tp30) REVERT: F 1368 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: F 1431 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.6118 (mp) REVERT: G 997 LEU cc_start: 0.5015 (OUTLIER) cc_final: 0.4806 (pp) REVERT: G 1178 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6445 (tp30) REVERT: G 1243 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.6544 (ttt) REVERT: G 1368 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.6837 (mp10) REVERT: H 998 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.6124 (tp) REVERT: H 1176 TYR cc_start: 0.5124 (OUTLIER) cc_final: 0.3554 (t80) REVERT: H 1213 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6459 (mp) REVERT: H 1368 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7100 (mp10) REVERT: I 997 LEU cc_start: 0.4766 (OUTLIER) cc_final: 0.4459 (pp) REVERT: I 1176 TYR cc_start: 0.5006 (OUTLIER) cc_final: 0.3516 (t80) REVERT: I 1213 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6583 (mp) REVERT: I 1368 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7086 (mp10) REVERT: J 1123 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7177 (mm) REVERT: J 1178 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6427 (tp30) REVERT: J 1243 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.6562 (ttt) REVERT: J 1368 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.6826 (mp10) outliers start: 256 outliers final: 153 residues processed: 586 average time/residue: 0.4634 time to fit residues: 444.5447 Evaluate side-chains 518 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 331 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1005 ARG Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1176 TYR Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1243 MET Chi-restraints excluded: chain A residue 1257 HIS Chi-restraints excluded: chain A residue 1368 GLN Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1005 ARG Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1094 GLU Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1123 LEU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1178 GLU Chi-restraints excluded: chain B residue 1186 ILE Chi-restraints excluded: chain B residue 1257 HIS Chi-restraints excluded: chain B residue 1368 GLN Chi-restraints excluded: chain B residue 1374 VAL Chi-restraints excluded: chain B residue 1471 ARG Chi-restraints excluded: chain C residue 893 LEU Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 997 LEU Chi-restraints excluded: chain C residue 1005 ARG Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1123 LEU Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1176 TYR Chi-restraints excluded: chain C residue 1186 ILE Chi-restraints excluded: chain C residue 1213 LEU Chi-restraints excluded: chain C residue 1257 HIS Chi-restraints excluded: chain C residue 1285 LEU Chi-restraints excluded: chain C residue 1364 HIS Chi-restraints excluded: chain C residue 1368 GLN Chi-restraints excluded: chain C residue 1431 LEU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 979 VAL Chi-restraints excluded: chain D residue 988 ILE Chi-restraints excluded: chain D residue 997 LEU Chi-restraints excluded: chain D residue 1005 ARG Chi-restraints excluded: chain D residue 1025 LEU Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1094 GLU Chi-restraints excluded: chain D residue 1119 LEU Chi-restraints excluded: chain D residue 1123 LEU Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1176 TYR Chi-restraints excluded: chain D residue 1186 ILE Chi-restraints excluded: chain D residue 1213 LEU Chi-restraints excluded: chain D residue 1257 HIS Chi-restraints excluded: chain D residue 1285 LEU Chi-restraints excluded: chain D residue 1286 TYR Chi-restraints excluded: chain D residue 1348 GLU Chi-restraints excluded: chain D residue 1364 HIS Chi-restraints excluded: chain D residue 1368 GLN Chi-restraints excluded: chain D residue 1387 GLN Chi-restraints excluded: chain D residue 1431 LEU Chi-restraints excluded: chain D residue 1471 ARG Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 998 LEU Chi-restraints excluded: chain E residue 1005 ARG Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1094 GLU Chi-restraints excluded: chain E residue 1119 LEU Chi-restraints excluded: chain E residue 1123 LEU Chi-restraints excluded: chain E residue 1160 VAL Chi-restraints excluded: chain E residue 1176 TYR Chi-restraints excluded: chain E residue 1178 GLU Chi-restraints excluded: chain E residue 1186 ILE Chi-restraints excluded: chain E residue 1257 HIS Chi-restraints excluded: chain E residue 1368 GLN Chi-restraints excluded: chain E residue 1374 VAL Chi-restraints excluded: chain E residue 1471 ARG Chi-restraints excluded: chain F residue 853 THR Chi-restraints excluded: chain F residue 893 LEU Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 998 LEU Chi-restraints excluded: chain F residue 1005 ARG Chi-restraints excluded: chain F residue 1067 SER Chi-restraints excluded: chain F residue 1094 GLU Chi-restraints excluded: chain F residue 1119 LEU Chi-restraints excluded: chain F residue 1123 LEU Chi-restraints excluded: chain F residue 1160 VAL Chi-restraints excluded: chain F residue 1176 TYR Chi-restraints excluded: chain F residue 1186 ILE Chi-restraints excluded: chain F residue 1213 LEU Chi-restraints excluded: chain F residue 1243 MET Chi-restraints excluded: chain F residue 1257 HIS Chi-restraints excluded: chain F residue 1368 GLN Chi-restraints excluded: chain F residue 1431 LEU Chi-restraints excluded: chain F residue 1471 ARG Chi-restraints excluded: chain G residue 893 LEU Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 997 LEU Chi-restraints excluded: chain G residue 1005 ARG Chi-restraints excluded: chain G residue 1025 LEU Chi-restraints excluded: chain G residue 1087 LEU Chi-restraints excluded: chain G residue 1119 LEU Chi-restraints excluded: chain G residue 1178 GLU Chi-restraints excluded: chain G residue 1186 ILE Chi-restraints excluded: chain G residue 1213 LEU Chi-restraints excluded: chain G residue 1243 MET Chi-restraints excluded: chain G residue 1257 HIS Chi-restraints excluded: chain G residue 1285 LEU Chi-restraints excluded: chain G residue 1364 HIS Chi-restraints excluded: chain G residue 1368 GLN Chi-restraints excluded: chain G residue 1387 GLN Chi-restraints excluded: chain H residue 853 THR Chi-restraints excluded: chain H residue 893 LEU Chi-restraints excluded: chain H residue 896 PHE Chi-restraints excluded: chain H residue 979 VAL Chi-restraints excluded: chain H residue 998 LEU Chi-restraints excluded: chain H residue 1005 ARG Chi-restraints excluded: chain H residue 1025 LEU Chi-restraints excluded: chain H residue 1067 SER Chi-restraints excluded: chain H residue 1087 LEU Chi-restraints excluded: chain H residue 1094 GLU Chi-restraints excluded: chain H residue 1119 LEU Chi-restraints excluded: chain H residue 1123 LEU Chi-restraints excluded: chain H residue 1160 VAL Chi-restraints excluded: chain H residue 1176 TYR Chi-restraints excluded: chain H residue 1186 ILE Chi-restraints excluded: chain H residue 1213 LEU Chi-restraints excluded: chain H residue 1257 HIS Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1286 TYR Chi-restraints excluded: chain H residue 1364 HIS Chi-restraints excluded: chain H residue 1368 GLN Chi-restraints excluded: chain H residue 1374 VAL Chi-restraints excluded: chain H residue 1431 LEU Chi-restraints excluded: chain H residue 1471 ARG Chi-restraints excluded: chain I residue 893 LEU Chi-restraints excluded: chain I residue 979 VAL Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain I residue 1005 ARG Chi-restraints excluded: chain I residue 1025 LEU Chi-restraints excluded: chain I residue 1087 LEU Chi-restraints excluded: chain I residue 1094 GLU Chi-restraints excluded: chain I residue 1119 LEU Chi-restraints excluded: chain I residue 1123 LEU Chi-restraints excluded: chain I residue 1160 VAL Chi-restraints excluded: chain I residue 1176 TYR Chi-restraints excluded: chain I residue 1186 ILE Chi-restraints excluded: chain I residue 1213 LEU Chi-restraints excluded: chain I residue 1257 HIS Chi-restraints excluded: chain I residue 1285 LEU Chi-restraints excluded: chain I residue 1286 TYR Chi-restraints excluded: chain I residue 1364 HIS Chi-restraints excluded: chain I residue 1368 GLN Chi-restraints excluded: chain I residue 1431 LEU Chi-restraints excluded: chain J residue 893 LEU Chi-restraints excluded: chain J residue 952 MET Chi-restraints excluded: chain J residue 979 VAL Chi-restraints excluded: chain J residue 1005 ARG Chi-restraints excluded: chain J residue 1025 LEU Chi-restraints excluded: chain J residue 1087 LEU Chi-restraints excluded: chain J residue 1119 LEU Chi-restraints excluded: chain J residue 1123 LEU Chi-restraints excluded: chain J residue 1178 GLU Chi-restraints excluded: chain J residue 1186 ILE Chi-restraints excluded: chain J residue 1213 LEU Chi-restraints excluded: chain J residue 1243 MET Chi-restraints excluded: chain J residue 1257 HIS Chi-restraints excluded: chain J residue 1285 LEU Chi-restraints excluded: chain J residue 1364 HIS Chi-restraints excluded: chain J residue 1368 GLN Chi-restraints excluded: chain J residue 1387 GLN Chi-restraints excluded: chain J residue 1461 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 476 optimal weight: 0.7980 chunk 362 optimal weight: 0.8980 chunk 250 optimal weight: 9.9990 chunk 53 optimal weight: 0.1980 chunk 230 optimal weight: 8.9990 chunk 323 optimal weight: 7.9990 chunk 483 optimal weight: 6.9990 chunk 512 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 458 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 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 857 HIS C 857 HIS C1203 HIS D1203 HIS D1485 GLN E 857 HIS E1203 HIS F1203 HIS G 857 HIS H1203 HIS I 857 HIS I1099 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 42890 Z= 0.159 Angle : 0.554 8.815 58090 Z= 0.267 Chirality : 0.036 0.143 6530 Planarity : 0.004 0.057 7410 Dihedral : 4.097 16.714 5660 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.59 % Allowed : 26.45 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.12), residues: 5210 helix: 0.57 (0.08), residues: 3940 sheet: None (None), residues: 0 loop : -1.59 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 961 HIS 0.004 0.001 HIS G1257 PHE 0.038 0.001 PHE J 974 TYR 0.012 0.001 TYR G1282 ARG 0.005 0.000 ARG E1386 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10420 Ramachandran restraints generated. 5210 Oldfield, 0 Emsley, 5210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10420 Ramachandran restraints generated. 5210 Oldfield, 0 Emsley, 5210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 376 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1176 TYR cc_start: 0.4228 (OUTLIER) cc_final: 0.4014 (t80) REVERT: A 1202 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8109 (tt) REVERT: A 1286 TYR cc_start: 0.7326 (OUTLIER) cc_final: 0.6540 (m-80) REVERT: A 1368 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7359 (mp10) REVERT: B 1202 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7978 (tt) REVERT: B 1471 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.6091 (tmm-80) REVERT: C 1176 TYR cc_start: 0.3757 (OUTLIER) cc_final: 0.3549 (t80) REVERT: C 1202 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8258 (tt) REVERT: C 1368 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7373 (mp10) REVERT: D 905 MET cc_start: 0.5256 (ttt) cc_final: 0.5052 (ttt) REVERT: D 1176 TYR cc_start: 0.3765 (OUTLIER) cc_final: 0.3468 (t80) REVERT: D 1202 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8183 (tt) REVERT: D 1368 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7412 (mp10) REVERT: D 1471 ARG cc_start: 0.5958 (OUTLIER) cc_final: 0.5757 (tmm-80) REVERT: E 1202 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8002 (tt) REVERT: E 1387 GLN cc_start: 0.6333 (OUTLIER) cc_final: 0.5587 (pt0) REVERT: E 1471 ARG cc_start: 0.6316 (OUTLIER) cc_final: 0.6097 (tmm-80) REVERT: F 1178 GLU cc_start: 0.6736 (tp30) cc_final: 0.6436 (tp30) REVERT: F 1202 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8102 (tt) REVERT: F 1286 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6595 (m-80) REVERT: F 1368 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7400 (mp10) REVERT: G 896 PHE cc_start: 0.6868 (OUTLIER) cc_final: 0.5642 (m-80) REVERT: G 1368 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6739 (mp10) REVERT: H 1176 TYR cc_start: 0.4036 (OUTLIER) cc_final: 0.3180 (t80) REVERT: H 1213 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6314 (tp) REVERT: H 1368 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: I 1176 TYR cc_start: 0.4177 (OUTLIER) cc_final: 0.3330 (t80) REVERT: I 1213 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6324 (tp) REVERT: I 1368 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: J 896 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.5327 (m-80) REVERT: J 1368 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6692 (mp10) outliers start: 247 outliers final: 114 residues processed: 584 average time/residue: 0.4256 time to fit residues: 411.3087 Evaluate side-chains 489 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 346 time to evaluate : 3.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1176 TYR Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1286 TYR Chi-restraints excluded: chain A residue 1368 GLN Chi-restraints excluded: chain A residue 1482 MET Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 959 HIS Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1123 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1285 LEU Chi-restraints excluded: chain B residue 1286 TYR Chi-restraints excluded: chain B residue 1291 SER Chi-restraints excluded: chain B residue 1431 LEU Chi-restraints excluded: chain B residue 1471 ARG Chi-restraints excluded: chain C residue 893 LEU Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 988 ILE Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1123 LEU Chi-restraints excluded: chain C residue 1176 TYR Chi-restraints excluded: chain C residue 1202 LEU Chi-restraints excluded: chain C residue 1213 LEU Chi-restraints excluded: chain C residue 1286 TYR Chi-restraints excluded: chain C residue 1364 HIS Chi-restraints excluded: chain C residue 1368 GLN Chi-restraints excluded: chain C residue 1387 GLN Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 959 HIS Chi-restraints excluded: chain D residue 979 VAL Chi-restraints excluded: chain D residue 988 ILE Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1094 GLU Chi-restraints excluded: chain D residue 1119 LEU Chi-restraints excluded: chain D residue 1123 LEU Chi-restraints excluded: chain D residue 1176 TYR Chi-restraints excluded: chain D residue 1202 LEU Chi-restraints excluded: chain D residue 1213 LEU Chi-restraints excluded: chain D residue 1286 TYR Chi-restraints excluded: chain D residue 1364 HIS Chi-restraints excluded: chain D residue 1368 GLN Chi-restraints excluded: chain D residue 1387 GLN Chi-restraints excluded: chain D residue 1471 ARG Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 988 ILE Chi-restraints excluded: chain E residue 1119 LEU Chi-restraints excluded: chain E residue 1123 LEU Chi-restraints excluded: chain E residue 1202 LEU Chi-restraints excluded: chain E residue 1213 LEU Chi-restraints excluded: chain E residue 1285 LEU Chi-restraints excluded: chain E residue 1286 TYR Chi-restraints excluded: chain E residue 1291 SER Chi-restraints excluded: chain E residue 1387 GLN Chi-restraints excluded: chain E residue 1431 LEU Chi-restraints excluded: chain E residue 1471 ARG Chi-restraints excluded: chain F residue 853 THR Chi-restraints excluded: chain F residue 893 LEU Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 988 ILE Chi-restraints excluded: chain F residue 1094 GLU Chi-restraints excluded: chain F residue 1119 LEU Chi-restraints excluded: chain F residue 1123 LEU Chi-restraints excluded: chain F residue 1160 VAL Chi-restraints excluded: chain F residue 1202 LEU Chi-restraints excluded: chain F residue 1285 LEU Chi-restraints excluded: chain F residue 1286 TYR Chi-restraints excluded: chain F residue 1348 GLU Chi-restraints excluded: chain F residue 1368 GLN Chi-restraints excluded: chain G residue 893 LEU Chi-restraints excluded: chain G residue 896 PHE Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 988 ILE Chi-restraints excluded: chain G residue 1119 LEU Chi-restraints excluded: chain G residue 1160 VAL Chi-restraints excluded: chain G residue 1176 TYR Chi-restraints excluded: chain G residue 1213 LEU Chi-restraints excluded: chain G residue 1285 LEU Chi-restraints excluded: chain G residue 1286 TYR Chi-restraints excluded: chain G residue 1364 HIS Chi-restraints excluded: chain G residue 1368 GLN Chi-restraints excluded: chain G residue 1374 VAL Chi-restraints excluded: chain G residue 1387 GLN Chi-restraints excluded: chain G residue 1489 LEU Chi-restraints excluded: chain H residue 853 THR Chi-restraints excluded: chain H residue 893 LEU Chi-restraints excluded: chain H residue 959 HIS Chi-restraints excluded: chain H residue 979 VAL Chi-restraints excluded: chain H residue 988 ILE Chi-restraints excluded: chain H residue 1119 LEU Chi-restraints excluded: chain H residue 1123 LEU Chi-restraints excluded: chain H residue 1176 TYR Chi-restraints excluded: chain H residue 1213 LEU Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1286 TYR Chi-restraints excluded: chain H residue 1348 GLU Chi-restraints excluded: chain H residue 1368 GLN Chi-restraints excluded: chain I residue 893 LEU Chi-restraints excluded: chain I residue 896 PHE Chi-restraints excluded: chain I residue 959 HIS Chi-restraints excluded: chain I residue 979 VAL Chi-restraints excluded: chain I residue 988 ILE Chi-restraints excluded: chain I residue 1119 LEU Chi-restraints excluded: chain I residue 1123 LEU Chi-restraints excluded: chain I residue 1176 TYR Chi-restraints excluded: chain I residue 1213 LEU Chi-restraints excluded: chain I residue 1285 LEU Chi-restraints excluded: chain I residue 1286 TYR Chi-restraints excluded: chain I residue 1368 GLN Chi-restraints excluded: chain I residue 1374 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 893 LEU Chi-restraints excluded: chain J residue 896 PHE Chi-restraints excluded: chain J residue 952 MET Chi-restraints excluded: chain J residue 959 HIS Chi-restraints excluded: chain J residue 979 VAL Chi-restraints excluded: chain J residue 988 ILE Chi-restraints excluded: chain J residue 1087 LEU Chi-restraints excluded: chain J residue 1119 LEU Chi-restraints excluded: chain J residue 1160 VAL Chi-restraints excluded: chain J residue 1176 TYR Chi-restraints excluded: chain J residue 1213 LEU Chi-restraints excluded: chain J residue 1285 LEU Chi-restraints excluded: chain J residue 1286 TYR Chi-restraints excluded: chain J residue 1364 HIS Chi-restraints excluded: chain J residue 1368 GLN Chi-restraints excluded: chain J residue 1374 VAL Chi-restraints excluded: chain J residue 1387 GLN Chi-restraints excluded: chain J residue 1461 LEU Chi-restraints excluded: chain J residue 1489 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 426 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 381 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 437 optimal weight: 0.9990 chunk 354 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 459 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1203 HIS G1203 HIS H 892 HIS I1099 ASN I1203 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 42890 Z= 0.171 Angle : 0.573 14.700 58090 Z= 0.272 Chirality : 0.036 0.141 6530 Planarity : 0.004 0.053 7410 Dihedral : 3.998 16.671 5660 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.86 % Allowed : 26.33 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.12), residues: 5210 helix: 0.73 (0.08), residues: 3950 sheet: None (None), residues: 0 loop : -1.60 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 963 HIS 0.004 0.001 HIS H1257 PHE 0.040 0.001 PHE J 974 TYR 0.013 0.001 TYR G1282 ARG 0.005 0.000 ARG F1035 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10420 Ramachandran restraints generated. 5210 Oldfield, 0 Emsley, 5210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10420 Ramachandran restraints generated. 5210 Oldfield, 0 Emsley, 5210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 370 time to evaluate : 3.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1176 TYR cc_start: 0.4245 (OUTLIER) cc_final: 0.3992 (t80) REVERT: A 1202 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8142 (tt) REVERT: A 1286 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6502 (m-80) REVERT: A 1368 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: A 1489 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6739 (mp) REVERT: B 1202 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8009 (tt) REVERT: B 1387 GLN cc_start: 0.6363 (OUTLIER) cc_final: 0.5571 (pt0) REVERT: B 1471 ARG cc_start: 0.6172 (OUTLIER) cc_final: 0.5754 (tmm-80) REVERT: C 1005 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.6373 (mtp180) REVERT: C 1176 TYR cc_start: 0.3807 (OUTLIER) cc_final: 0.3447 (t80) REVERT: C 1186 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6065 (pt) REVERT: C 1202 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8365 (tt) REVERT: C 1368 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7439 (mp10) REVERT: D 1176 TYR cc_start: 0.3895 (OUTLIER) cc_final: 0.3394 (t80) REVERT: D 1186 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6184 (pt) REVERT: D 1202 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8279 (tt) REVERT: D 1207 ASP cc_start: 0.6137 (OUTLIER) cc_final: 0.5523 (m-30) REVERT: D 1368 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7025 (mt0) REVERT: D 1471 ARG cc_start: 0.6103 (OUTLIER) cc_final: 0.5875 (tmm-80) REVERT: E 857 HIS cc_start: 0.6061 (m-70) cc_final: 0.5791 (m170) REVERT: E 1087 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6413 (mm) REVERT: E 1202 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8007 (tt) REVERT: E 1471 ARG cc_start: 0.6328 (OUTLIER) cc_final: 0.5924 (tmm-80) REVERT: F 1202 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8130 (tt) REVERT: F 1286 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6502 (m-80) REVERT: F 1368 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7384 (mp10) REVERT: G 896 PHE cc_start: 0.6885 (OUTLIER) cc_final: 0.5648 (m-80) REVERT: G 997 LEU cc_start: 0.4662 (OUTLIER) cc_final: 0.4417 (pp) REVERT: G 1005 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.6059 (mtp180) REVERT: G 1368 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.6761 (mp10) REVERT: H 1213 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6603 (tp) REVERT: H 1368 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7242 (mp10) REVERT: H 1471 ARG cc_start: 0.6173 (OUTLIER) cc_final: 0.5962 (tmm-80) REVERT: I 1213 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6637 (mp) REVERT: I 1368 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7234 (mp10) REVERT: J 896 PHE cc_start: 0.6742 (OUTLIER) cc_final: 0.5347 (m-80) REVERT: J 1368 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6714 (mp10) outliers start: 259 outliers final: 156 residues processed: 600 average time/residue: 0.4658 time to fit residues: 460.0001 Evaluate side-chains 548 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 356 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1176 TYR Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1286 TYR Chi-restraints excluded: chain A residue 1291 SER Chi-restraints excluded: chain A residue 1348 GLU Chi-restraints excluded: chain A residue 1368 GLN Chi-restraints excluded: chain A residue 1380 THR Chi-restraints excluded: chain A residue 1482 MET Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1005 ARG Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1123 LEU Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1286 TYR Chi-restraints excluded: chain B residue 1291 SER Chi-restraints excluded: chain B residue 1348 GLU Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1387 GLN Chi-restraints excluded: chain B residue 1431 LEU Chi-restraints excluded: chain B residue 1471 ARG Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 893 LEU Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 988 ILE Chi-restraints excluded: chain C residue 1005 ARG Chi-restraints excluded: chain C residue 1067 SER Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1123 LEU Chi-restraints excluded: chain C residue 1176 TYR Chi-restraints excluded: chain C residue 1186 ILE Chi-restraints excluded: chain C residue 1202 LEU Chi-restraints excluded: chain C residue 1213 LEU Chi-restraints excluded: chain C residue 1285 LEU Chi-restraints excluded: chain C residue 1286 TYR Chi-restraints excluded: chain C residue 1291 SER Chi-restraints excluded: chain C residue 1348 GLU Chi-restraints excluded: chain C residue 1364 HIS Chi-restraints excluded: chain C residue 1368 GLN Chi-restraints excluded: chain C residue 1374 VAL Chi-restraints excluded: chain C residue 1380 THR Chi-restraints excluded: chain C residue 1387 GLN Chi-restraints excluded: chain C residue 1431 LEU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 979 VAL Chi-restraints excluded: chain D residue 988 ILE Chi-restraints excluded: chain D residue 1005 ARG Chi-restraints excluded: chain D residue 1067 SER Chi-restraints excluded: chain D residue 1094 GLU Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 LEU Chi-restraints excluded: chain D residue 1123 LEU Chi-restraints excluded: chain D residue 1160 VAL Chi-restraints excluded: chain D residue 1176 TYR Chi-restraints excluded: chain D residue 1186 ILE Chi-restraints excluded: chain D residue 1202 LEU Chi-restraints excluded: chain D residue 1207 ASP Chi-restraints excluded: chain D residue 1213 LEU Chi-restraints excluded: chain D residue 1285 LEU Chi-restraints excluded: chain D residue 1286 TYR Chi-restraints excluded: chain D residue 1291 SER Chi-restraints excluded: chain D residue 1364 HIS Chi-restraints excluded: chain D residue 1368 GLN Chi-restraints excluded: chain D residue 1387 GLN Chi-restraints excluded: chain D residue 1431 LEU Chi-restraints excluded: chain D residue 1471 ARG Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 988 ILE Chi-restraints excluded: chain E residue 1005 ARG Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1119 LEU Chi-restraints excluded: chain E residue 1123 LEU Chi-restraints excluded: chain E residue 1176 TYR Chi-restraints excluded: chain E residue 1202 LEU Chi-restraints excluded: chain E residue 1213 LEU Chi-restraints excluded: chain E residue 1285 LEU Chi-restraints excluded: chain E residue 1286 TYR Chi-restraints excluded: chain E residue 1291 SER Chi-restraints excluded: chain E residue 1380 THR Chi-restraints excluded: chain E residue 1431 LEU Chi-restraints excluded: chain E residue 1471 ARG Chi-restraints excluded: chain E residue 1489 LEU Chi-restraints excluded: chain F residue 853 THR Chi-restraints excluded: chain F residue 893 LEU Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 988 ILE Chi-restraints excluded: chain F residue 1094 GLU Chi-restraints excluded: chain F residue 1119 LEU Chi-restraints excluded: chain F residue 1123 LEU Chi-restraints excluded: chain F residue 1186 ILE Chi-restraints excluded: chain F residue 1202 LEU Chi-restraints excluded: chain F residue 1285 LEU Chi-restraints excluded: chain F residue 1286 TYR Chi-restraints excluded: chain F residue 1291 SER Chi-restraints excluded: chain F residue 1348 GLU Chi-restraints excluded: chain F residue 1368 GLN Chi-restraints excluded: chain F residue 1380 THR Chi-restraints excluded: chain G residue 893 LEU Chi-restraints excluded: chain G residue 896 PHE Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 988 ILE Chi-restraints excluded: chain G residue 997 LEU Chi-restraints excluded: chain G residue 1005 ARG Chi-restraints excluded: chain G residue 1067 SER Chi-restraints excluded: chain G residue 1087 LEU Chi-restraints excluded: chain G residue 1119 LEU Chi-restraints excluded: chain G residue 1176 TYR Chi-restraints excluded: chain G residue 1213 LEU Chi-restraints excluded: chain G residue 1285 LEU Chi-restraints excluded: chain G residue 1286 TYR Chi-restraints excluded: chain G residue 1291 SER Chi-restraints excluded: chain G residue 1353 LEU Chi-restraints excluded: chain G residue 1364 HIS Chi-restraints excluded: chain G residue 1368 GLN Chi-restraints excluded: chain G residue 1374 VAL Chi-restraints excluded: chain G residue 1387 GLN Chi-restraints excluded: chain G residue 1489 LEU Chi-restraints excluded: chain H residue 893 LEU Chi-restraints excluded: chain H residue 979 VAL Chi-restraints excluded: chain H residue 988 ILE Chi-restraints excluded: chain H residue 1005 ARG Chi-restraints excluded: chain H residue 1087 LEU Chi-restraints excluded: chain H residue 1119 LEU Chi-restraints excluded: chain H residue 1123 LEU Chi-restraints excluded: chain H residue 1160 VAL Chi-restraints excluded: chain H residue 1186 ILE Chi-restraints excluded: chain H residue 1213 LEU Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1286 TYR Chi-restraints excluded: chain H residue 1291 SER Chi-restraints excluded: chain H residue 1348 GLU Chi-restraints excluded: chain H residue 1364 HIS Chi-restraints excluded: chain H residue 1368 GLN Chi-restraints excluded: chain H residue 1471 ARG Chi-restraints excluded: chain I residue 893 LEU Chi-restraints excluded: chain I residue 896 PHE Chi-restraints excluded: chain I residue 979 VAL Chi-restraints excluded: chain I residue 988 ILE Chi-restraints excluded: chain I residue 1005 ARG Chi-restraints excluded: chain I residue 1068 LEU Chi-restraints excluded: chain I residue 1102 VAL Chi-restraints excluded: chain I residue 1119 LEU Chi-restraints excluded: chain I residue 1123 LEU Chi-restraints excluded: chain I residue 1186 ILE Chi-restraints excluded: chain I residue 1213 LEU Chi-restraints excluded: chain I residue 1285 LEU Chi-restraints excluded: chain I residue 1286 TYR Chi-restraints excluded: chain I residue 1291 SER Chi-restraints excluded: chain I residue 1348 GLU Chi-restraints excluded: chain I residue 1353 LEU Chi-restraints excluded: chain I residue 1364 HIS Chi-restraints excluded: chain I residue 1368 GLN Chi-restraints excluded: chain I residue 1374 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 893 LEU Chi-restraints excluded: chain J residue 896 PHE Chi-restraints excluded: chain J residue 979 VAL Chi-restraints excluded: chain J residue 988 ILE Chi-restraints excluded: chain J residue 1005 ARG Chi-restraints excluded: chain J residue 1067 SER Chi-restraints excluded: chain J residue 1087 LEU Chi-restraints excluded: chain J residue 1119 LEU Chi-restraints excluded: chain J residue 1131 LEU Chi-restraints excluded: chain J residue 1176 TYR Chi-restraints excluded: chain J residue 1213 LEU Chi-restraints excluded: chain J residue 1285 LEU Chi-restraints excluded: chain J residue 1286 TYR Chi-restraints excluded: chain J residue 1291 SER Chi-restraints excluded: chain J residue 1364 HIS Chi-restraints excluded: chain J residue 1368 GLN Chi-restraints excluded: chain J residue 1374 VAL Chi-restraints excluded: chain J residue 1387 GLN Chi-restraints excluded: chain J residue 1461 LEU Chi-restraints excluded: chain J residue 1489 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 172 optimal weight: 1.9990 chunk 461 optimal weight: 0.0070 chunk 101 optimal weight: 0.0050 chunk 300 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 512 optimal weight: 0.9980 chunk 425 optimal weight: 20.0000 chunk 237 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 169 optimal weight: 0.1980 chunk 269 optimal weight: 6.9990 overall best weight: 0.4414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 892 HIS I 892 HIS I1099 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 42890 Z= 0.148 Angle : 0.541 12.045 58090 Z= 0.259 Chirality : 0.036 0.297 6530 Planarity : 0.004 0.050 7410 Dihedral : 3.856 15.654 5660 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.23 % Allowed : 26.72 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.12), residues: 5210 helix: 1.02 (0.08), residues: 4000 sheet: None (None), residues: 0 loop : -1.56 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 963 HIS 0.003 0.000 HIS H1257 PHE 0.039 0.001 PHE J 974 TYR 0.012 0.001 TYR E1282 ARG 0.005 0.000 ARG B1386 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10420 Ramachandran restraints generated. 5210 Oldfield, 0 Emsley, 5210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10420 Ramachandran restraints generated. 5210 Oldfield, 0 Emsley, 5210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 393 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1124 LEU cc_start: 0.7423 (mm) cc_final: 0.7170 (mm) REVERT: A 1286 TYR cc_start: 0.7275 (OUTLIER) cc_final: 0.6475 (m-80) REVERT: A 1368 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6880 (mp10) REVERT: B 857 HIS cc_start: 0.5945 (m90) cc_final: 0.5630 (m170) REVERT: B 1207 ASP cc_start: 0.6134 (OUTLIER) cc_final: 0.5672 (m-30) REVERT: B 1387 GLN cc_start: 0.6247 (OUTLIER) cc_final: 0.5465 (pt0) REVERT: C 1202 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8262 (tt) REVERT: C 1207 ASP cc_start: 0.6015 (OUTLIER) cc_final: 0.5569 (m-30) REVERT: C 1368 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6850 (mt0) REVERT: D 905 MET cc_start: 0.5105 (ttt) cc_final: 0.4879 (ttt) REVERT: D 1368 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.6844 (mt0) REVERT: E 857 HIS cc_start: 0.6145 (m-70) cc_final: 0.5918 (m170) REVERT: E 1087 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6355 (mm) REVERT: E 1387 GLN cc_start: 0.6321 (OUTLIER) cc_final: 0.5556 (pt0) REVERT: F 857 HIS cc_start: 0.5995 (m90) cc_final: 0.5706 (m170) REVERT: F 1202 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8148 (tt) REVERT: F 1207 ASP cc_start: 0.6020 (OUTLIER) cc_final: 0.5587 (m-30) REVERT: F 1286 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.6542 (m-80) REVERT: F 1368 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: G 896 PHE cc_start: 0.6829 (OUTLIER) cc_final: 0.5490 (m-80) REVERT: G 1207 ASP cc_start: 0.5728 (OUTLIER) cc_final: 0.5360 (m-30) REVERT: G 1368 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6664 (mp10) REVERT: H 1176 TYR cc_start: 0.3829 (OUTLIER) cc_final: 0.3114 (t80) REVERT: H 1368 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6852 (mp10) REVERT: I 857 HIS cc_start: 0.5772 (m90) cc_final: 0.5456 (m170) REVERT: I 1176 TYR cc_start: 0.3754 (OUTLIER) cc_final: 0.3052 (t80) REVERT: J 896 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.5276 (m-80) REVERT: J 904 ARG cc_start: 0.6018 (ttp80) cc_final: 0.5804 (mtm110) REVERT: J 1005 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.6326 (mtp180) REVERT: J 1207 ASP cc_start: 0.5589 (OUTLIER) cc_final: 0.5212 (m-30) REVERT: J 1368 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6693 (mp10) outliers start: 231 outliers final: 140 residues processed: 589 average time/residue: 0.4251 time to fit residues: 411.0812 Evaluate side-chains 529 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 365 time to evaluate : 3.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 959 HIS Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1286 TYR Chi-restraints excluded: chain A residue 1291 SER Chi-restraints excluded: chain A residue 1348 GLU Chi-restraints excluded: chain A residue 1368 GLN Chi-restraints excluded: chain A residue 1482 MET Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 1005 ARG Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1123 LEU Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1186 ILE Chi-restraints excluded: chain B residue 1207 ASP Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1285 LEU Chi-restraints excluded: chain B residue 1286 TYR Chi-restraints excluded: chain B residue 1291 SER Chi-restraints excluded: chain B residue 1348 GLU Chi-restraints excluded: chain B residue 1387 GLN Chi-restraints excluded: chain B residue 1482 MET Chi-restraints excluded: chain C residue 853 THR Chi-restraints excluded: chain C residue 893 LEU Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 988 ILE Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1123 LEU Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1202 LEU Chi-restraints excluded: chain C residue 1207 ASP Chi-restraints excluded: chain C residue 1285 LEU Chi-restraints excluded: chain C residue 1286 TYR Chi-restraints excluded: chain C residue 1291 SER Chi-restraints excluded: chain C residue 1364 HIS Chi-restraints excluded: chain C residue 1368 GLN Chi-restraints excluded: chain C residue 1374 VAL Chi-restraints excluded: chain C residue 1387 GLN Chi-restraints excluded: chain C residue 1431 LEU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 893 LEU Chi-restraints excluded: chain D residue 959 HIS Chi-restraints excluded: chain D residue 979 VAL Chi-restraints excluded: chain D residue 988 ILE Chi-restraints excluded: chain D residue 1094 GLU Chi-restraints excluded: chain D residue 1119 LEU Chi-restraints excluded: chain D residue 1123 LEU Chi-restraints excluded: chain D residue 1285 LEU Chi-restraints excluded: chain D residue 1286 TYR Chi-restraints excluded: chain D residue 1291 SER Chi-restraints excluded: chain D residue 1348 GLU Chi-restraints excluded: chain D residue 1364 HIS Chi-restraints excluded: chain D residue 1368 GLN Chi-restraints excluded: chain D residue 1387 GLN Chi-restraints excluded: chain D residue 1431 LEU Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 988 ILE Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1119 LEU Chi-restraints excluded: chain E residue 1123 LEU Chi-restraints excluded: chain E residue 1176 TYR Chi-restraints excluded: chain E residue 1213 LEU Chi-restraints excluded: chain E residue 1285 LEU Chi-restraints excluded: chain E residue 1286 TYR Chi-restraints excluded: chain E residue 1291 SER Chi-restraints excluded: chain E residue 1348 GLU Chi-restraints excluded: chain E residue 1387 GLN Chi-restraints excluded: chain E residue 1431 LEU Chi-restraints excluded: chain F residue 853 THR Chi-restraints excluded: chain F residue 893 LEU Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 988 ILE Chi-restraints excluded: chain F residue 1094 GLU Chi-restraints excluded: chain F residue 1119 LEU Chi-restraints excluded: chain F residue 1123 LEU Chi-restraints excluded: chain F residue 1160 VAL Chi-restraints excluded: chain F residue 1202 LEU Chi-restraints excluded: chain F residue 1207 ASP Chi-restraints excluded: chain F residue 1286 TYR Chi-restraints excluded: chain F residue 1291 SER Chi-restraints excluded: chain F residue 1348 GLU Chi-restraints excluded: chain F residue 1368 GLN Chi-restraints excluded: chain F residue 1489 LEU Chi-restraints excluded: chain G residue 893 LEU Chi-restraints excluded: chain G residue 896 PHE Chi-restraints excluded: chain G residue 959 HIS Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 988 ILE Chi-restraints excluded: chain G residue 1119 LEU Chi-restraints excluded: chain G residue 1176 TYR Chi-restraints excluded: chain G residue 1207 ASP Chi-restraints excluded: chain G residue 1213 LEU Chi-restraints excluded: chain G residue 1285 LEU Chi-restraints excluded: chain G residue 1286 TYR Chi-restraints excluded: chain G residue 1353 LEU Chi-restraints excluded: chain G residue 1364 HIS Chi-restraints excluded: chain G residue 1368 GLN Chi-restraints excluded: chain G residue 1374 VAL Chi-restraints excluded: chain G residue 1387 GLN Chi-restraints excluded: chain G residue 1489 LEU Chi-restraints excluded: chain H residue 853 THR Chi-restraints excluded: chain H residue 893 LEU Chi-restraints excluded: chain H residue 979 VAL Chi-restraints excluded: chain H residue 988 ILE Chi-restraints excluded: chain H residue 1102 VAL Chi-restraints excluded: chain H residue 1119 LEU Chi-restraints excluded: chain H residue 1123 LEU Chi-restraints excluded: chain H residue 1160 VAL Chi-restraints excluded: chain H residue 1176 TYR Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1286 TYR Chi-restraints excluded: chain H residue 1291 SER Chi-restraints excluded: chain H residue 1348 GLU Chi-restraints excluded: chain H residue 1353 LEU Chi-restraints excluded: chain H residue 1368 GLN Chi-restraints excluded: chain I residue 896 PHE Chi-restraints excluded: chain I residue 959 HIS Chi-restraints excluded: chain I residue 979 VAL Chi-restraints excluded: chain I residue 988 ILE Chi-restraints excluded: chain I residue 1067 SER Chi-restraints excluded: chain I residue 1068 LEU Chi-restraints excluded: chain I residue 1119 LEU Chi-restraints excluded: chain I residue 1123 LEU Chi-restraints excluded: chain I residue 1160 VAL Chi-restraints excluded: chain I residue 1176 TYR Chi-restraints excluded: chain I residue 1285 LEU Chi-restraints excluded: chain I residue 1286 TYR Chi-restraints excluded: chain I residue 1291 SER Chi-restraints excluded: chain I residue 1348 GLU Chi-restraints excluded: chain I residue 1353 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 893 LEU Chi-restraints excluded: chain J residue 896 PHE Chi-restraints excluded: chain J residue 952 MET Chi-restraints excluded: chain J residue 959 HIS Chi-restraints excluded: chain J residue 979 VAL Chi-restraints excluded: chain J residue 988 ILE Chi-restraints excluded: chain J residue 1005 ARG Chi-restraints excluded: chain J residue 1119 LEU Chi-restraints excluded: chain J residue 1131 LEU Chi-restraints excluded: chain J residue 1176 TYR Chi-restraints excluded: chain J residue 1186 ILE Chi-restraints excluded: chain J residue 1207 ASP Chi-restraints excluded: chain J residue 1213 LEU Chi-restraints excluded: chain J residue 1285 LEU Chi-restraints excluded: chain J residue 1286 TYR Chi-restraints excluded: chain J residue 1353 LEU Chi-restraints excluded: chain J residue 1364 HIS Chi-restraints excluded: chain J residue 1368 GLN Chi-restraints excluded: chain J residue 1374 VAL Chi-restraints excluded: chain J residue 1380 THR Chi-restraints excluded: chain J residue 1387 GLN Chi-restraints excluded: chain J residue 1461 LEU Chi-restraints excluded: chain J residue 1489 LEU Chi-restraints excluded: chain J residue 1490 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.8044 > 50: distance: 43 - 60: 7.638 distance: 46 - 51: 8.636 distance: 47 - 69: 25.265 distance: 51 - 52: 31.608 distance: 52 - 53: 4.819 distance: 53 - 54: 27.939 distance: 53 - 55: 7.260 distance: 54 - 78: 16.865 distance: 55 - 56: 32.237 distance: 56 - 57: 22.932 distance: 56 - 59: 5.976 distance: 57 - 58: 14.629 distance: 57 - 60: 16.783 distance: 58 - 83: 19.582 distance: 60 - 61: 11.278 distance: 61 - 62: 17.433 distance: 61 - 64: 6.383 distance: 62 - 63: 22.621 distance: 62 - 69: 13.580 distance: 64 - 65: 23.854 distance: 65 - 66: 15.441 distance: 66 - 67: 7.031 distance: 66 - 68: 6.842 distance: 70 - 71: 15.822 distance: 70 - 73: 9.332 distance: 71 - 72: 12.992 distance: 71 - 78: 9.873 distance: 73 - 74: 11.193 distance: 74 - 75: 16.162 distance: 75 - 76: 6.846 distance: 75 - 77: 8.432 distance: 78 - 79: 16.813 distance: 79 - 80: 3.433 distance: 79 - 82: 36.430 distance: 80 - 81: 6.236 distance: 80 - 83: 15.635 distance: 83 - 84: 4.772 distance: 84 - 85: 16.872 distance: 84 - 87: 7.142 distance: 85 - 86: 9.759 distance: 85 - 91: 16.154 distance: 87 - 88: 12.562 distance: 88 - 89: 7.642 distance: 88 - 90: 9.202 distance: 91 - 92: 18.842 distance: 92 - 93: 18.789 distance: 92 - 95: 16.388 distance: 93 - 100: 18.694 distance: 95 - 96: 22.547 distance: 96 - 97: 3.807 distance: 97 - 98: 7.361 distance: 97 - 99: 20.704 distance: 100 - 101: 20.144 distance: 101 - 102: 19.470 distance: 101 - 104: 13.862 distance: 102 - 103: 33.706 distance: 102 - 108: 33.606 distance: 104 - 105: 29.816 distance: 105 - 106: 10.421 distance: 105 - 107: 22.592 distance: 108 - 109: 3.857 distance: 109 - 110: 10.177 distance: 109 - 112: 6.661 distance: 110 - 111: 38.203 distance: 110 - 118: 32.243 distance: 112 - 113: 14.839 distance: 113 - 114: 22.869 distance: 113 - 115: 20.501 distance: 114 - 116: 11.363 distance: 115 - 117: 21.815 distance: 116 - 117: 19.457 distance: 118 - 119: 10.754 distance: 119 - 120: 9.321 distance: 119 - 122: 6.190 distance: 120 - 121: 4.032 distance: 120 - 127: 34.685 distance: 122 - 123: 10.956 distance: 123 - 124: 7.484 distance: 124 - 125: 30.454 distance: 124 - 126: 36.841